comparative analysis of human protein-coding and noncoding rnas between brain and 10 mixed cell lines by rna-seq比较分析人类蛋白质编码和非编码rna在大脑和10混合rna-seq细胞系.pdfVIP

Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq 1 1 2 1 1 1 1 1 Geng Chen , Kangping Yin , Leming Shi , Yuanzhang Fang , Ya Qi , Peng Li , Jian Luo , Bing He , Mingyao Liu1, Tieliu Shi1,3* 1 Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai, China, 2 National Center for Toxicological Research, United States of America Food and Drug Administration, Jefferson, Arkansas, United States of America, 3 Shanghai Information Center for Life Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, China Abstract In their expression process, different genes can generate diverse functional products, including various protein-coding or noncoding RNAs. Here, we investigated the protein-coding capacities and the expression levels of their isoforms for human known genes, the conservation and disease association of long noncoding RNAs (ncRNAs) with two transcriptome sequencing datasets from human brain tissues and 10 mixed cell lines. Comparative analysis revealed that about two-thirds of the genes expressed between brain and cell lines are the same, but less than one-third of their isoforms are identical. Besides those genes specially expressed in brain and cell lines, about 66% of genes expressed in common encoded different isoforms. Moreover, most genes dominantly expressed one isoform and some genes only generated protein-coding (or noncoding) RNAs in one sample but not in another. We found 282 human genes could encode both protein-coding and noncoding RNAs through alternative splicing i