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The role of tetraspanin CD81 in malignant transformation is best studied in colorectal cancer, and it appears that other transcripts beside the fully coding mRNA may also be dysregulated in malignant cells. Recent data from a comprehensive pan‐cancer transcriptome analysis demonstrated differential activity of two alternative CD81 gene promoters in malignant versus nonmalignant gut mucosa. The promoter active in gut mucosa gives rise to transcripts CD81‐203 and CD81‐213, while the promoter active in colon and rectal cancer gives rise to transcripts CD81‐205 and CD81‐215. Our study aimed to explore the biomarker potential of the transcripts from the alternative CD81 gene promoters in colon cancer, as well as to investigate their structure and potential function using in silico tools. The analysis of the transcripts' expression in several colon cell lines cultivated in 2D and 3D and a set of colon cancer and healthy gut mucosa samples by qPCR and RNA sequencing suggested their low expression and stromal origin. Expression patterns in tumor and nontumor tissue along with in silico data suppose that the transcript CD81‐215 may be a noncoding RNA of stromal origin with possible involvement in signaling related to malignant transformation. Significance statement: Elements of the noncoding transcriptome are increasingly being accepted as the factors contributing to the complexity of the genome, but their role remains unexplored in spite of demonstrated relevance for many diseases, including cancer. Noncoding transcripts harbor vast potential for application in personalized medicine, both as prospective therapeutics and therapeutic targets. The differential expression of the transcript CD81‐215 in tumor and nontumor tissue, along with in silico predictions of its structure, localization, and interaction partners, point to the possible involvement of this molecule in colorectal carcinogenesis and its biomarker potential. [ABSTRACT FROM AUTHOR]

The regulation of apoptosis (the programmed cell death) is dependent on the crucial involvement of BCL2 and BAX. The Bax-248G>A and Bcl-2-938 C>A polymorphic variations in the promoter sequences of the Bax and Bcl-2 gene have been recently associated with low Bax expression, progression to advanced stages, treatment resistance, and shortened overall survival rate in some hematological malignancies, including chronic myeloid leukemia (CML) and other myeloproliferative neoplasms. Chronic inflammation has been linked to various stages of carcinogenesis wherein pro-inflammatory cytokines play diverse roles in influencing cancer microenvironment leading to cell invasion and cancer progression. Cytokines such as TNF-α and IL-8 have been implicated in cancer growth in both solid and hematological malignancies with studies showing their elevated levels in patients. Genomic approaches have in recent years provided significant knowledge with the regard to the association of certain SNPs (single nucleotide polymerphisms) either in a gene or its promoter that can influence its expression, with the risk and susceptibility to human diseases including cancer. This study has investigated the consequences of promoter SNPs in apoptosis genes Bax-248G>A (rs4645878)/Bcl-2-938C>A (rs2279115) and pro-inflammatory cytokines TNF-α rs1800629 G>A/IL-8 rs4073 T>A on the risk and susceptibility towards hematological cancers. The study design has 235 individuals both male and female enrolled as subjects that had 113 cases of MPDs (myeloproliferative disorders) and 122 healthy individuals as controls. The genotyping studies were conducted through ARMS PCR (amplification-refractory mutation system PCR). The Bcl-2-938 C>A polymorphism showed up in 22% of patients in the study, while it was observed in only 10% of normal controls. This difference in genotype and allele frequency between the two groups was significant (p = 0.025). Similarly, the Bax-248G>A polymorphism was detected in 6.48% of the patients and 4.54% of the normal controls, with a significant difference in genotype and allele frequency between the groups (p = 0.048). The results suggest that the Bcl-2-938 C>A variant is linked to an elevated risk of MPDs in the codominant, dominant, and recessive inheritance models. Moreover, the study indicated allele A as risk allele which can significantly increase the risk of MPDs unlike the C allele. In case of Bax gene covariants, these were associated with an increased risk of MPDs in the codominant inheritance model and dominant inheritance model. It was found that the allele A significantly enhanced the risk of MPDs unlike the G allele. The frequencies of IL-8 rs4073 T>A in patients was found to be TT (16.39%), AT (36.88%) and AA (46.72%), compared to controls who were more likely to have frequencies of TT (39.34%), AT (37.70%) and AA (22.95%) as such, respectively. There was a notable overrepresentation of the AA genotype and GG homozygotes among patients compared to controls in TNF-α polymorphic variants, with 6.55% of patients having the AA genotype and 84% of patients being GG homozygotes, compared to 1.63% and 69%, respectively in controls. The data from the current study provide partial but important evidence that polymorphisms in apoptotic genes Bcl-2-938C>A and Bax-248G>A and pro-inflammatory cytokines IL-8 rs4073 T>A and TNF-α G>A may help predict the clinical outcomes of patients and determine the significance of such polymorphic variations in the risk of myeloproliferative diseases and their role as prognostic markers in disease management using a case-control study approach.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease characterized by synovitis, cartilage damage and bone resorption. Methylation of deoxyribonucleic acid plays a crucial role in repressing gene expression. Receptor activator of nuclear factor-kappa ligand (RANKL) controls bone homeostasis. To assess the serum level of RANKL and its gene promoter methylation in RA patients and to determine its association with clinical characteristics and disease activity. The study included 40 RA patients and 40 control. The disease activity score (DAS28) was assessed. Frequency of RANKL gene promoter methylation was determined by quantitative methylation specific PCR (QMSP) and serum RANKL level by enzyme linked immunosorbant assay (ELISA). Patients mean age was 46.8 ± 10.6 years, 36 females and 4 males (F:M 9:1) with median disease duration 4.5 years. Positive rheumatoid factor, anti-cyclic citrullinated peptide and C-reactive protein were present in 65 %, 75 % and 55 % of cases. Methylation percentage of RANKL gene promoter was significantly lower in patients (3.4 %) than in controls (3.7 %)(p = 0.035) while serum level was significantly increased in patients (9.1 ng/ml,5.3–11.8 ng/ml) than in controls (5.7 ng/ml, 4.5–8 ng/ml)(p = 0.003). RANKL methylation frequency was inversely associated with serum level (rs = -0.21,p = 0.06). There was no significant correlation of RANKL serum level and methylation with DAS28 (r = 0.03,p = 0.87 and r = 0.06,p = 0.73 respectively). RANKL serum level (>9.5 ng/ml) and methylation percentage (≤9%) significantly discriminate RA cases from control (sensitivity 47.5 %, specificity 91.9 %; p = 0.001 and sensitivity 100 %, specificity 40 %; p = 0.03 respectively). RA patients expressed elevated serum RANKL with low methylation. [ABSTRACT FROM AUTHOR]

Insulin receptor (IR) signaling is central to normal metabolic control and dysregulated in prevalent chronic diseases. IR binds insulin at the cell surface and transduces rapid signaling via cytoplasmic kinases. However, mechanisms mediating long-term effects of insulin remain unclear. Here, we show that IR associates with RNA polymerase II in the nucleus, with striking enrichment at promoters genome-wide. The target genes were highly enriched for insulin-related functions including lipid metabolism and protein synthesis and diseases including diabetes, neurodegeneration, and cancer. IR chromatin binding was increased by insulin and impaired in an insulin-resistant disease model. Promoter binding by IR was mediated by coregulator host cell factor-1 (HCF-1) and transcription factors, revealing an HCF-1-dependent pathway for gene regulation by insulin. These results show that IR interacts with transcriptional machinery at promoters and identify a pathway regulating genes linked to insulin's effects in physiology and disease.

Abstract Background Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members. Results Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species. Conclusions Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes.

In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. The aim of this work was to identify epigenetic events in which promoter or gene body DNA methylation induces gene expression changes that drive melanocyte malignant transformation and metastasis. We previously developed a linear mouse model of melanoma progression consisting of spontaneously immortalized melanocytes, premalignant melanocytes, a nonmetastatic tumorigenic, and a metastatic cell line. Here, through the integrative analysis of methylome and transcriptome data, we identified the relationship between promoter and/or gene body DNA methylation alterations and gene expression in early, intermediate, and late stages of melanoma progression. We identified adenylate cyclase type 3 (Adcy3) and inositol polyphosphate 4‐phosphatase type II (Inpp4b), which affect tumor growth and metastatic potential, respectively. Importantly, the gene expression and DNA methylation profiles found in this murine model of melanoma progression were correlated with available clinical data from large population‐based primary melanoma cohorts, revealing potential prognostic markers.

Fragaria chiloensis is a native species from Chile and has interesting attributes such as good taste, aroma, and exotic white color. As the maternal relative of commercial strawberry, it is interesting to understand its ripening physiology. Changes in physiological parameters (size, soluble solids, acidity, and firmness) were followed during the development and ripening of F. chiloensis fruit, noticing a fast and intense softening that severely limits its post-harvest shelf life. The content of abscisic acid (ABA) was quantified along its development and displayed an incremental pattern, meanwhile a descendant profile was determined for auxin. To clarify the role of ABA on F. chiloensis softening, detached immature fruits (C2 stage, low ABA levels) were treated with exogenous ABA and changes in firmness were followed during storage at 20 °C. Fruit firmness reduction was accelerated by ABA treatment compared to non-treated fruit, and consistent with that, a clear induction in the accumulation of transcripts of cell wall disassembly genes such as FcPG, FcRGL1, and FcExp5 was observed. In parallel, there was an increment in the transcript level of transcription factors (TFs) such as FcNAC1, FcSEP3, and FcSHP. Good correlations were determined between firmness reduction and the expression of cell wall genes and TFs. Bioinformatic analysis reveals the presence of cis elements responding to ABA in the promoter regions of cell wall disassembly genes and FcNAC1. This indicates that ABA accelerates the set of transcriptional changes leading to softening on this non-climacteric fruit and suggests that these TFs could act as molecular mediators. [ABSTRACT FROM AUTHOR]

More than 50 lysosomal storage diseases (LSDs) are associated with lysosomal dysfunctions with the frequency of 1:5,000 live births. As a result of missing enzyme activity, the lysosome dysfunction accumulates undegraded or partially degraded molecules, affecting the entire body. Most of them are life-threatening diseases where patients could die within the first or second decade of life. Approximately 20 LSDs have the approved treatments, which do not provide the cure for the disorder. Therefore, the delivery of missing genes through gene therapy is a promising approach for LSDs. Over the years, ex vivo lentiviral-mediated gene therapy for LSDs has been approached using different strategies. Several clinical trials for LSDs are under investigation.Ex vivo lentiviral-mediated gene therapy needs optimization in dose, time of delivery, and promoter-driven expression. Choosing suitable promoters seems to be one of the important factors for the effective expression of the dysfunctional enzyme. This review summarizes the research on therapy for LSDs that has used different lentiviral vectors, emphasizing gene promoters.

Background: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members. Results: Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species. Conclusions: Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes. [ABSTRACT FROM AUTHOR]

Junction epithelium (JE) is located apical to the bottom of the gingival sulcus and binds enamel to hemidesmosomes to protect the periodontal tissue from bacterial infection. Function of odontogenic ameloblast-associated protein (ODAM) is suggested by its expression sites (JE and maturation stage ameloblasts) to be involved in the adhesion between the JE and enamel, and odontogenesis. To analyze the changes in ODAM gene and protein expressions in inflamed gingiva, Ca9-22 gingival epithelial cells were stimulated with 1 ng/ml interleukin-1β (IL-1β) for 3–24 h, and ODAM mRNA and protein levels were analyzed by real-time PCR and Western blotting. Luciferase (LUC) constructs were made ligating various lengths of human ODAM gene promoters and performed LUC analyses in Ca9-22 cells. Gel shift and chromatin immunoprecipitation (ChIP) assays were performed. IL-1β induced ODAM mRNA and protein levels at 6–24 h. IL-1β increased LUC activities of the ODAM gene promoter constructs from − 85 to − 950. These activities were blocked by protein kinase A, tyrosine kinase, mitogen-activated protein (MAP) kinase kinase and phosphoinositide 3-kinase inhibitors. Gel shift and ChIP assays showed that IL-1β induced CCAAT/enhancer-binding protein (C/EBP) β and Yin Yang1 (YY1) binding to C/EBP1, 2, 3, and YY1 elements. These data indicate that IL-1β stimulates ODAM gene transcription mediated through C/EBP1, C/EBP2, C/EBP3, and YY1 elements in the human ODAM gene promoter. [ABSTRACT FROM AUTHOR]

In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. The aim of this work was to identify epigenetic events in which promoter or gene body DNA methylation induces gene expression changes that drive melanocyte malignant transformation and metastasis. We previously developed a linear mouse model of melanoma progression consisting of spontaneously immortalized melanocytes, premalignant melanocytes, a nonmetastatic tumorigenic, and a metastatic cell line. Here, through the integrative analysis of methylome and transcriptome data, we identified the relationship between promoter and/or gene body DNA methylation alterations and gene expression in early, intermediate, and late stages of melanoma progression. We identified adenylate cyclase type 3 (Adcy3) and inositol polyphosphate 4-phosphatase type II (Inpp4b), which affect tumor growth and metastatic potential, respectively. Importantly, the gene expression and DNA methylation profiles found in this murine model of melanoma progression were correlated with available clinical data from large population-based primary melanoma cohorts, revealing potential prognostic markers. [ABSTRACT FROM AUTHOR]

Kalmegh (Andrographis paniculata) spatiotemporally produces medicinally-important ent -labdane-related diterpenoids (ent- LRDs); andrographolide (AD), 14-deoxy-11,12-didehydroandrographolide (DDAD), neoandrographolide (NAD). ApCPS1 and ApCPS2, the ent -copalyl pyrophosphate (ent -CPP)-producing class II diterpene synthases (diTPSs) were identified, but their contributions to ent -CPP precursor supply for ent- LRD biosynthesis were not well understood. Here, we characterized ApCPS4, an additional ent -CPP-forming diTPS. Further, we elucidated in planta function of the ent -CPP-producing diTPSs (ApCPS1,2,4) by integrating transcript-metabolite co-profiles, biochemical analysis and gene functional characterization. ApCPS1,2,4 localized to the plastids, where diterpenoid biosynthesis occurs in plants, but ApCPS1,2,4 transcript expression patterns and ent -LRD contents revealed a strong correlation of ApCPS2 expression and ent -LRD accumulation in kalmegh. ApCPS1,2,4 upstream sequences differentially activated β-glucuronidase (GUS) in Arabidopsis and transiently-transformed kalmegh. Similar to higher expression of ApCPS1 in kalmegh stem, ApCPS1 upstream sequence activated GUS in stem/hypocotyl of Arabidopsis and kalmegh. However, ApCPS2,4 upstream sequences weakly activated GUS expression in Arabidopsis, which was not well correlated with ApCPS2,4 transcript expression in kalmegh tissues. Whereas, ApCPS2,4 upstream sequences could activate GUS expression at a considerable level in kalmegh leaf and roots/calyx, respectively, suggesting the involvement of transcriptional regulator(s) of ApCPS2,4 that might participate in kalmegh-specific diterpenoid pathway. Interestingly, ApCPS2 -silenced kalmegh showed a drastic reduction in AD, DDAD and NAD contents and compromised defense against insect herbivore Spodoptera litura. However, ent -LRD contents and herbivore defense in ApCPS1 or ApCPS4 -silenced plants remained largely unaltered. Overall, these results suggested an important role of ApCPS2 in producing ent -CPP for medicinal ent -LRD biosynthesis and defense against insect herbivore. • This work clarifies the roles of A. paniculata ent -copalyl pyrophosphate synthases in medicinal diterpenoid biosynthesis. • ApCPS4 was biochemically characterized as an ent -copalyl pyrophosphate synthase. • ApCPS1,2,4 localized in the plastids and their upstream sequences differentially activated β-glucuronidase. • ApCPS2 transcript expression strongly correlated with diterpenoid levels in tissues. • ApCPS2 silencing led to a drastic reduction in diterpenoid levels and compromised defense to insect herbivore. [ABSTRACT FROM AUTHOR]

Abstract Objective Calcitonin receptor-like receptor (CRLR) regulates vasoconstriction and dilatation; the expression increases during hypoxia via activation of hypoxia response element (HRE) in CRLR gene promoter region. Variant in HRE, as well short tandem repeat (STR) variants near HRE in CRLR alters the gene expression. This study focused on a case–control study to investigate the expression of genetic typing CLRL promoter variant in pregnant women with severe preeclampsia and normal pregnancies, we also tried to describe interesting findings of the genetic expression in anemic patients in the severe preeclampsia group. Our aimed to observe the correlation of CRLR gene promoter variant and anemia in severe preeclampsia. Results There was no nucleotide variant in HRE; CACA box prior to HRE varied in length (15–24); CACA box with length > 20 was used as cut off point. Hb was lower in CACA box length ≥ 21 (10.33 ± 1.57) vs.

Abstract Genetic modification of Rhodococcus jostii RHA1 was carried out in order to optimise the production of pyridine-2,4-dicarboxylic acid and pyridine-2,5-dicarboxylic acid bioproducts from lignin or lignocellulose breakdown, via insertion of either the Sphingobium SYK-6 ligAB genes or Paenibacillus praA gene respectively. Insertion of inducible plasmid pTipQC2 expression vector containing either ligAB or praA genes into a ΔpcaHG R. jostii RHA1 gene deletion strain gave 2–threefold higher titres of PDCA production from lignocellulose (200–287 mg/L), compared to plasmid expression in wild-type R. jostii RHA1. The ligAB genes were inserted in place of the chromosomal pcaHG genes encoding protocatechuate 3,4-dioxygenase, under the control of inducible Picl or PnitA promoters, or a constitutive Ptpc5 promoter, producing 2,4-PDCA products using either wheat straw lignocellulose or commercial soda lignin as carbon source. Insertion of Amycolatopsis sp. 75iv2 dyp2 gene on a pTipQC2 expression plasmid led to enhanced titres of 2,4-PDCA products, due to enhanced rate of lignin degradation. Growth in minimal media containing wheat straw lignocellulose led to the production of 2,4-PDCA in 330 mg/L titre in 40 h, with > tenfold enhanced productivity, compared with plasmid-based expression of ligAB genes in wild-type R. jostii RHA1. Production of 2,4-PDCA was also observed using several different polymeric lignins as carbon sources, and a titre of 240 mg/L was observed using a commercially available soda lignin as feedstock.

Objective: Odontogenic ameloblast-associated protein (ODAM) is produced by maturation stage ameloblasts and junctional epithelium (JE). The function of ODAM is thought to be involved in the attachment of teeth and JE. To elucidate transcriptional regulation of human ODAM gene in inflamed gingiva, we have analyzed the effects of TNF-α on the expression of ODAM gene in Ca9-22 and Sa3 gingival epithelial cells. Materials and methods: Total RNAs were extracted from Ca9-22 and Sa3 cells after stimulation by TNF-α (10 ng/ml). ODAM mRNA and protein levels were analyzed by qPCR and Western blotting. Luciferase (LUC) analyses were performed using LUC constructs inserted in various lengths of ODAM gene promoter. Gel shift and chromatin immunoprecipitation (ChIP) assays were carried out. Results: TNF-α increased ODAM mRNA and protein levels at 3 to 24 h. TNF-α induced LUC activities of the ODAM gene promoter constructs, and the activities were inhibited by protein kinase A, tyrosine kinase, MEK1/2, PI3-kinase and NF-κB inhibitors. Gel shift and ChIP assays revealed that TNF-α increased CCAAT/enhancer-binding protein (C/EBP) β and Yin Yang1 (YY1) binding to three kinds of C/EBPs and YY1 elements. Conclusion: These results demonstrate that TNF-α stimulates ODAM gene transcription via C/EBPs and YY1 elements in the human ODAM gene promoter. [ABSTRACT FROM AUTHOR]

The estimation of hypermethylation of the cell cycle (RASSF1A, p16/INK4A, p14/ARF) and detoxification (GSTP1) gene promoters was carried out in blood leukocytes of humans exposed to radiation as a result of the Chernobyl accident (98 individuals: accident liquidators, 76 individuals; adult residents of the territories with radionuclide contamination, 135–688 kBq/m2, 22 individuals) depending on their cytogenetic status. The results of multiple regression analysis ("Frequency of aberrations ~ age + number of hypermethylated genes") indicate a correlation of the total level of chromosomal type aberrations with the considered epigenetic disturbances (β = 0.256; р = 0.011), but not with age (β = –0.138; p = 0.165). The frequency of these cytogenetic disorders increases with an increase in the number of methylated loci. Thus, a positive association between the damages to the genome induced by radiation exposure in the range of small and medium doses (long time ago) and hypermethylation of promoters of the genes of the main protective systems of the cells was detected. [ABSTRACT FROM AUTHOR]

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan. [ABSTRACT FROM AUTHOR]

Background: The promoter region is a key element of gene expression regulation. In mammals, most of the genes present, at the level of their promoter, a large number of islands CpG. Age also is seen as another factor for developing breast cell cancer reaching the tumour stage. Aim: This study aimed to explore the hypermethylation of the BRCA1/2 promoter gene in women breast cancer and correlation with age and tumour stage. Materials and methods: Fifty biopsies were derived from Moroccan women treated for breast carcinoma, the DNA extracted was treated by bisulphite and the targeted BRCA1/2 Amplicons were amplified by specific methylation primers (MSP). Results: The result shows that 62% of the samples were BRCA1 methylated in addition and negative result for BRCA2, these positive epigenetic factor were remarkable in women over 47 years and at the stage of malignant tumour. Conclusion: These results show that half of the methylated samples are positive with a majority of over 47 years old, and confirms that age might be an additional factor for breast cancer development. [ABSTRACT FROM AUTHOR]

Background: The epoxyeicosatrienoic acids (EETs) have antihypertensive, anti-inflammatory, and organ protective properties and their circulation levels are related to hypertension, diabetes mellitus, cardiovascular diseases, and preeclampsia. Soluble epoxide hydrolase (sEH) catalyses the degradation of EETs to less biologically active dihydroxyeicosatrienoic acids. Here, we sequenced the promoter region of EPHX2 to investigate the association between promoter sequence alterations that we thought to affect the expression levels of the enzyme and preeclampsia (PE). Methods: Nucleotide sequencing of the promoter region of the EPHX2, spanning from position -671 to +30, was performed on 100 pregnant women with PE and, 20 or more weeks pregnant normotensive, healthy women (n=100). Results: Pregnant women who carry rs4149235, rs4149232, rs73227309, and rs62504268 polymorphisms have 4.4, 2.4, 2.3, and 2.8 times significantly increased risk of PE, respectively. CCGG (OR: 3.11; 95% CI: 1.12-8.62) and CCCA (OR: 0.45; 95% CI: 0.36-0.55) haplotypes were associated with an increased and decreased risk of PE, respectively. Conclusions: Four SNPs (rs4149232, rs4149235, rs73227309, and rs62504268) in the promoter region of the EPHX2, and CCGG and CCCA haplotypes of these 4 SNPs were significantly associated with PE. These SNPs in the promoter region may affect sEH expression and thus enzyme activity and may play a role in PE pathogenesis by causing individual differences in EET levels. However, future studies are needed to confirm our findings and examine the effect of these SNPs on the sEH expression and/or enzyme activity.

BackgroundAcute myocardial infarction (AMI), a common complex disease caused by an interaction between genetic and environmental factors, is a serious type of coronary artery disease and is also a leading cause of death worldwide. Autophagy-related 16-like 1 (ATG16L1) is a key regulatory factor of autophagy and plays an important role in induced autophagy. In the cardiovascular system, autophagy is essential to preserve the homeostasis and function of the heart and blood vessels. No studies have hitherto examined the association between AMI and ATG16L1 gene promoter.MethodsWe conducted a case-control study, using polymerase chain reaction and sequencing techniques, dual luciferase reporter assay, and electrophoretic mobility shift assay, to analyze genetic and functional variation in the ATG16L1 gene promoter between AMI and controls. A variety of statistical analyses were used to analyze the allele and genotype frequencies and the relationship between single-nucleotide polymorphisms (SNPs) and AMI.ResultsIn all, 10 SNPs and two DNA-sequence variants (DSVs) were identified in 688 subjects, and three ATG16L1 gene promoter mutations [g.233250693 T > C (rs185213911), g.233250946 G > A (rs568956599), g.233251133 C > G (rs1301744254)] that were identified in AMI patients significantly altered the transcriptional activity of ATG16L1 gene promoter in HEH2, HEK-293, and H9c2 cells (P < 0.05). Further electrophoretic mobility shift assays indicated that the SNPs affected the binding of transcription factors (P < 0.01).ConclusionATG16L1 gene promoter mutations in AMI patients may affect the binding of transcription factors and change the transcriptional activity of the ATG16L1 gene, changing the level of autophagy and contributing to the occurrence and development of AMI as rare and low-frequency risk factors.

Background: Acute myocardial infarction (AMI), a common complex disease caused by an interaction between genetic and environmental factors, is a serious type of coronary artery disease and is also a leading cause of death worldwide. Autophagy-related 16-like 1 (ATG16L1) is a key regulatory factor of autophagy and plays an important role in induced autophagy. In the cardiovascular system, autophagy is essential to preserve the homeostasis and function of the heart and blood vessels. No studies have hitherto examined the association between AMI and ATG16L1 gene promoter. Methods: We conducted a case-control study, using polymerase chain reaction and sequencing techniques, dual luciferase reporter assay, and electrophoretic mobility shift assay, to analyze genetic and functional variation in the ATG16L1 gene promoter between AMI and controls. A variety of statistical analyses were used to analyze the allele and genotype frequencies and the relationship between single-nucleotide polymorphisms (SNPs) and AMI. Results: In all, 10 SNPs and two DNA-sequence variants (DSVs) were identified in 688 subjects, and three ATG16L1 gene promoter mutations [g.233250693 T > C (rs185213911), g.233250946 G > A (rs568956599), g.233251133 C > G (rs1301744254)] that were identified in AMI patients significantly altered the transcriptional activity of ATG16L1 gene promoter in HEH2, HEK-293, and H9c2 cells (P < 0.05). Further electrophoretic mobility shift assays indicated that the SNPs affected the binding of transcription factors (P < 0.01). Conclusion: ATG16L1 gene promoter mutations in AMI patients may affect the binding of transcription factors and change the transcriptional activity of the ATG16L1 gene, changing the level of autophagy and contributing to the occurrence and development of AMI as rare and low-frequency risk factors. [ABSTRACT FROM AUTHOR]

Abstract Myostatin (MSTN) is one of the key factors regulating myogenesis. Because of its role as a negative regulator of muscle mass deposition, much interest has been given to its protein and, in recent years, several studies have analysed MSTN gene regulation. This review discusses the MSTN gene promoter, focusing on its structure in several animal species, both vertebrate and invertebrate. We report the important binding sites considering their degree of phylogenetic conservation and roles they play in the promoter activity. Finally, we discuss recent studies focusing on MSTN gene regulation via promoter manipulation and the potential applications they have both in medicine and agriculture.

Amelotin (AMTN) is an enamel protein that is localized in junctional epithelium (JE) of gingiva and suggested to be involved in the attachment between JE and tooth enamel. MicroRNA is a small non-coding RNA that regulates gene expression at post-transcriptional level by binding to the 3′-untranslated region (3′-UTR) of target mRNAs. In this study, we have analyzed the effects of miR-200b on the expression of AMTN in human gingival epithelial (Ca9-22) cells. Total RNAs and proteins were extracted from Ca9-22 cells transfected with miR-200b expression plasmid or miR-200b inhibitor and stimulated by TNF-α (10 ng/ml, 12 h). AMTN and inhibitor of kappa-B kinase beta (IKKβ) mRNA and protein levels were measured by qPCR and Western blot. Human AMTN 3′-UTR that contains putative miR-200b target sites were cloned downstream of -353AMTN luciferase (LUC) plasmid. Ca9-22 cells were transfected with -353AMTN 3′-UTR LUC constructs and miR-200b expression plasmid, and LUC activities were measured with or without stimulation by TNF-α. TNF-α-induced AMTN mRNA levels were partially inhibited by miR-200b overexpression and enhanced by miR-200b inhibitor. TNF-α-induced IKKβ mRNA and protein levels were almost completely inhibited by miR-200b. Transcriptional activities of -353AMTN 3′-UTR LUC constructs were induced by TNF-α and partially inhibited by miR-200b. IKKβ inhibitor IMD0354 and NF-κB inhibitor triptolide decreased TNF-α-induced LUC activities. Furthermore, both inhibitors reduced AMTN mRNA levels in the presence or absence of TNF-α. These results suggest that miR-200b suppresses AMTN expression by targeting to AMTN and IKKβ mRNAs in the human gingival epithelial cells. [ABSTRACT FROM AUTHOR]

Genetic modification of Rhodococcus jostii RHA1 was carried out in order to optimise the production of pyridine-2,4-dicarboxylic acid and pyridine-2,5-dicarboxylic acid bioproducts from lignin or lignocellulose breakdown, via insertion of either the Sphingobium SYK-6 ligAB genes or Paenibacillus praA gene respectively. Insertion of inducible plasmid pTipQC2 expression vector containing either ligAB or praA genes into a ΔpcaHG R. jostii RHA1 gene deletion strain gave 2–threefold higher titres of PDCA production from lignocellulose (200–287 mg/L), compared to plasmid expression in wild-type R. jostii RHA1. The ligAB genes were inserted in place of the chromosomal pcaHG genes encoding protocatechuate 3,4-dioxygenase, under the control of inducible Picl or PnitA promoters, or a constitutive Ptpc5 promoter, producing 2,4-PDCA products using either wheat straw lignocellulose or commercial soda lignin as carbon source. Insertion of Amycolatopsis sp. 75iv2 dyp2 gene on a pTipQC2 expression plasmid led to enhanced titres of 2,4-PDCA products, due to enhanced rate of lignin degradation. Growth in minimal media containing wheat straw lignocellulose led to the production of 2,4-PDCA in 330 mg/L titre in 40 h, with > tenfold enhanced productivity, compared with plasmid-based expression of ligAB genes in wild-type R. jostii RHA1. Production of 2,4-PDCA was also observed using several different polymeric lignins as carbon sources, and a titre of 240 mg/L was observed using a commercially available soda lignin as feedstock. [ABSTRACT FROM AUTHOR]

• Peripheral IFN-γ stimulation can promote cognitive and behavioral functions in mice. • STAT1 binds to the target gene of β-catenin promoter (−218∼−204 bp), which plays a positive regulatory effect on β-catenin. • IFN-γ can regulate wnt/β-catenin signaling pathways through STAT1 activation to promote NSCs' proliferation, differentiation. Interferon-gamma (IFN-γ) is critical for central nervous system (CNS) functions and it may be a promising treatment to stimulate CNS regeneration. However, previous studies reported inconsistent results, and the molecular mechanisms remain controversial. Here we show that IFN-γ-treated mice via intraperitoneal injection have elevated IFN-γ level in central hippocampus and superior cognitive behaviors IFN-γ could activates the level of protein expression of Wnt7a, β-catenin, and CyclinD1 in Wnt/β-catenin signaling pathway of mice hippocampus. Functional and mechanism analysis in vitro revealed that IFN-γ promoted the proliferation and differentiation in primary cultured neural stem cells (NSCs). STAT1 was accountable for IFN-γ-induced activation of the β-catenin promoter, and IFN-γ increased the binding affinity of STAT1 to β-catenin promoter based on luciferase activity and chromatin immunoprecipitation. Our results suggest that IFN-γ exerts many effects ranging from cognitive function in vivo to NSC proliferation, self-renewal, and differentiation in vitro. It does so by recruiting STAT1 to the β-catenin promoter, enhancing cis-regulation by STAT1, and ultimately activating Wnt/β-catenin signaling. In this study, we first found that STAT1 was recruited into the promoter of β-catenin to activate β-catenin expression, and this effect was regulated by IFN-γ. It is also discovered firstly that Wnt/β-catenin and JAK/STAT pathways form cross-links through STAT1. Promoting neurogenesis through immune stimulation might be a promising strategy for repairing the diseased/injured CNS. This study provides a scientific basis for immunomodulation to promote nerve regeneration and offer a new therapeutic direction for central nervous system regeneration. [ABSTRACT FROM AUTHOR]

Ubiquitous eukaryotic non-coding circular RNAs are involved in numerous co- and post-transcriptional regulatory mechanisms. Recently, we reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica, with 3′ss–5′ss ligation points and 5′ss GU-rich elements essential for their biogenesis and their suggested role in transcription regulation. Here, we explored how flicRNAs impact gene expression regulation. Using CLIP assays, followed by qRT-PCR, we identified that the RabX13 control flicRNA and virulence-associated flicRNAs were bound to the HA-tagged RNA Pol II C-terminus domain in E. histolytica transformants. The U2 snRNA was also present in such complexes, indicating that they belonged to transcription initiation/elongation complexes. Correspondingly, inhibition of the second step of splicing using boric acid reduced flicRNA formation and modified the expression of their parental genes and non-related genes. flicRNAs were also recovered from chromatin immunoprecipitation eluates, indicating that the flicRNA-Pol II complex was formed in the promoter of their cognate genes. Finally, two flicRNAs were found to be cytosolic, whose functions remain to be uncovered. Here, we provide novel evidence of the role of flicRNAs in gene expression regulation in cis, apparently in a widespread fashion, as an element bound to the RNA polymerase II transcription initiation complex, in E. histolytica.

Background: The epoxyeicosatrienoic acids (EETs) have antihypertensive, anti-inflammatory, and organ protective properties and their circulation levels are related to hypertension, diabetes mellitus, cardiovascular diseases, and preeclampsia. Soluble epoxide hydrolase (sEH) catalyses the degradation of EETs to less biologically active dihydroxyeicosatrienoic acids. Here, we sequenced the promoter region of EPHX2 to investigate the association between promoter sequence alterations that we thought to affect the expression levels of the enzyme and preeclampsia (PE). Methods: Nucleotide sequencing of the promoter region of the EPHX2, spanning from position -671 to +30, was performed on 100 pregnant women with PE and, 20 or more weeks pregnant normotensive, healthy women (n = 100). Results: Pregnant women who carry rs4149235, rs4149232, rs73227309, and rs62504268 polymorphisms have 4.4, 2.4, 2.3, and 2.8 times significantly increased risk of PE, respectively. CCGG (OR: 3.11; 95% Cl: 1.12-8.62) and CCCA (OR: 0.45; 95% Cl: 0.36-0.55) haplotypes were associated with an increased and decreased risk of PE, respectively. Conclusions: Four SNPs (rs4149232, rs4149235, rs73227309, and rs62504268) in the promoter region of the EPHX2, and CCGG and CCCA haplotypes of these 4 SNPs were significantly associated with PE. These SNPs in the promoter region may affect sEH expression and thus enzyme activity and may play a role in PE pathogenesis by causing individual differences in EET levels. However, future studies are needed to confirm our findings and examine the effect of these SNPs on the sEH expression and/or enzyme activity. [ABSTRACT FROM AUTHOR]

Fish are a major source of beneficial n-3 LC-PUFA in human diet, and there is considerable interest to elucidate the mechanism and regulatory aspects of LC-PUFA biosynthesis in farmed species. Long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis involves the activities of two groups of enzymes, the fatty acyl desaturase (Fads) and elongase of very long-chain fatty acid (Elovl). The promoters of elovl5 elongase, which catalyses the rate-limiting reaction of elongating polyunsaturated fatty acid (PUFA), have been previously described and characterized from several marine and diadromous teleost species. We report here the cloning and characterization of elovl5 promoter from two freshwater fish species, the carnivorous snakehead fish (Channa striata) and zebrafish. Results show the presence of sterol-responsive elements (SRE) in the core regulatory region of both promoters, suggesting the importance of sterol regulatory element-binding protein (Srebp) in the regulation of elovl5 for both species. Mutagenesis luciferase and electrophoretic mobility shift assays further validate the role of SRE for basal transcriptional activation. In addition, several Sp1-binding sites located in close proximity with SRE were present in the snakehead promoter, with one having a potential synergy with SRE in the regulation of elovl5 expression. The core zebrafish elovl5 promoter fragment also directed in vivo expression in the yolk syncytial layer of developing zebrafish embryos. [ABSTRACT FROM AUTHOR]

Epilepsy is a major health burden, calling for new mechanistic insights and therapies. CRISPR-mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can effectively treat acquired focal epilepsy, focusing on ion channels because their manipulation is known be effective in changing network hyperactivity and hypersynchronziation. We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonic-clonic seizures in a model of temporal lobe epilepsy, and rescued cognitive impairment and transcriptomic alterations associated with chronic epilepsy. The focal treatment minimizes concerns about off-target effects in other organs and brain areas. This study provides the proof-of-principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability. [ABSTRACT FROM AUTHOR]

Cyprinus carpio is world’s most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from “Gene” and “RefSeq” databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.

Small molecules able to bind non-canonical G-quadruplex DNA structures (G4) have been recently tested as novel potential agents for the treatment of prostate cancer thanks to their repression of aberrant androgen receptor gene. However, metastatic castration-resistant prostate cancer (mCRPC), a letal form of prostate cancer, is still incurable. Here we tested two naphthalenediimide derivatives, previously reported as multitarget agents, on a couple of relevant mCRPC cell models (DU145 and PC-3). We showed that these compounds interfere with the RAS/MEK/ERK and PI3K/AKT pathways. Interestingly, both these two biological processes depend upon Epidermal Growth Factor Receptor (EGFR) activation. By means of biological and analytical tools we showed that our compounds are efficient inducers of the structural transition of the EGFR promoter towards a G-quadruplex conformation, ultimately leading to a reduction of the receptor production. The overall result is an interesting cytotoxic profile for these two derivatives. Thanks to their activity at different steps, these compounds can open the way to novel therapeutic approaches for mCRPC that could contribute to escape resistance to selective treatments. Image 1 • NDI can target multiple cellular G-quadruplexes. • In NDI-treated mCRPC cells the expression level of EGFR is reduced. • NDI-treatment can help to escape some resistance mechanisms. • Distinct biological outcomes characterize NDI-treated mCRPC cells. • Cell defense programs may impact on NDI biological activity. [ABSTRACT FROM AUTHOR]

Gene promoter methylation is a common epigenetic event, taking place in the early phase of tumorigenesis, which has a great potential as a diagnostic and prognostic cancer biomarker. In this umbrella review, we provide an overview on the association between gene-promoter methylation of protein-coding genes and cancer risk based on currently available meta-analyses data on gene promoter methylation. We searched MEDLINE via PubMed and the Cochrane Database of Systematic Reviews for meta-analyses that examine the association between gene-promoter methylation and cancer, published until January 2019 in English. We used AMSTAR to assess the quality of the included studies and applied a set of pre-specified criteria to evaluate the magnitude of each association. We provide a comprehensive overview of 80 unique combinations between 22 different genes and 18 cancer outcomes, all of which indicated a positive association between promoter hypermethylation and cancer. In total, the 70 meta-analyses produced significant results under a random-effects model with odds ratios that ranged from 1.94 to 26.60, with the summary effect being in favor of the unmethylated group in all cases. Three of the strong evidence associations involve RASSF1 methylation on bladder cancer risk (OR = 18.46; 95% CI: 12.69–26.85; I2 = 0%), MGMT methylation on NSCLC (OR = 4.25; 95% CI: 2.83–6.38; I2 = 22.4%) and RARB methylation on prostate cancer (OR = 6.87; 95% CI: 4.68–10.08; I2 = 0%). Meta-analyses showed a moderate quality, AMSTAR score ranging from 4 to 9 (Mdn = 8; IQR: 7.0 to 8.0). As primary studies and meta-analyses on the subject accumulate, more genetic loci may be found to be highly associated with specific cancer types and hence the biomarker sets will become wider. • Overview of 80 unique combinations between 22 genes and 18 cancer outcomes • All showed a positive association between promoter hypermethylation and cancer. • Strong evidence linked methylation of MGMT , RASSF1 and RARB to various cancers. • Quality of studies was moderate, AMSTAR ranged from 4 to 9 (Mdn = 8; IQR: 7 to 8). [ABSTRACT FROM AUTHOR]

Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes. [ABSTRACT FROM AUTHOR]

The cohesin protein complex mediates sister chromatid cohesion to ensure accurate chromosome segregation, and also influences gene transcription in higher eukaryotes. Modest deficits in cohesin function that do not alter chromosome segregation cause significant birth defects. The mechanisms by which cohesin participates in gene regulation have been studied in Drosophila , revealing that it is involved in gene activation by transcriptional enhancers and epigenetic gene silencing mediated by Polycomb group proteins. Recent studies reveal that early DNA replication origins are important for determining which genes associate with cohesin, and suggest that cohesin at replication origins is important for establishing both sister chromatid cohesion and enhancer–promoter communication. Cohesin participates in gene activation and Polycomb repressive complex function via multiple mechanisms. Cohesin association with transcriptional enhancers and gene promoters is linked to their proximity to early DNA replication origins. Cohesin association with early replication origins may be important for establishing both sister chromatid cohesion and enhancer–promoter communication. [ABSTRACT FROM AUTHOR]

Highlights • Aberrant DNA methylation patterns are a hallmark of diseases, such as cancer, Alzheimer's disease, and cardiovascular disease, and mathematical analysis of the mechanics of DNA methylation has the potential to give new insights into these mechanisms. • We develop a fast and robust methodology for selecting computational models for DNA methylation. • We demonstrate the effectiveness of the method on recovering parameter values associated with the processes which underpin DNA methylation. • Our work opens the possibility for further biological experimentation based on our finding that the parameters which govern DNA methylation are influenced by gene promoter methylation levels. • Our work showcases the utility of Bayesian analysis and its application to complex biological problems. Abstract Epigenetics is coming to the fore as a key process which underpins health. In particular emerging experimental evidence has associated alterations to DNA methylation status with healthspan and aging. Mammalian DNA methylation status is maintained by an intricate array of biochemical and molecular processes. It can be argued changes to these fundamental cellular processes ultimately drive the formation of aberrant DNA methylation patterns, which are a hallmark of diseases, such as cancer, Alzheimer's disease and cardiovascular disease. In recent years mathematical models have been used as effective tools to help advance our understanding of the dynamics which underpin DNA methylation. In this paper we present linear and nonlinear models which encapsulate the dynamics of the molecular mechanisms which define DNA methylation. Applying a recently developed Bayesian algorithm for parameter estimation and model selection, we are able to estimate distributions of parameters which include nominal parameter values. Using limited noisy observations, the method also identified which methylation model the observations originated from, signaling that our method has practical applications in identifying what models best match the biological data for DNA methylation. [ABSTRACT FROM AUTHOR]

Junctional epithelium (JE) develops from reduced enamel epithelium during tooth formation and is critical for the maintenance of healthy periodontal tissue through ensuring appropriate immune responses and the rapid turnover of gingival epithelial cells. We have previously shown a relationship between inflammatory cytokines and expression of JE‐specific genes, such as amelotin (AMTN), in gingival epithelial cells. Here, we elucidated the effects of Porphyromonas gingivalis‐derived lipopolysaccharide (PgLPS) on Amtn gene transcription and the interaction of transcription factors. To determine the molecular basis of transcriptional regulation of the Amtn gene by PgLPS, we performed real‐time PCR and carried out luciferase assays using a mouse Amtn gene promoter linked to a luciferase reporter gene in mouse gingival epithelial GE1 cells. Gel mobility shift and chromatin immunoprecipitation assays were performed to identify response elements bound to LPS‐induced transcription factors. Next, we analyzed protein levels of the LPS‐induced transcription factors and the interaction of transcription factors by western blotting and immunoprecipitation. LPS increased Amtn mRNA levels and elevated luciferase activities of constructs containing regions between −116 and −238 of the mouse Amtn gene promoter. CCAAT/enhancer‐binding protein (C/EBP) 1–, C/EBP2– and Ying Yang 1 (YY1)–nuclear protein complexes were increased by LPS treatment. Furthermore, we identified LPS‐modulated interactions with C/EBPβ, YY1 and Smad3. These results demonstrate that PgLPS regulates Amtn gene transcription via binding of C/EBPβ–Smad3 and YY1–Smad3 complexes to C/EBP1, C/EBP2 and YY1 response elements in the mouse Amtn gene promoter. Porphyromonas gingivalis lipopolysaccharide (LPS)‐induced physical interactions between CCAAT/enhancer‐binding protein β (C/EBPβ), Ying Yang 1 (YY1) and Smad3 upregulate amelotin (Amtn) gene transcription via mitogen‐activated protein kinase kinase 1/2 (MEK1/2), phosphatidylinositol 3‐kinase (PI3‐K) and Smad2/3 pathways in gingival epithelial cells. These findings raise the possibility of an association between induced C/EBPβ and YY1 in inflammation and a constitutive interaction with Smad3 in gingival epithelial cells. [ABSTRACT FROM AUTHOR]

It has become impossible to review all the existing literature on Voltage-Dependent Anion selective Channel (VDAC) in a single article. A real Renaissance of studies brings this protein to the center of decisive knowledge both for cell physiology and therapeutic application. This review, after highlighting the similarities between the cellular context and the study methods of the solute carriers present in the inner membrane and VDAC in the outer membrane of the mitochondria, will focus on the isoforms of VDAC and their biochemical characteristics. In particular, the possible reasons for their evolutionary onset will be discussed. The variations in their post-translational modifications and the differences between the regulatory regions of their genes, probably the key to understanding the current presence of these genes, will be described. Finally, the situation in the higher eukaryotes will be compared to that of yeast, a unicellular eukaryote, where there is only one active isoform and the role of VDAC in energy metabolism is better understood.

The human (h) placental lactogenic hormone chorionic somatomammotropin (CS) is highly produced during pregnancy and acts as a metabolic adaptor in response to maternal insulin resistance. Maternal obesity can exacerbate this "resistance", and a >75% decrease in CS RNA levels was observed in term placentas from obese vs. lean women. The genes coding for hCS (hCS-A and hCS-B) and placental growth hormone (hGH-V) as well as the hCS-L pseudogene and pituitary growth hormone (GH) gene (hGH-N) are located at a single locus on chromosome 17. Three remote hypersensitive sites (HS III-V) located >28 kb upstream of hGH-N as well as local hCS gene promoter and enhancer regions are implicated in hCS gene expression. A placentaspecific chromosomal architecture, including interaction between HS III-V and hCS but not hGH gene promoters, was detected in placentas from lean women (BMI <25 kg/m2) by using the chromosome conformation capture assay. This architecture was disrupted by prepregnancy maternal obesity (BMI >35 kg/m²), resulting in a predominant interaction between HS III and the hGH-N promoter, which was also observed in nonplacental tissues. This was accompanied by a decrease in hCS levels, which was consistent with reduced RNA polymerase II and CCAAT/enhancer-binding protein-β association with individual hCS promoter and enhancer sequences, respectively. Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS. [ABSTRACT FROM AUTHOR]

Transcription of vitellogenin ( vtg ) genes are initiated when estradiol-17β (E 2 )-estrogen receptor (ER) complexes bind estrogen response elements (ERE) located in the gene promoter region. Transcriptional regulation of dual vtg subtypes (major salmonid A-type vtg : vtgAs ; minor C-type vtg : vtgC ) by E 2 was investigated under co-expression of a potential major transcriptional factor, erα1 , in cutthroat trout. Two forms of trout vtgAs promoters (1 and 2) and one vtgC promoter were sequenced. These promoters structurally differ based on the number of EREs present. The vtgAs promoter 1 exhibited the highest maximal transcriptional activity by in vitro gene reporter assays. The concentration of E 2 that induces 50% of gene reporter activity (half-maximal effective concentrations, EC 50 ) was similar among all vtg promoters and also to the EC 50 of E 2 administered to induce vtg transcription in vivo . This study revealed a difference in transcriptional properties of multiple vtg promoters for the first time in a salmonid species, providing the basis to understand mechanisms underlying regulation of vitellogenesis via dual vtg gene expression. [ABSTRACT FROM AUTHOR]

The present study aimed to explore the effects of Helicobacter pylori (H. pylori) infection on the expression of transcription factor GATA binding protein 3 (GATA-3) and connexin 32 (Cx32) in cultured gastric mucosa cells, and their association with each other. GES-1 cells were co-cultured with East Asian type cytotoxin-associated gene A+ H. pylori in the H. pylori group, and without H. pylori culture in the control group. Additionally, Mongolian gerbils were gavaged with H. pylori, and later the gastric antrum tissues were collected. The GATA-3 and Cx32 mRNA and protein expression levels were detected by a reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively. The scratch labeling fluorescent dye tracer (SLDT) technique was used to detect the gap junctional intercellular communication (GJIC) function. GATA-3 small interfering RNA (siRNA) was transfected into BGC823 cells and its effect on Cx32 expression levels was detected. The impact of GATA-3 on Cx32 promoter transcriptional activity was detected using a dual luciferase reporter assay. The results revealed that H. pylori infection increased GATA-3 expression and decreased Cx32 expression in GES-1 cells and in animal gastric tissues compared with their respective controls, whilst in BGC823 cells, GATA-3 siRNA increased Cx32 expression compared with the control. In the SLDT experiment of GES-1 cells with H. pylori infection, the fluorescent dye was primarily limited to a single cell row close to the scratch, and only a limited amount of dye passing to the second cell row, indicating that the GJIC function was substantially reduced or absent compared with the control group, where the fluorescence dye transferred to the neighboring cells of 3-4 rows, indicating a stronger GJIC function comparatively. GATA-3 inhibited the expression of the luciferase reporter gene, compared with the controls, suggesting that GATA-3 inhibited the expression of Cx32 by binding to Cx32 promoter sites. These results indicated that H. pylori-increased GATA-3 expression, which downregulated Cx32 expression, may serve an important function in gastric carcinogenesis, and GATA-3 siRNA may serve a function in the prevention and treatment of gastric cancer. [ABSTRACT FROM AUTHOR]

Although it is difficult to detect αvβ6 integrin (αvβ6) in normal epithelia cells, its expression is upregulated during wound healing and carcinogenesis. Overexpression of αvβ6 has been demonstrated in epithelial cell carcinomas, such as adenocarcinoma of the colon and ovary. However, the expression of αvβ6 has not been reported in hepatocellular carcinoma (HCC). We previously indicated that LPA may induce αvβ6-mediated TGF-β1 signaling mechanisms during the pathogenesis of lung injury and fibrosis. In addition, transforming growth factor-β1 (TGF-β1) and lysophosphatidic acid (LPA) have been demonstrated to participate in the progression of HCC. In the present study, we hypothesized that TGF-β1 and LPA would serve a key role in the subunit integrin β6 (Itgβ6) transcriptional regulatory mechanism in HCC. It was identified that human HCC tissues and Hep-3B cells expressed Itgβ6. Treatment of Hep-3B with TGF-β1 or LPA increased the expression of Itgβ6. Furthermore, truncation experiments indicated a positive regulatory region at −326 to −157 bp of the Itgβ6 promoter. TGF-β1 and LPA increased transcriptional activation at this regulatory region. To the best of our knowledge, the present study was the first to demonstrate Itgβ6 expression in HCC, and the data indicate that TGF-β1 and LPA regulate Itgβ6 expression through the Itgβ6 gene promoter, which is an important factor in the development of HCC. [ABSTRACT FROM AUTHOR]

One of the major causes of tooth loss is chronic inflammation of the periodontium, the tissues surrounding the tooth. Amelotin (AMTN) is a tooth enamel protein which is expressed in maturation‐stage ameloblasts and also in the internal basal lamina of junctional epithelium, a unique epithelial structure attached to the tooth surface which protects against the constant microbiological challenge to the periodontium. Localization of AMTN suggests that its function could be involved in the dentogingival attachment. The purpose of this study was to investigate the effect of interleukin‐1β (IL‐1β) on AMTN gene transcription in human gingival epithelial Ca9‐22 cells. IL‐1β increased AMTN mRNA and protein levels at 3 h, and the levels reached maximum at 6 and 12 h. IL‐1β induced luciferase activities of human AMTN gene promoter constructs (−211, −353, −501, −769, and −950AMTN), but these activities were partially inhibited in −353AMTN constructs that included 3‐bp mutations in CCAAT/enhancer binding protein 1 (C/EBP1), C/EBP2, and Ying Yang 1 (YY1) elements. Transcriptional activities induced by IL‐1β were abrogated by protein kinase A (PKA), tyrosine kinase, mitogen‐activated protein kinase kinase (MEK1/2), and phosphatidylinositol 3‐kinase (PI3K) inhibitors. Gel shift and ChIP assays showed that IL‐1β increased C/EBPβ binding to C/EBP1 and C/EBP2, and YY1 binding to YY1 elements after 3 h, and that these DNA–protein interactions were inhibited by PKA, tyrosine kinase, MEK1/2, and PI3K inhibitors. These results demonstrated that IL‐1β increases AMTN gene transcription in human gingival epithelial cells mediated through C/EBP1, C/EBP2, and YY1 elements in the human AMTN gene promoter. [ABSTRACT FROM AUTHOR]

Objective: Amelotin (AMTN) is an enamel protein that is localized in the basal lamina of ameloblasts in their maturation stage and the internal basal lamina of junctional epithelium (JE) and it is suggested that AMTN could be involved in the dentogingival attachment. To elucidate the transcriptional regulation of human AMTN gene in inflamed gingiva, we have analyzed the effect of tumor necrosis factor-α (TNF-α) on the expression of AMTN gene in Ca9-22 and Sa3 human gingival epithelial cells.Materials and methods: Total RNAs were extracted from Ca9-22 and Sa3 cells after stimulation by TNF-α (10 ng/ml). AMTN mRNA and protein levels were measured by real-time PCR and Western blotting. Transient transfection analyses were completed using the various lengths of human AMTN gene promoter constructs with or without TNF-α. Gel mobility shift and chromatin immunoprecipitation assays were performed to investigate the transcription factors bindings to the human AMTN gene promoter by TNF-α.Results: TNF-α (10 ng/ml) increased AMTN mRNA and protein levels after 12 h. TNF-α induced luciferase activities of human AMTN gene promoter constructs (− 211AMTN, − 353AMTN, and − 501AMTN). TNF-α-induced luciferase activities were partially inhibited in the mutation − 353AMTN constructs that included 3-bp mutations in CCAAT enhancer-binding protein 1 (C/EBP1), C/EBP2 and Ying Yang 1 (YY1) elements. Transcriptional activities induced by TNF-α were inhibited by protein kinase A, Src-tyrosine kinase, MEK1/2, p38 kinase, NF-κB, and PI3-kinase inhibitors. Gel shift assays showed that TNF-α increased nuclear proteins binding to two types of C/EBP elements (C/EBP1 and C/EBP2) and YY1 element. The results of the chromatin immunoprecipitation assays showed that C/EBPβ binding to C/EBP1 and C/EBP2, and YY1 binding to YY1 were increased by TNF-α.Conclusions: These findings demonstrated that TNF-α stimulates AMTN gene transcription in human gingival epithelial cells via C/EBP1, C/EBP2, and YY1 elements in the human AMTN gene promoter. [ABSTRACT FROM AUTHOR]

Follicular dendritic cell‐secreted protein (FDC‐SP) is a secreted protein expressed in follicular dendritic cells, periodontal ligament and junctional epithelium. To elucidate the transcriptional regulation of the human FDC‐SP gene by tumor necrosis factor‐α (TNF‐α), we conducted real‐time PCR, Western blotting, transient transfection analyses with chimeric constructs of the FDC‐SP gene promoter linked to a luciferase reporter gene, gel mobility shift and chromatin immunoprecipitation assays using Ca9‐22 gingival epithelial cells. TNF‐α (10 ng/ml) induced FDC‐SP mRNA and protein levels at 3 hr and reached maximum at 12 hr. In transient transfection assays, TNF‐α (12 hr) increased the LUC activities of constructs between −116FDCSP and −948FDCSP including the human FDC‐SP gene promoter. Transcriptional stimulations by TNF‐α were partially inhibited in the −345FDCSP constructs that included 3‐bp mutations in the YY1, GATA, CCAAT enhancer‐binding protein 2 (C/EBP2) and C/EBP3. Transcriptional activities induced by TNF‐α were inhibited by tyrosine kinase, MEK1/2 and phosphoinositide 3‐kinase inhibitors. The results of ChIP assays showed that YY1, GATA and C/EBPβ transcription factors interacted with the YY1, GATA, C/EBP2 and C/EBP3 elements that were increased by TNF‐α. These studies show that TNF‐α stimulates human FDC‐SP gene transcription by targeting YY1, GATA, C/EBP2 and C/EBP3 in the FDC‐SP gene promoter. [ABSTRACT FROM AUTHOR]

Bone sialoprotein (BSP) is a glycoprotein associated with mineralized tissues. In this study, we investigated the regulation of Bsp transcription by calcium hydroxide [Ca(OH)2] in rat osteosarcoma‐derived osteoblast‐like ROS 17/2.8 cells and stromal bone marrow cells. Application of Ca(OH)2 (0.4 mM) increased the levels of runt‐related transcription factor 2 (Runx2) and BspmRNAs at 3 and 6 h and the level of BSP protein at 12 h. Transient transfection analyses were performed using chimeric constructs encompassing different regions of the rat Bsp gene promoter ligated to a luciferase reporter gene. It was found that Ca(OH)2 increased the luciferase activities of the pLUC3 and pLUC4 constructs. Introduction of 2‐bp mutations to the luciferase construct showed that the effects of Ca(OH)2 were mediated by cAMP response‐element (CRE) and fibroblast growth factor 2 (FGF2) response element (FRE). Luciferase activities induced by Ca(OH)2 were blocked by protein kinase C (PKC), protein kinase A (PKA), phosphoinositide‐3‐kinase (PI3‐K), and extracellular signal‐regulated kinase 1/2 (ERK1/2) inhibitors and by calcium‐sensing receptor (CASR) antagonists. Gel‐shift analyses showed that Ca(OH)2 increased binding of nuclear protein to CRE and FRE. Dexamethasone‐induced mineralization in stromal bone marrow cells was abrogated by CASR antagonists. These studies demonstrate that Ca(OH)2 regulates Bsp transcription via the CASR by targeting CRE and FRE in the rat Bsp gene promoter. [ABSTRACT FROM AUTHOR]