Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
The Rhinogobius (Perciformes, Gobiidae), is a species-rich freshwater gobiid genus. In this article, the complete mitochondrial genome (mtDNA) of the Rhinogobius cliffordpopei was first determined. The mtDNA of R. cliffordpopei consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. In the phylogenetic tree, R. cliffordpopei firstly joined with R. brunneus, and next clustered with R. giurinus. Then, they constituted Gobiidae clade with the rest other six species. This relationship consists of taxonomic status. The results would provide basal molecular data for the future research of adaptive evolution in Rhinogobius.
BackgroundSimilar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking.ResultsIn this study, the mRNA and lncRNA expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs.ConclusionsWe found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain.
KEYWORDSzebrafish, brain, the dimorphic patterns, mRNA and lncRNAs, high-throughput transcriptome sequencing 2 Abstract Background: Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking. Results: In this study, the mRNA and lncRNAs expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs. Conclusions: We found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain. Consent for publicationNot applicable. Publisher's NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
We performed a survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods. We discovered 74 new bacterial species and reconstructed their draft genomes, which were obtained from the 75 reconstructed almost complete metagenomic assembly genomes (MAG) in the soil and water samples. Proteobacteria and Actinobacteria were found to be the most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. To our surprise, Pandoravirus salinus was found in the soil microbial community. We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway.
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