PT  - JOURNAL ARTICLE
AU  - Wan-Hsin Liu
AU  - Zing Tsung-Yeh Tsai
AU  - Huai-Kuang Tsai
TI  - Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs
AID  - 10.1101/163626
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 163626
4099  - http://biorxiv.org/content/early/2017/07/17/163626.short
4100  - http://biorxiv.org/content/early/2017/07/17/163626.full
AB  - Background The regulatory roles of long intergenic noncoding RNAs (lincRNAs) in humans have been revealed through the use of advanced sequencing technology. Recently, three possible scenarios of lincRNA origin have been proposed: de novo origination from intergenic regions, duplication from long noncoding RNA, and pseudogenization from protein. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudo genized protein-coding sequence to lincRNA. Due to the non-mutually exclusive nature that these three scenarios have, accompanied by the need of systematic investigation of lincRNA origination, we conduct a comparative genomics study to investigate the evolution of human lincRNAs.Results Combining with syntenic analysis and stringent Blastn e-value cutoff, we found that the majority of lincRNAs are aligned to the intergenic regions of other species. Interestingly, 193 human lincRNAs could have protein-coding orthologs in at least two of nine vertebrates. Transposable elements in these conserved regions in human genome are much less than expectation. Moreover, 19% of these lincRNAs have overlaps with or are close to pseudogenes in the human genome.Conclusions We suggest that a notable portion of lincRNAs could be derived from pseudogenized protein-coding genes. Furthermore, based on our computational analysis, we hypothesize that a subset of these lincRNAs could have potential to regulate their paralogs by functioning as competing endogenous RNAs. Our results provide evolutionary evidence of the relationship between human lincRNAs and protein-coding genes.List of abbreviationslincRNAlong intergenic noncoding RNATEtransposable elementlncRNAlong non-coding RNAORFopen reading frameceRNAcompeting endogenous RNA