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This study conducted a survey for establishing in-situ and ex-situ conservation measures for northern linage plants that are vulnerable to climate change and for designating Forest Genetic Resource Reserve for 25 algific talus slope sites, which are specific areas of forest biodiversity. The survey was conducted in South Korea within a distance of 50 m to the east, west, north, and south from the core area where wind blows to the algific talus slopes. The study was conducted once or twice per season from April 2016 to November 2021. Vascular plants of 25 algific talus slope sites in South Korea included a total of 1,052 taxa of 125 families, 486 genera, 947 species, 23 subsp., 75 var., and 7 f. The maximum surveyed area was 0.09 km2, accounting for only 0.00014% of the 62,860 km2 forest area in Korea, but comprise 22.27% of the 4,724 species of vascular plants in Korea. The algific talus slopes are areas rich in forest biodiversity. Six taxa were categorized as endangered, including Paeonia obovata Maxim. Sixty-seven taxa, including Astilboides tabularis (Hemsl.) Engl.; 58 taxa endemic to the Korean Peninsula, including Weigela subsessilis (Nakai) L.H. Bailey; and 317 taxa of floristic target plants were categorized as rare plants in the Red list. Further, 181 taxa were identified as northern linage plants and 32 taxa, including Sillaphyton podagraria (H. Boissieu) Pimenov, were limestone area plants. Regarding alien plants, 75 taxa, including Oenothera biennis L., were identified, and the naturalization and urbanization rates were 7.13% and 12.12%, respectively. Plants specific to the phytogeography of the 25 algific talus slope sites in this study were Vaccinium vitis-idaea L., Rosa koreana Kom., Syringa villosa Vahl subsp. wolfii (C.K. Schneid.) Y. Chen & D.Y. Hong, Lonicera chrysantha Turcz. ex Ledeb., Tephroseris flammea (Turcz. ex DC.) Holub, among others.

Long noncoding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. How these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA Firre displays distinct expression and localization patterns in human and mouse. Single molecule RNA FISH reveals that in a range of cell lines, mouse Firre (mFirre) is predominantly nuclear, while human FIRRE (hFIRRE) is distributed between the cytoplasm and nucleus. This localization pattern is maintained in human/mouse hybrid cells expressing both human and mouse Firre, implying that the localization of the lncRNA is species autonomous. We find that the majority of hFIRRE transcripts in the cytoplasm are comprised of isoforms that are enriched in RRD repeats. We furthermore determine that in various tissues, mFirre is more highly expressed than its human counterpart. Our data illustrate that the rapid evolution of syntenic lncRNAs can lead to variations in lncRNA localization and abundance, which in turn may result in disparate lncRNA functions even in closely related species.

Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to molecular biology. Here, we present MPRNA-immunoprecipitation (MPRNA-IP), an adaptation of the previously developed massively parallel RNA assay (MPRNA), and a new avenue for in vivo high-throughput dissection of RNA-protein interactions. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, we are able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest including NORAD, MS2, and human telomerase RNA, and we describe statistical models for identifying RNA domains and parsing the structural contributions of RNA in these interactions. By blending modern and classical approaches, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions.

Certain transcription factors are proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a transcription factor critical for maintenance of pluripotency and neurogenesis, has been found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. Here we demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain in vitro. These interactions are primarily with double-stranded RNA in a non-sequence specific fashion, mediated by a similar but not identical interaction surface. We further determined that Sox2 directly binds RNA in mouse embryonic stem cells by UV-cross-linked immunoprecipitation of Sox2 and more than a thousand Sox2-RNA interactions in vivo were identified using fRIP-seq. Together, these data reveal that Sox2 employs a high-affinity/low-specificity paradigm for RNA binding in vitro and in vivo., Some transcription factors have been proposed to functionally interact with RNA to facilitate proper regulation of gene expression. Here the authors demonstrate that human Sox2 interact directly and with high affinity to RNAs through its HMG DNA-binding domain.

The rapid and unexpected spread of SARS-CoV-2 worldwide has caused unprecedented disruption to daily life and has brought forward critical challenges for public health. The disease was the largest cause of death in the United States in early 2021. Likewise, the COVID-19 pandemic has highlighted the need for rapid and accurate diagnoses at scales larger than ever before. To improve the availability of current gold standard diagnostic testing methods, the development of point-of-care devices that can maintain gold standard sensitivity while reducing the cost and providing portability is much needed. In this work, we combine the amplification capabilities of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) techniques with high-sensitivity end-point detection of crumpled graphene field-effect transistors (cgFETs) to develop a portable detection cell. This electrical detection method takes advantage of the ability of graphene to adsorb single-stranded DNA due to noncovalent π–π bonds but not double-stranded DNA. These devices have demonstrated the ability to detect the presence of the SARS-CoV-2 virus in a range from 10 to 104 copies/μL in 20 viral transport medium (VTM) clinical samples. As a result, we achieved 100% PPV, NPV, sensitivity, and specificity with 10 positive and 10 negative VTM clinical samples. Further, the cgFET devices can differentiate between positive and negative VTM clinical samples in 35 min based on the Dirac point shift. Likewise, the improved sensing capabilities of the crumpled gFET were compared with those of the traditional flat gFET devices.

Long noncoding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. How these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA

DNA methylation has long been recognized as a tumor-promoting factor when aberrantly regulated in the promoter region of genes. However, the effect of intragenic DNA methylation remains poorly understood on the clinical aspects of cancer. Here, we first evaluated the significance of intragenic DNA methylation for survival outcomes of cancer patients in a genome-wide manner. Glioblastoma patients with hypermethylated intragenic regions exhibited better survival than hypomethylated patients. Enrichment analyses of intragenic DNA methylation profiles with epigenetic signatures prioritized the intragenic DNA methylation of ZMIZ1 as a possible glioblastoma prognostic marker that is independent of MGMT methylation in IDH1 wild-type patients. This intragenic region harbored molecular signatures of alternative transcription across many cell types. Furthermore, we found that the intragenic region of ZMIZ1 can serve as a molecular marker in multiple cancers including astrocytomas, bladder cancer and renal cell carcinoma according to DNA methylation status. Finally, in vitro and in vivo experiments uncovered the role of ZMIZ1 as a driver of tumor cell migration. Altogether, our results identify ZMIZ1 as a prognostic marker in cancer and highlight the clinical significance of intragenic methylation in cancer.

The study of survival outliers of glioblastoma can provide important clues on gliomagenesis as well as on the ways to alter clinical course of this almost uniformly lethal cancer type. However, there has been little consensus on genetic and epigenetic signatures of the long-term survival outliers of glioblastoma. Although the two classical molecular markers of glioblastoma including isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation are associated with overall survival rate of glioblastoma patients, they are not specific to the survival outliers. In this study, we compared the two groups of survival outliers of glioblastoma with IDH wild-type, consisting of the glioblastoma patients who lived longer than 3 years (n = 17) and the patients who lived less than 1 year (n = 12) in terms of genome-wide DNA methylation profile. Statistical analyses were performed to identify differentially methylated sites between the two groups. Functional implication of DNA methylation patterns specific to long-term survivors of glioblastoma were investigated by comprehensive enrichment analyses with genomic and epigenomic features. We found that the genome of long-term survivors of glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. In the long-term survival glioblastoma-specific sites distant from CGI, somatic mutations of glioblastoma are enriched with higher DNA methylation, suggesting that the hypomethylation in long-term survival glioblastoma can contribute to reduce the rate of somatic mutation. On the other hand, the hypermethylation near CGIs associates with transcriptional downregulation of genes involved in cancer progression pathways. Using independent cohorts of IDH1/2- wild type glioblastoma, we also showed that these two patterns of DNA methylation can be used as molecular markers of long-term survival glioblastoma. Our results provide extended understanding of DNA methylation, especially of DNA hypomethylation, in cancer genome and reveal clinical importance of DNA methylation pattern as prognostic markers of glioblastoma. Electronic supplementary material The online version of this article (10.1186/s40478-019-0744-0) contains supplementary material, which is available to authorized users.

BackgroundAlu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the role of Alu has not been studied comprehensively in brain tumor because an evolutionary perspective has been the subject of little research in brain tumor. We aim to investigate the relevance of Alu to the gliomagenesis.MethodsUsing a total of 41 pairs of neurotypicial brain tissue samples and samples of diverse gliomas, we performed strand-specific RNA-seq and analyzed two Alu-associated post-transcriptional regulations, A-to-I editing and circular RNAs, and Alu expression in a genome-wide way. ResultsWe found that while both A-to-I editing and circular RNA are decreased overall in gliomas, grade 2 oligodendrogliomas do not show this same pattern of global changes. Instead, in comparison with other gliomas, oligodendrogliomas showed a higher proportion of perturbed Alu RNA. Adenosine deaminase acting on RNA 2 (ADAR2) was down-regulated in gliomas other than grade 2 oligodendrogliomas, contributing to the observed Alu-associated perturbation. ConclusionsOur results demonstrate that Alu is associated with glioma development and grade 2 oligodendroglioma exhibits a unique pattern of Alu-associated post-transcriptional regulations, which provides an insight to gliomagenesis from the perspective of an evolutionary genetic element.

Many chromatin-binding proteins and protein complexes that regulate transcription also bind RNA. One of these, Polycomb repressive complex 2 (PRC2), deposits the H3K27me3 mark of facultative heterochromatin and is required for stem cell differentiation. PRC2 binds RNAs broadly in vivo and in vitro. Yet, the biological importance of this RNA binding remains unsettled. Here, we tackle this question in human induced pluripotent stem cells by using multiple complementary approaches. Perturbation of RNA-PRC2 interaction by RNase A, by a chemical inhibitor of transcription or by an RNA-binding-defective mutant all disrupted PRC2 chromatin occupancy and localization genome wide. The physiological relevance of PRC2-RNA interactions is further underscored by a cardiomyocyte differentiation defect upon genetic disruption. We conclude that PRC2 requires RNA binding for chromatin localization in human pluripotent stem cells and in turn for defining cellular state.

Additional file 15: Fig. S10. Loss of TUG1 expression in infertile human males. Heatmap of microarray data from three different probe sets showing decreased expression of TUG1 in sperm from infertile teratozoospermic men (T) compared to fertile (normospermic) individuals (ND). In all cases, p < 4.39 x10-4.

Additional file 3: Fig. S3. Overview of the Tug1 locus in mouse. UCSC genome browser showing the murineTug1 locus. The three predominate Tug1 isoforms are depicted (black) and the Tug1 transgene (tg(Tug1)) is shown (blue). For Tug1 knockout, the longest annotated Tug1 isoform was replaced by a lacZ reporter cassette, leaving the promotor and first exon intact. The deleted region is indicated by red dashed lines. The open reading frame (ORF) encoding the TUG1-BOAT protein and PhyloCSF scores for the (-2) frame across the locus are depicted (grey). Chromosomal coordinates (mm10) are shown.

Additional file 2: Fig. S2. In vivo expression pattern of Tug1 during murine embryogenesis. RNA in situ hybridization of Tug1 RNA using a digoxigenin-labeled antisense RNA probe in mouse embryos at different developmental stages. Embryonic day (E)8.5, E9.5, E10.5, E11.5, and E12.5 are shown.

Additional file 4: Fig. S4. Morphology analysis of Tug1-/- mice and sperm (A) Body mass (g) measurements over 11 weeks of male and female Tug1-/- mice compared to wild type littermates. Males: Tug1-/- (n = 7); WT (n = 8). Females: Tug1-/- (n = 3), WT (n = 7). Significant p values at specific time points are indicated (*). (B) Representative images from adult male mice (12 weeks old) show normal physiological appearance of external genitalia and reproductive tracks in Tug1-/- compared to WT. Seminal vesicles (SV), vas deferens (VD), bladder (B), testicle (T), epididymis (E), anterior prostate (AP). (C) Box plots of body mass (g) (left panel), relative testis mass (testis mass / body mass; middle panel) and total sperm count for wild type (n = 9) and Tug1-/- males. (D) Box plots of the percentage of different sperm morphological abnormalities for wild type (n = 9) and Tug1-/- (n = 8) males. Significant (*) p value (Wilcoxon rank sum test) is indicated.

RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis., LncRNA loci potentially contain multiple modes that can exert function, including DNA regulatory elements. Here, the authors generated genetic models in mice to dissect the role of the syntenically conserved lncRNA Firre in the context of hematopoiesis.

The aim of this work was to study the effect of heat and moisture treatment (HMT) on carotenoids, phenolic content and antioxidant capacity of ground, orange maize. Total carotenoid content (TCC) of untreated sample (53.39 mg/kg) was 2.2 times higher than measured in treated orange maize f (24.61 mg/kg). The rates of degradation with HMT were in the following order: β-carotene > β-cryptoxanthin > zeaxanthin > lutein. There was a significant interaction between longer heating time and higher moisture content on carotenoid degradation (p

Transcriptome compartmentalization by the nuclear membrane provides both stochastic and functional buffering of transcript activity in the cytoplasm and has recently been implicated in neurodegenerative disease processes. Although many mechanisms regulating transcript compartmentalization are also prevalent in brain development, the extent to which subcellular localization differs as the brain matures has yet to be addressed. To characterize the nuclear and cytoplasmic transcriptomes during brain development, we sequenced both RNA fractions from homogenate prenatal and adult human postmortem cortex using PolyA+ and RiboZero library preparation methods. We find that while many genes are differentially expressed by fraction and developmental expression changes are similarly detectable in nuclear and cytoplasmic RNA, the compartmented transcriptomes become more distinct as the brain matures, perhaps reflecting increased utilization of nuclear retention as a regulatory strategy in adult brain. We examined potential mechanisms of this developmental divergence including alternative splicing, RNA editing, nuclear pore composition, RNA binding protein motif enrichment, and RNA secondary structure. Intron retention is associated with greater nuclear abundance in a subset of transcripts, as is enrichment for several splicing factor binding motifs. Finally, we examined disease association with fraction-regulated gene sets and found nuclear-enriched genes were also preferentially enriched in gene sets associated with neurodevelopmental psychiatric diseases. These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an underappreciated role in developmental regulation of gene expression in brain, particularly in genes whose dysregulation is related to neuropsychiatric disorders.

BackgroundSeveral long noncoding RNAs (lncRNAs) have been shown to function as central components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, their functions remain largely uncharacterized. This is compounded by the fact that identifying lncRNA loci that have robust and reproducible phenotypes when mutated has been a challenge.ResultsWe previously generated a cohort of 20 lncRNA loci knockout mice. Here, we extend our initial study and provide a more detailed analysis of the highly conserved lncRNA locus, Taurine Upregulated Gene 1 (Tug1). We report that Tug1 knockout male mice are sterile with complete penetrance due to a low sperm count and abnormal sperm morphology. Having identified a lncRNA loci with a robust phenotype, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region (DNA, RNA, protein, or the act of transcription) have activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors three distinct regulatory activities – two noncoding and one coding: (i) a cis DNA repressor that regulates many neighboring genes, (ii) a lncRNA that can regulate genes by a trans-based function, and finally (iii) Tug1 encodes an evolutionary conserved peptide that when overexpressed impacts mitochondrial membrane potential.ConclusionsOur results reveal an essential role for the Tug1 locus in male fertility and uncover three distinct regulatory activities in the Tug1 locus, thus highlighting the complexity present at lncRNA loci.

Figures S1. Classification of the sites in the 450â k bead array according to CGI. Figure S2. The cells and histone marks obtained from ENCODE. Figure S3. Volcano plot of differences between STS-GBM and LTS-GBM in DNA methylation level (beta). Figure S4. Proportion of the number of significant sites according to chromosomes. Figure S5. The relation between the ChIP-seq signal of H3K9me3 and the DNA methylation level (beta) for the hyper-methylated sites in U87 cell line. Figure S6. Enrichment of significant differential sites in gene regions. Figure S7. Distribution of Pearson correlation coefficients between DNA methylation level (beta) and gene expression measured by RNA-seq (FPKM) across GBM samples in TCGA. Figure S8. Distribution of Z-score of DNA methylation of the sample with somatic mutation. Table S1. Sample information. Table S3. Gene Ontology (GO) results of the hypo-methylated sites. (PDF 2060 kb)

The provitamin A potential of landrace orange maize from different locations (A, B, C and D) of central Malawi has been evaluated. Physicochemical compositions, color, total carotenoid content (TCC), carotenoid profiles, and oxygen radical absorbance capacity (ORAC) and 2,2-diphenyl-1-picryhydrazyl (DPPH) free radical scavenging activity as antioxidant capacities of maize were determined. Color values of orange maize had correlations with β-cryptoxanthin (r>0.36). TCC of white and orange maize averaged 2.12 and 59.5 mg/kg, respectively. Lutein was the most abundant carotenoid (47.8%) in orange maize, followed by zeaxanthin (24.2%), β-carotene (16.4%) and β-cryptoxanthin (11.6%). Location D showed the highest levels of lutein, zeaxanthin and antioxidant capacity. Provitamin A content of orange maize met the target level (15 μg/g) of biofortification. Retinol activity equivalent (RAE) from β-cryptoxanthin and β-carotene in orange maize averaged 81.73 μg/100g. In conclusion, orange maize has the potential to be a natural source of provitamin A.

BACKGROUND: The study of survival outliers of glioblastoma (GBM) can have important implications on gliomagenesis as well as in the identification of ways to alter clinical course on this almost uniformly lethal cancer type. However, current studied epigenetic and genetic signatures of the GBM outliers have failed to identify unifying criteria to characterize this unique group of patients. MATERIAL AND METHODS: We compared global DNA methylation patterns of IDH wild-type (IDH WT) GBM patients who lived longer than 3 years (n=17, LTS-GBM) with patients who lived less than 1 year (n=12, STS-GBM), and performed comprehensive enrichment analyses with genomic and epigenomic signatures in conjunction with available open source data. The analysis result was further validated with an independent set of 10 LTS-GBM samples. RESULTS: We found that the genome of LTS-GBM is differentially methylated relative to STS-GBM depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct signature of histone mark enrichment, and oncogenic aspects in gliomagenesis. The hypomethylation pattern at the region distant from CGI is associated with H3K9me3 enrichment and lower rates of de novo mutations, while the hypermethylation at CGIs is associated with H3K27ac and correlates with transcriptional downregulation of genes involved in cancer progression pathways. CONCLUSION: These results extend our understanding of DNA methylation of survival outliers in glioblastoma in a genome-wide level and provide insight on the potential impact of DNA hypomethylation in cancer genome.

The study of survival outliers of glioblastoma (GBM) can have important implications on gliomagenesis as well as in the identification of ways to alter clinical course on this almost uniformly lethal cancer type. However, current studied epigenetic and genetic signatures of the GBM outliers have failed to identify unifying criteria to characterize this unique group of patients. In this study, we profiled the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma and performed comprehensive enrichment analyses with genomic and epigenomic signatures. We found that the genome of long-term survivors in glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. The hypomethylation pattern at the region distant from CGI is associated with lower rates of de novo mutations while the hypermethylation at CGIs correlates with transcriptional downregulation of genes involved in cancer progression pathways. These results extend our understanding of DNA methylation of survival outliers in glioblastoma in a genome-wide level, and provide insight on the potential impact of DNA hypomethylation in cancer genome.

Fluorescence-guided surgery using 5-aminolevulinic acid (5-ALA) is now a widely-used modality for glioblastoma (GBM) treatment. However, intratumoral heterogeneity of fluorescence intensity may reflect different onco-metabolic programs. Here, we investigated the metabolic mechanism underlying the heterogeneity of 5-ALA fluorescence in GBM. Using an in-house developed fluorescence quantification system for tumor tissues, we collected 3 types of GBM tissues on the basis of their fluorescence intensity, which was characterized as strong, weak, and none. Expression profiling by RNA-sequencing revealed 77 genes with a proportional relationship and 509 genes with an inverse relationship between gene expression and fluorescence intensity. Functional analysis and in vitro experiments confirmed glutaminase 2 (GLS2) as a key gene associated with the fluorescence heterogeneity. Subsequent metabolite profiling discovered that insufficient NADPH due to GLS2 underexpression was responsible for the delayed metabolism of 5-ALA and accumulation of protoporphyrin IX (PpIX) in the high fluorescence area. The expression level of GLS2 and related NADPH production capacity is associated with the regional heterogeneity of 5-ALA fluorescence in GBM.

Background Since high-throughput protein-protein interaction (PPI) data has recently become available for humans, there has been a growing interest in combining PPI data with other genome-wide data. In particular, the identification of phenotype-related PPI subnetworks using gene expression data has been of great concern. Successful integration for the identification of significant subnetworks requires the use of a search algorithm with a proper scoring method. Here we propose a multivariate analysis of variance (MANOVA)-based scoring method with a greedy search for identifying differentially expressed PPI subnetworks. Results Given the MANOVA-based scoring method, we performed a greedy search to identify the subnetworks with the maximum scores in the PPI network. Our approach was successfully applied to human microarray datasets. Each identified subnetwork was annotated with the Gene Ontology (GO) term, resulting in the phenotype-related functional pathway or complex. We also compared these results with those of other scoring methods such as t statistic- and mutual information-based scoring methods. The MANOVA-based method produced subnetworks with a larger number of proteins than the other methods. Furthermore, the subnetworks identified by the MANOVA-based method tended to consist of highly correlated proteins. Conclusion This article proposes a MANOVA-based scoring method to combine PPI data with expression data using a greedy search. This method is recommended for the highly sensitive detection of large subnetworks.