Tissue-Specific Alternative Splicing Analysis Reveals the Diversity of Chromosome 18 Transcriptome

The
Chromosome-centric Human Proteome Project (C-HPP) is aimed
to identify the variety of protein products and transcripts of the
number of chromosomes. The Russian part of C-HPP is devoted to the
study of the human chromosome 18. Using widely accepted Tophat and
SpliceGrapher, a tool for accurate splice sites and alternative mRNA
isoforms prediction, we performed the extensive mining of the splice
variants of chromosome 18 transcripts and encoded protein products
in liver, brain, lung, kidney, blood, testis, derma, and skeletal
muscles. About 6.1 billion of the reads represented by 450 billion
of the bases have been analyzed. The relative frequencies of splice
events as well as gene expression profiles in normal tissues are evaluated.
Using ExPASy PROSITE, the novel features and possible functional sites
of previously unknown splice variants were highlighted. A set of unique
proteotypic peptides enabling the identification of novel alternative
protein species using mass-spectrometry is constructed. The revealed
data will be integrated into the gene-centric knowledgebase of the
Russian part of C-HPP available at http://kb18.ru and http://www.splicing.zz.mu/.

以染色体为中心的人类蛋白质组计划（Chromosome-centric Human Proteome Project, C-HPP）旨在鉴定人类各染色体对应的各类蛋白质产物与转录本。C-HPP的俄罗斯分支专注于人类18号染色体的相关研究。研究团队采用学界公认的Tophat以及用于精准预测剪接位点和可变mRNA剪接异构体的工具SpliceGrapher，对肝脏、大脑、肺脏、肾脏、血液、睾丸、真皮以及骨骼肌中18号染色体转录本的剪接变异体及其编码的蛋白质产物开展了大规模挖掘。本次分析共处理约61亿条读段，对应总碱基量达4500亿个。研究同时评估了正常组织中剪接事件的相对频率与基因表达谱。借助ExPASy PROSITE数据库，研究团队对此前未被报道的剪接变异体的新型特征与潜在功能位点进行了标注。此外，研究构建了一套专属的蛋白质组特征肽段集，可通过质谱（mass-spectrometry）技术实现新型可变蛋白质亚型的鉴定。本研究获得的相关数据将整合至C-HPP俄罗斯分支的以基因为中心的知识库，该知识库可通过http://kb18.ru与http://www.splicing.zz.mu/访问。