ArticleBMC genomics2017
Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Defective biological networks associated with pseudogene-derived lncRNAs in cancer drug resistance: Promising prospects for their clinical targets in cancer therapy.Genes & diseases · 2026Review
- The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.Nature communications · 2025Article
- An ancestral genomic sequence that serves as a nucleation site for de novo gene birth.PloS one · 2022Article
- The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules?Life (Basel, Switzerland) · 2021Review
- LncRNA EBLN3P promotes the progression of osteosarcoma through modifying the miR-224-5p/Rab10 signaling axis.Scientific reports · 2021Article
- A Methodology to Study Pseudogenized lincRNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Overcoming challenges and dogmas to understand the functions of pseudogenes.Nature reviews. Genetics · 2020Review
- Formation of human long intergenic non-coding RNA genes, pseudogenes, and protein genes: Ancestral sequences are key players.PloS one · 2020Article
- Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds.G3 (Bethesda, Md.) · 2019Article
- The Genetics and Epigenetics of 22q11.2 Deletion Syndrome.Frontiers in genetics · 2019Review
- Identification of transcribed protein coding sequence remnants within lincRNAs.Nucleic acids research · 2018Article
- Formation of a Family of Long Intergenic Noncoding RNA Genes with an Embedded Translocation Breakpoint Motif in Human Chromosomal Low Copy Repeats of 22q11.2-Some Surprises and Questions.Non-coding RNA · 2018Article
- Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets.Oncotarget · 2018Article
- MicroRNAs, long noncoding RNAs, and circular RNAs: potential tumor biomarkers and targets for colorectal cancer.Cancer management and research · 2018Review
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3 authors.
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Abstract
backgroundThe 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 origins have been proposed: de novo origination from intergenic regions, duplication from other long noncoding RNAs, and pseudogenization from protein-coding genes. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudogenized protein-coding sequence to lincRNA. Due to the non-mutually exclusive nature of these three scenarios and the need of systematic investigation of lincRNA origination, we conducted a comparative genomics study to investigate the evolution of human lincRNAs.
resultsCombining with syntenic analysis and stringent Blastn e-value cutoff, we found that the majority of lincRNAs are aligned to 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.
conclusionsWe 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.
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