The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs.
Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.
Department of Bioinformatics and Biostatistics, School of Life Sciences &Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, Shanghai 200235, China.
Qianqian
Q
Ning
Department of Bioinformatics and Biostatistics, School of Life Sciences &Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, Shanghai 200235, China.|Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
Yixue
Y
Li
Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Zhen
Z
Wang
Medical oncology department, shanghai pulmonary hospital, cancer institute, Tongji University Medical School, Shanghai 200433, China.
Songwen
S
Zhou
Biomedical Information Research Center, Children's Hospital of Shanghai, Shanghai 200062, China.
Hong
H
Sun
Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200062, China.
Guangjun
G
Yu
D063646:Carcinogenesis / Q000235:genetics; D019143:Evolution, Molecular; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D016366:Open Reading Frames / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*
D062085:RNA, Long Noncoding