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Background: MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis., Results: In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones., Conclusions: Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism.

MicroRNAs (miRNAs) are short noncoding RNAs that play important roles in cellular processes and disease pathogenesis via the control of specific targeted gene expression. The miR-196s miRNA is encoded at three paralogous loci in three HOX clusters and acts as an oncogenic miRNA in cancer progression. Recent studies have demonstrated that the expression of miR-196b increases cell proliferation and survival in leukemic cells. Here, we used a sequential methylation analysis to reveal that the methylation status correlated well with miR-196b expression in different cell lines. Treatment with the demethylating drug 5-Aza-dC reactivated miR-196b transcription in methylation-silenced cells. Using in vitro methylation approach, we further provide evidences that promoter hypermethylation represses miR-196b transcriptional activation tightly in human cancer cell lines. We also demonstrate that the expression of miR-196b is significantly elevated in gastric cancer and that hypomethylation status of miR-196b CpG islands frequently is observed in primary gastric tumors. Our results provide important information on miR-196s regulation and demonstrate that abnormal DNA hypomethylation induces overexpression of miR-196b in gastric cancer., (© 2010 Wiley-Liss, Inc.)

Sco-CHH and Sco-CHH-L (CHH-like peptide), two structural variants of the crustacean hyperglycemic hormone family identified in the mud crab (Scylla olivacea), are presumably alternatively spliced gene products. In this study, Sco-CHH and Sco-CHH-L were isolated from the tissues using high performance liquid chromatography. Identity of the native peptides was confirmed using mass spectrometric (MS) analyses of purified materials and of trypsin-digested peptide fragments. Additionally, characterizations using circular dichroism (CD) spectrometry revealed that the 2 peptides have similar CD spectral profiles, showing they are composed mainly of alpha-helices, and are similarly thermo-stable with a melting temperature of 74-75 degrees C. Results of bioassays indicated that Sco-CHH exerted hyperglycemic and molt-inhibiting activity, whereas Sco-CHH-L did not. Further, recombinant Sco-CHH-Gly (rSco-CHH-Gly, a glycine extended Sco-CHH) and Sco-CHH-L (rSco-CHH-L) were produced using an Escherichia coli expression system, refolded, and purified. rSco-CHH-Gly was further alpha-amidated at the C-terminal end to produce rSco-CHH. MS analyses of enzyme-digested peptide fragments of rSco-CHH-Gly and rSco-CHH-L showed that the two peptides share a common disulfide bond pattern: C7-C43, C23-C39, and C26-C52. Circular dichroism analyses and hyperglycemic assay revealed that rSco-CHH and rSco-CHH-L resemble their native counterparts, in terms of CD spectral profiles, melting curve profiles, and biological activity. rSco-CHH-Gly has a lower alpha-helical content (32%) than rSco-CHH (47%), a structural deviation that may be responsible for the significant decrease in the biological activity of rSco-CHH-Gly. Finally, modeled structure of Sco-CHH and Sco-CHH-L indicated that they are similarly folded, each with an N-terminal tail region and 4 alpha-helices. Putative surface residues located in corresponding positions of Sco-CHH and Sco-CHH-L but with side chains of different properties were identified. The combined results support the notion that Sco-CHH and Sco-CHH-L are functionally different, but resemble each other at higher-level structures. Functional diversity between the 2 peptides is probably due to critical residues located in the C-terminus. The availability of large amounts of recombinant proteins will permit additional functional and structural studies of these CHH family peptides., (Copyright 2010 Elsevier Inc. All rights reserved.)

Background: Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms., Results: By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices., Conclusion: Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence.

Aim: To examine the antitumor effect of 4'-chloro-3,5-dihydroxystilbene, a resveratrol derivative, on lung adenocarcinoma A549 cells., Methods: The cytotoxic IC(50) was determined by direct cell counting. Flow cytometry, monodansylcadaverine (MDC) staining, transfection, Western blot and a proteasome activity assay were used to study the cellular mechanism of 4'-chloro-3,5-dihydroxystilbene. A xenograft nude mouse model was used to analyze the antitumor effect in vivo., Results: 4'-Chloro-3,5-dihydroxystilbene induced a rapid and persistent increase in the intracellular reactive oxygen species in the cells, but the cell death could not be inhibited by two antioxidant agents. The derivative caused sub-G(1) formation, a decrease in the mitochondria membrane potential and poly (ADP-ribose) polymerase degradation, and the caspase inhibitor Z-VAD-FMK could partially prevent cell death. It also induced a significant increase in intracellular acidic vacuoles, LC3-II formation and intracellular GFP-LC3 aggregation. An autophagic inhibitor partially reversed cell death. Additionally, 4'-chloro-3,5-dihydroxystilbene induced the accumulation of ubiquitinated conjugates and inhibited proteasome activity in cells. In an in vivo study, 4'-chloro-3,5-dihydroxystilbene retarded tumor growth in nude mice., Conclusion: These data suggest that the resveratrol derivative 4'-chloro-3,5-dihydroxystilbene could be developed as an anti-tumor compound.

Many of the known microRNAs (miRNAs) are encoded by polycistronic transcripts and are thought to be co-expressed. In this study, we discovered that the expression of a large miRNA cluster (C19MC) on human chromosome 19 is upregulated by the demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-dC), in AGS gastric cancer cells. We found that C19MC was rarely expressed in most cells, but its expression was restored through DNA demethylation. We confirmed that this miRNA cluster was mainly expressed in the placenta, as previously reported. Furthermore, its expression pattern was highly correlated with the methylation state of a distal CpG-rich region located about 17.6 kb upstream of the miRNA cluster. Using combined bisulfite restriction analysis (COBRA) and bisulfite-sequencing techniques, we determined that this CpG-rich region is hypermethylated in the AGS and HeLa cells, but hypomethylated in the placenta tissue. In conclusion, we demonstrated that the expression pattern of the C19MC was activated in human cancer cells through demethylation of a CpG-rich region.

Bacterial adherence to epithelial cells is a key virulence trait of pathogenic bacteria. The type 1 fimbriae and the P-fimbriae of uropathogenic Escherichia coli (UPEC) have both been described to be important for the establishment of urinary tract infections (UTI). To explore the interactions between the host and bacterium responsible for the different environments of UPEC invasion, we examined the effect of pH and osmolarity on UPEC strain J96 fimbrial expression, and subsequent J96-induced interleukin-8 (IL-8) expression in different uroepithelial cells. The J96 strain grown in high pH with low osmolarity condition was favorable for the expression of type 1 fimbriae; whereas J96 grown in low pH with high osmolarity condition was beneficial for P fimbriae expression. Type 1 fimbriated J96 specifically invaded bladder 5637 epithelial cells and induced IL-8 expression. On the contrary, P fimbriated J96 invaded renal 786-O epithelial cells and induced IL-8 expression effectively. Type 1 fimbriated J96-induced IL-8 induction involved the p38, as well as ERK, JNK pathways, which leads to AP-1-mediated gene expression. P fimbriated J96-induced augmentation of IL-8 expression mainly involved p38-mediated AP-1 and NF-kappaB transcriptional activation. These results indicate that different expression of fimbriae in J96 trigger differential IL-8 gene regulation pathways in different uroepithelial cells.

Wogonin, a naturally occurring plant flavonoid, is isolated from Chinese herbal plants Scutellaria baicalensis Georgi and S. barbata D. Don. The extract of S. baicalensis Georgi has been added to an assortment of health drinks or food supplements. Wogonin has been reported to exhibit anticancer and anti-inflammatory properties. Cyclooxygenase-2 (COX-2) is a key enzyme in the production of prostaglandins in inflammatory conditions. In this study, the effect of wogonin on phorbol 12-myristate 13-acetate (PMA)-induced COX-2 expression was investigated. It showed that wogonin inhibited PMA-induced COX-2 protein and mRNA levels in human lung epithelial cancer cells, and the mechanism of this inhibition was at the transcriptional level by using COX-2 gene promoter assay. Among various signal inhibitors, the mitogen-activated protein kinase kinase 1/2 (MEK1/2) inhibitor U0126 also inhibited PMA-induced COX-2 expression and COX-2 promoter activation. The activity of AP-1-driven promoter, but not nuclear factor-kappa B (NF-kappaB), was inhibited by U0126. The data indicated that MEK1/2-AP-1 is very important for PMA-induced COX-2 expression. Wogonin also inhibited PMA-induced AP-1 activation and the expression of c-Jun, a key component of AP-1. Taken together, it is suggested that wogonin inhibits PMA-induced COX-2 gene expression by inhibiting c-Jun expression and AP-1 activation in A549 cells.

ING4 (inhibitor of growth 4) is a candidate tumor suppressor gene that is implicated as a repressor of cell growth, angiogenesis, cell spreading and cell migration and can suppress loss of contact inhibition in vitro. Another group and we identified four wobble-splicing isoforms of ING4 generated by alternative splicing at two tandem splice sites, GC(N)(7)GT and NAGNAG, which caused canonical (GT-AG) and non-canonical (GC-AG) splice site wobbling selection. Expression of the four ING4 wobble-splicing isoforms did not vary significantly in any of the cell lines examined. Here we show that ING4_v1 is translocated to the nucleolus, indicating that ING4 contains an intrinsic nucleolar localization signal. We further demonstrate that the subcellular localization of ING4 is modulated by two wobble-splicing events at the exon 4-5 boundary, causing displacement from the nucleolus to the nucleus. We also observed that ING4 is degraded through the ubiquitin-proteasome pathway and that it is subjected to N-terminal ubiquitination. We demonstrate that nucleolar accumulation of ING4 prolongs its half-life, but lack of nucleolar targeting potentially increases ING4 degradation. Taken together, our data suggest that the two wobble-splicing events at the exon 4-5 boundary influence subnuclear localization and degradation of ING4.

Two full-length cDNA sequences encoding a crustacean hyperglycemic hormone (CHH) precursor were cloned from tissues of the mud crab Scylla olivacea. Sco-CHH (S. olivacea CHH) was cloned from eyestalk ganglia, whereas Sco-CHH-L (S. olivacea CHH-like peptide) was cloned from extra-eyestalk tissues (pericardial organ and thoracic ganglia). Each conceptually translated precursor is expected to be processed into a signal peptide, a CHH precursor-related peptide (CPRP), and a mature CHH or CHH-like peptide. The two precursors are identical in amino acid sequence through the 40th residue of the mature peptide, but different from each other substantially in the C-terminus. Both CHH variants contain the six highly conserved cysteine residues characteristic of the CHH family peptides, and share higher sequence identities with other brachyuran CHH sequences than with those of other taxonomic groups. As determined by reverse transcription-polymerase chain reaction (RT-PCR), the transcripts of Sco-CHH and Sco-CHH-L were present in eyestalk ganglia and several extra-eyestalk tissues (the thoracic ganglia, pericardial organ, brain, circumesophageal connectives, and gut). Sco-CHH was the predominant form in eyestalk ganglia, while Sco-CHH-L was the predominant form in several extra-eyestalk tissues. Neither transcript was expressed in the muscle, hepatopancreas, ovary, testis, heart, or gill. Antisera were raised against synthetic peptides corresponding to a stretch of sequence-specific to the C-terminus of Sco-CHH or Sco-CHH-L. Western blot analyses of tissues expressing Sco-CHH and Sco-CHH-L detected a Sco-CHH immunoreactive protein in the sinus gland, and a Sco-CHH-L immunoreactive protein in the pericardial organ. Immunohistochemical analyses of the eyestalk ganglia localized both Sco-CHH and Sco-CHH-L immunoreactivity to the sinus gland, and only Sco-CHH immunoreactivity to the X-organ somata; analyses of the pericardial organs also localized both Sco-CHH and Sco-CHH-L immunoreactivity to the anterior and posterior bars, as well as to longitudinal trunks joining the two bars. The combined data provided supporting evidence that Sco-CHH and Sco-CHH-L are co-localized in the same tissue.

Alternative splicing involving the 3' tandem splice site NAGNAG sequence may play a role in the structure-function diversity of proteins. However, how 3' tandem splice site utilization is determined is not well understood. We previously demonstrated that 3' NAGNAG-based wobble splicing occurs mostly in a tissue- and developmental stage-independent manner. Bioinformatic analysis reveals that the nucleotide preceding the AG dinucleotide may influence 3' splice site utilization; this is also supported by an in vivo splicing assay. Moreover, we found that the intron sequence plays an important role in 3' splice site selection for NAGNAG wobble splicing. Mutations of the region between the branch site and the NAGNAG 3' splice site, indeed, affected the ratio of the distal/proximal AG selection. Finally, we found that single nucleotide polymorphisms around the NAGNAG motif could affect the splice site choice, which may lead to a change in mRNA patterns and influence protein function. We conclude that the NAGNAG motif and its upstream region to the branch point sequence are required for 3' tandem splice site selection.

Alternative splicing is an important mechanism mediating the function of genes in multicellular organisms. Recently, we discovered a new splicing-junction wobble mechanism that generates subtle alterations in mRNA by randomly selecting tandem 5' and 3' splicing-junction sites. Here we developed a sensitive approach to identify such splicing-junction wobble isoforms using polymerase chain reaction amplification with fluorescence-labeled primers encompassing the wobble-splicing boundary and capillary electrophoresis. Using the ING4 wobble isoforms as an example, we demonstrated that capillary electrophoresis can precisely separate DNA fragments with a small difference in size (<3 nt) and can be used to quantify the expression ratio, which thus measures the distribution of each splicing-junction wobble isoform in tissues. Based on our analyses of several genes, the relative ratio of each wobble-splicing isoform tends to be constant among various tissues. The occasional observed tissue heterogeneity of wobble-splicing transcripts can be generated only by genomic single-nucleotide polymorphisms around the splicing junction.

Agkicetin-C, a potent glycoprotein Ib antagonist from the venom of the Chinese pit viper, Deinagkistrodon acutus, has been purified and characterized (5). It is a disulfide-linked heterodimer containing subunits of 132 and of 123 amino acid residues. Herein, the complete amino acid sequences were resolved by cloning and nucleotide sequencing of the cDNAs. The sequences of its subunits are homologous to those of other snake venom proteins of the C-type (Ca2+-dependent) lectin superfamily. A three-dimensional model of agkicetin-C was constructed based on the crystal structure of habu coagulation factor IX/X-binding protein. By careful alignment of all the related sequences available and comparing the 3D-model of agkicetin-C with structures of other homologous proteins of different functions, some variable residues of agkicetin-C were identified, which possibly are responsible for the specificity of this distinct subtype of the C-type lectin-like venom proteins.