Computational Analysis Of Post-transcriptional Regulation Coordinated By RNA-binding Proteins

Transcriptome and post-transcriptional regulation are tightly connected in eukaryotic cells.From their birth to degradation,transcripts are always bound by various RNA-binding proteins(RBPs)and other RNA molecules,which play key roles in nearly all post-transcriptional regulation events,including splicing,polyadenylation,subcellular localization and degradation.The precise post-regulations increase the complexity of the transcriptomes,making the eukaryotic cells display various phenotypes and quick response to stress conditions.Recently,the advance of high-throughput sequencing technologies makes it possible to study the transcriptome and post-transcriptional regulation in an integrative manner.We could quantify the gene expression levels more precisely using RNA-seq technology.And we could obtain transcriptome-wide RBP binding sites with high resolution through CLIP-seq technologies.In this study,we investigated the transcriptome and post-transcriptional regulation using large-scale CLIP-seq and RNA-seq data sets.First,we constructed CLIPdb and POSTAR as comprehensive data resource for exploring post-transcriptional regulation coordinated by RBPs.CLIPdb aims to provide transcriptome-wide RBP binding sites with high resolution.We collected 395 publicly available CLIP-seq data sets for 111 RBPs from four species(human,mouse,worm and yeast),and applied a unified computational method to identify transcriptome-wide binding sites.POSTAR supplies the largest collection of experimentally probed and computationally predicted RBP binding sites in human and mouse transcriptomes.POSTAR annotates the RBP binding sites using extensive information of various molecular regulatory events,genomic variants and gene-function associations.We then developed a computational framework to describe the global interactions between RBPs and structured RNAs at single-nucleotide resolution.We found that the RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionary conserved signatures,often facilitate a specific RNA structure conformation in vivo,and have association with the regulatory functions of RNA molecules.Finally,we used RNA-seq data from four mammalian species(human,chimpanzee,bonobo and mouse)to map the transcriptomes from various cell states,and identified sets of conserved cell state-associated RBPs and other types of key regulators,including transcription factors and and long non-coding RNAs.We found that the cell state-associated can serve as good cell state indicators.The biological functions of most RBPs in cell identity control have not been well studied.Through integrative analysis of high-throughput sequencing data,we uncover the complex mechanisms of RBP regulation at the post-transcriptional level,and the putative functions of RBPs in regulating the diversity of cell differentiation states.Our results provides valuable data resources for better understanding the transcriptome and post-transcriptional regulation.