MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that are involved in oncogenesis and show remarkable tissue specificity.miRNAs are approximately 22 nt non-coding RNAs, which regulate gene expression...MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that are involved in oncogenesis and show remarkable tissue specificity.miRNAs are approximately 22 nt non-coding RNAs, which regulate gene expression in a sequence-specific manner via translational inhibition or messenger RNA (mRNA) degradation, thus affecting various cellular processes.Since the discovery of their fundamental mechanisms of action, the field of miRNAs has opened a new era in the understanding of small noncoding RNAs.Recent evidence has shown that miRNA controls cell growth, apoptosis, and differentiation.Cancer is a complex genetic disease caused by abnormalities in gene structure and expression, moreover, miRNA expression correlates with cancers and could have a crucial function in tumor progression.Bioinformatic data indicate that each miRNA can control hundreds of target genes, but identification of the accurate miRNA targets will be crucial to exploit the emerging knowledge of miRNA contribution to cancer process.展开更多
RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In ...RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.展开更多
Long noncoding RNAs(lncRNAs)play important roles in human diseases including vascular disease.Given the large number of lncRNAs,however,whether the majority of them are associated with vascular disease remains unknown...Long noncoding RNAs(lncRNAs)play important roles in human diseases including vascular disease.Given the large number of lncRNAs,however,whether the majority of them are associated with vascular disease remains unknown.For this purpose,here we present a genomic location based bioinformatics method to predict the lncRNAs associated with vascular disease.We applied the presented method to globally screen the human lncRNAs potentially involved in vascular disease.As a result,we predicted 3043 putative vascular disease associated lncRNAs.To test the accuracy of the method,we selected 10 lncRNAs predicted to be implicated in proliferation and migration of vascular smooth muscle cells(VSMCs)for further experimental validation.The results confirmed that eight of the 10 lncRNAs(80%)are validated.This result suggests that the presented method has a reliable prediction performance.Finally,the presented bioinformatics method and the predicted vascular disease associated lncRNAs together may provide helps for not only better understanding of the roles of lncRNAs in vascular disease but also the identification of novel molecules for the diagnosis and therapy of vascular disease.展开更多
Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specif...Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.展开更多
Chaperonin-containing tailless complex polypeptide 1(CCT) is a group of genes involved in protein folding. It has been reported to be associated with the genesis and development of multiple tumors. However, the expres...Chaperonin-containing tailless complex polypeptide 1(CCT) is a group of genes involved in protein folding. It has been reported to be associated with the genesis and development of multiple tumors. However, the expression levels and functions of distinct CCTs involved in carcinogenesis and progression of hepatocellular carcinoma(HCC) have not been systematically analyzed. In the present study, we aimed to investigate the expression and mutation patterns, diagnostic and prognostic value, and functional enrichment of CCTs in HCC using ONCOMINE, GEPIA, the Human Protein Atlas, cBioPortal, Kaplan-Meier Plotter, and R language. The transcriptional and translational levels of all CCT family members were remarkably higher in HCC patients and related to the tumor stage. All CCT family members, especially CCT2 and CCT8, might serve as promising diagnostic, prognostic markers as well as therapeutic targets for HCC.展开更多
文摘MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that are involved in oncogenesis and show remarkable tissue specificity.miRNAs are approximately 22 nt non-coding RNAs, which regulate gene expression in a sequence-specific manner via translational inhibition or messenger RNA (mRNA) degradation, thus affecting various cellular processes.Since the discovery of their fundamental mechanisms of action, the field of miRNAs has opened a new era in the understanding of small noncoding RNAs.Recent evidence has shown that miRNA controls cell growth, apoptosis, and differentiation.Cancer is a complex genetic disease caused by abnormalities in gene structure and expression, moreover, miRNA expression correlates with cancers and could have a crucial function in tumor progression.Bioinformatic data indicate that each miRNA can control hundreds of target genes, but identification of the accurate miRNA targets will be crucial to exploit the emerging knowledge of miRNA contribution to cancer process.
基金supported by the National Science&Technology Pillar Program of China(2012BAD13B06)the Special Fund for Agroscientific Research in the Public Interest(201203009)
文摘RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.
基金supported by the National Natural Science Foundation of China(91339106)National High Technology Research and Development Program of China(2014AA021102)
文摘Long noncoding RNAs(lncRNAs)play important roles in human diseases including vascular disease.Given the large number of lncRNAs,however,whether the majority of them are associated with vascular disease remains unknown.For this purpose,here we present a genomic location based bioinformatics method to predict the lncRNAs associated with vascular disease.We applied the presented method to globally screen the human lncRNAs potentially involved in vascular disease.As a result,we predicted 3043 putative vascular disease associated lncRNAs.To test the accuracy of the method,we selected 10 lncRNAs predicted to be implicated in proliferation and migration of vascular smooth muscle cells(VSMCs)for further experimental validation.The results confirmed that eight of the 10 lncRNAs(80%)are validated.This result suggests that the presented method has a reliable prediction performance.Finally,the presented bioinformatics method and the predicted vascular disease associated lncRNAs together may provide helps for not only better understanding of the roles of lncRNAs in vascular disease but also the identification of novel molecules for the diagnosis and therapy of vascular disease.
基金supported by grants from the National Natural Science Foundation of China(31271318)Natural Science Foundation of Guangdong(S2012010008912)Foundation of Key Laboratory of Plant Resources Conservation and Sustainable Utilization,South China Botanical Garden,Chinese Academy of Sciences
文摘Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.
基金National Natural Science Foundation of China (Gr ant No. 81803535)Natural Science Foundation of Hunan Province of China (Grant No. 2018JJ6070)。
文摘Chaperonin-containing tailless complex polypeptide 1(CCT) is a group of genes involved in protein folding. It has been reported to be associated with the genesis and development of multiple tumors. However, the expression levels and functions of distinct CCTs involved in carcinogenesis and progression of hepatocellular carcinoma(HCC) have not been systematically analyzed. In the present study, we aimed to investigate the expression and mutation patterns, diagnostic and prognostic value, and functional enrichment of CCTs in HCC using ONCOMINE, GEPIA, the Human Protein Atlas, cBioPortal, Kaplan-Meier Plotter, and R language. The transcriptional and translational levels of all CCT family members were remarkably higher in HCC patients and related to the tumor stage. All CCT family members, especially CCT2 and CCT8, might serve as promising diagnostic, prognostic markers as well as therapeutic targets for HCC.
