| Title | Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates |
| Authors | Chen, Jia-Yu Shen, Qing Sunny Zhou, Wei-Zhen Peng, Jiguang He, Bin Z. Li, Yumei Liu, Chu-Jun Luan, Xuke Ding, Wanqiu Li, Shuxian Chen, Chunyan Tan, Bertrand Chin-Ming Zhang, Yong E. He, Aibin Li, Chuan-Yun |
| Affiliation | Peking Univ, Inst Mol Med, Beijing Key Lab Cardiometab Mol Med, Beijing 100871, Peoples R China. Peking Univ, Coll Life Sci, Natl Lab Prot Engn & Plant Genet Engn, Ctr Bioinformat, Beijing 100871, Peoples R China. Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA. Harvard Univ, Howard Hughes Med Inst, Cambridge, MA 02138 USA. Peking Tsinghua Ctr Life Sci, Beijing, Peoples R China. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China. Chang Gung Univ, Mol Med Res Ctr, Taoyuan, Taiwan. |
| Keywords | RHESUS MACAQUE GC-CONTENT DROSOPHILA-MELANOGASTER PEPTIDEATLAS PROJECT NONCODING RNAS HUMAN PROTEOME ORPHAN GENES EVOLUTION GENOME EXPRESSION |
| Issue Date | 2015 |
| Publisher | PLOS GENETICS |
| Citation | PLOS GENETICS.2015,11,(7). |
| Abstract | While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts. |
| URI | http://hdl.handle.net/20.500.11897/418646 |
| ISSN | 1553-7390 |
| DOI | 10.1371/journal.pgen.1005391 |
| Indexed | SCI(E) PubMed |
| Appears in Collections: | 分子医学研究所 生命科学学院 蛋白质与植物基因研究国家重点实验室 |
