MicroRNAs (miRNAs) are one family of short (21-23 nt) regulatory non-coding RNAs processed from long (70-110 nt) miRNA precursors (pre-miRNAs). Identifying true and false precursors plays an important role in computational identification of miRNAs. Some numerical features have been extracted from precursor sequences and their secondary structures to suit some classification methods; however, they may lose some usefully discriminative information hidden in sequences and structures. In this study, pre-miRNA sequences and their secondary structures are directly used to construct an exponential kernel based on weighted Levenshtein distance between two sequences. This string kernel is then combined with support vector machine (SVM) for detecting true and false pre-miRNAs. Based on 331 training samples of true and false human pre-miRNAs, 2 key parameters in SVM are selected by 5-fold cross validation and grid search, and 5 realizations with different 5-fold partitions are executed. Among 16 independent test sets from 3 human, 8 animal, 2 plant, 1 virus, and 2 artificially false human pre-miRNAs, our method statistically outperforms the previous SVM-based technique on 11 sets, including 3 human, 7 animal, and 1 false human pre-miRNAs. In particular, premiRNAs with multiple loops that were usually excluded in the previous work are correctly identified in this study with an accuracy of 92.66%.
Animals ; Artificial Intelligence ; Base Sequence ; Computational Biology ; Databases, Nucleic Acid ; Humans ; MicroRNAs ; chemistry ; genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors ; chemistry ; genetics ; Species Specificity

Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.
Animals ; Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotides ; metabolism ; Oocytes ; cytology ; metabolism ; Pseudouridine ; metabolism ; RNA Precursors ; metabolism ; RNA Splice Sites ; RNA Splicing ; RNA, Messenger ; genetics ; metabolism ; RNA, Small Nuclear ; genetics ; metabolism ; Ribonucleoproteins, Small Nuclear ; genetics ; metabolism ; Saccharomyces cerevisiae ; genetics ; metabolism ; Saccharomyces cerevisiae Proteins ; genetics ; metabolism ; Spliceosomes ; genetics ; metabolism ; Uridine ; analogs & derivatives ; metabolism ; Xenopus ; genetics ; metabolism

Folate, vitamin B12, and homocysteine (HCY) are involved in the metabolism of nucleic acid precursors and it has been hypothesized that they also influence telomere length, a biomarker of aging. However, previous studies have reported inconsistent findings, and data for older adults are limited. Our study aimed to evaluate associations between leukocyte telomere length (LTL) and serum folate, vitamin B12, and HCY levels among adults aged 55 years and over. In a cross-sectional study in 798 men and women aged 55-79 years, serum folate, vitamin B12, and HCY levels were measured using chemiluminescent immunometric assays, and relative LTL was assessed using quantitative real-time polymerase chain reaction. To evaluate associations between LTL and serum folate, vitamin B12, and HCY levels, multiple linear regression models were used. In multiple models adjusted for age, sex, serum high sensitive C-reactive protein (hs-CRP) levels, and other potential confounding factors, we found no association between LTL and serum folate, vitamin B12, and HCY levels. However, we did find a significant inverse association between HCY levels and LTL in participants with serum hs-CRP levels of > or = 2 mg/L (p < 0.05). Moreover, there was a trend toward an association between HCY and vitamin B12 levels in these individuals (p = 0.08). In those with serum hs-CRP levels of < 2 mg/L, HCY was inversely associated with vitamin B12 levels (p < 0.001) and had no association with LTL. Our findings suggest that increased serum HCY levels, when combined with the presence of systemic inflammation, may play a role in accelerating biological aging.
Adult* ; Aging ; C-Reactive Protein ; Cross-Sectional Studies ; Female ; Folic Acid ; Homocysteine* ; Humans ; Inflammation* ; Leukocytes* ; Linear Models ; Male ; Metabolism ; Nucleic Acid Precursors ; Real-Time Polymerase Chain Reaction ; Telomere* ; Vitamin B 12* ; Vitamin B Complex ; Vitamins*

OBJECTIVETo clone and identify the mouse gene homologous to human hepatitis B virus (HBV) pre-S1 protein-binding protein (PS1BP).

METHODSThe human PS1BP cDNA sequence was used as the reference sequence to search homologous mouse cDNA sequence from GenBank established by National Center for Biotechnology (NCBI), National Institute of Health (NIH), for its homologous cDNA sequences of mouse by BLASTn tool. The characteristics of mouse PS1BP protein primary structure were predicted by online software. Finally the genomic DNA structure of mouse PS1BP was deduced and compared.

RESULTSThe mouse PS1BP was identified and consisted of 1455 nt, coding a protein of 484 aa. The identity of human and mouse PS1BP protein is 84.92% (411/484). The genomic DNA of mouse PS1BP consisted of 3 exons and 2 introns.

CONCLUSIONThe identification and characterization of mouse PS1BP cDNA and genomic DNA pave a way for further study of their structures and functions.

Amino Acid Sequence ; Animals ; Base Sequence ; Carrier Proteins ; genetics ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; genetics ; Databases, Nucleic Acid ; Hepatitis B Surface Antigens ; genetics ; Hepatitis B virus ; genetics ; Humans ; Mice ; Molecular Sequence Data ; Protein Precursors ; genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid

Disappearance of hepatitis B surface antigens (HBsAg) in chronic hepatitis B usually indicates clearance of hepatitis B virus (HBV) infection. However, false HBsAg negativity with mutations in pre-S2 and 'a' determinant has been reported. It is also known that YMDD mutations decrease the production of HBV and escape detection of serum HBsAg. Here, we report overlapping gene mutations in a patient with HBsAg loss during the lamivudine therapy. After 36 months of lamivudine therapy in a 44-yrold Korean chronic hepatitis B patient, serum HBsAg turned negative while HBV DNA remained positive by a DNA probe method. Nucleotide sequence of serum HBV DNA was compared with the HBV genotype C subtype adr registered in NCBI AF 286594. Deletion of nucleotides 23 to 55 (amino acids 12 to 22) was identified in the pre-S2 region. Sequencing of the 'a' determinant revealed amino acid substitutions as I126S, T131N, M133T, and S136Y. Methionine of rtM204 in the P gene was substituted for isoleucine indicating YIDD mutation (rtM204I). We identified a HBV mutant composed of pre-S2 deletions and 'a' determinant substitutions with YMDD mutation. Our result suggests that false HBsAg negativity can be induced by combination of overlapping gene mutations during the lamivudine therapy.
Adult ; Amino Acid Sequence ; Anti-HIV Agents/therapeutic use ; Base Sequence ; Comparative Study ; DNA Mutational Analysis ; DNA, Viral/blood/chemistry/genetics ; DNA-Directed DNA Polymerase/genetics ; Gene Deletion ; Genes, Overlapping/*genetics ; Hepatitis B Surface Antigens/blood/*genetics ; Hepatitis B virus/*genetics ; Hepatitis B, Chronic/blood/*drug therapy/virology ; Humans ; Lamivudine/*therapeutic use ; Male ; Molecular Sequence Data ; *Mutation ; Protein Precursors/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Viral Proteins/genetics

No abstract available.
Animals ; Gonadotropin-Releasing Hormone* ; Mice* ; RNA Precursors*

Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell "housekeeping" machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
Humans ; Neoplasms/metabolism* ; RNA Precursors/metabolism* ; RNA Splicing ; RNA Splicing Factors/metabolism* ; Spliceosomes/metabolism*

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.
Alternative Splicing ; Cell Line ; Exons* ; Humans ; Least-Squares Analysis ; Protein Isoforms ; RNA Precursors ; RNA, Messenger ; Transcriptome

Alternative splicing of pre-mRNA is an important mechanism for regulating gene function at the post-transcription level and for producing proteomic diversity in higher eukaryotes. The alternative splicing is regulated by the interaction between diverse cis-acting elements and trans-acting factors. Alternative splicing events of oncogenes, tumor suppressor genes and metastasis suppressor genes are associated with the initiation and development of human neoplasms. The protein isoforms sourced from alternative splicing take part in regulating the gene transcription, cell cycle, apoptosis of cells, and playing a role in tumor growth. It is possible for molecular therapy to target directly isoforms of protein produced by alternative splicing or to interfere with the process of alternative splicing.
Alternative Splicing ; genetics ; Humans ; Neoplasms ; genetics ; RNA Precursors ; metabolism ; RNA, Neoplasm ; analysis ; Transcription, Genetic

T-cell internal antigen-1 (TIA-1) has roles in regulating alternative pre-mRNA splicing, mRNA translation, and stress granule (SG) formation in human cells. As an evolutionarily conserved response to environmental stress, SGs have been reported in various species. However, SG formation in chicken cells and the role of chicken TIA-1 (cTIA-1) in SG assembly has not been elucidated. In the present study, we cloned cTIA-1 and showed that it facilitates the assembly of canonical SGs in both human and chicken cells. Overexpression of the chicken prion-related domain (cPRD) of cTIA-1 that bore an N-terminal green fluorescent protein (GFP) tag (pntGFP-cPRD) or Flag tag (pFlag-cPRD) induced the production of typical SGs. However, C-terminal GFP-tagged cPRD induced notably large cytoplasmic granules that were devoid of endogenous G3BP1 and remained stable when exposed to cycloheximide, indicating that these were not typical SGs, and that the pntGFP tag influences cPRD localization. Finally, endogenous cTIA-1 was recruited to SGs in chicken cells and tissues under environmental stress. Taken together, our study provide evidence that cTIA-1 has a role in canonical SG formation in chicken cells and tissues. Our results also indicate that cPRD is necessary for SG aggregation.
Chickens ; Clone Cells ; Cycloheximide ; Cytoplasmic Granules ; Humans ; Protein Biosynthesis ; RNA Precursors ; RNA-Binding Proteins ; T-Lymphocytes