ArticleGenome biology2017
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 68 citations in OpenAlex.
- The landscape and evolutionary dynamics of derived lncRNAs in insects.Communications biology · 2025Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Mechanisms and progress of LncRNAs in prostate cancer development and diagnostic therapy.International urology and nephrology · 2025Review
- Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.Scientific reports · 2024Article
- Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs.Life science alliance · 2023Article
- Species-specific regulation of XIST by the JPX/FTX orthologs.Nucleic acids research · 2023Article
- Identification of long non-coding RNA-mRNA interactions and genome-wide lncRNA annotation in animal transcriptome profiling.Journal of animal science and technology · 2023Review
- LncRNA evolution and DNA methylation variation participate in photosynthesis pathways of distinct lineages ofForestry research · 2023Article
- Article
- Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation.NAR cancer · 2022Article
- The Genomics of Auditory Function and Disease.Annual review of genomics and human genetics · 2022Review
- The Conservation of Long Intergenic Non-Coding RNAs and Their Response toInternational journal of molecular sciences · 2022Article
- LncRNAs in domesticated animals: from dog to livestock species.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- The evolutionary landscape and expression pattern of plant lincRNAs.RNA biology · 2022Article
- The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules?Life (Basel, Switzerland) · 2021Review
- A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants.Nucleic acids research · 2021Article
- Long noncoding RNAs as tumorigenic factors and therapeutic targets for renal cell carcinoma.Cancer cell international · 2021Review
- A Methodology to Study Pseudogenized lincRNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Long non-coding RNAs in development and disease: conservation to mechanisms.The Journal of pathology · 2020Review
- Overcoming challenges and dogmas to understand the functions of pseudogenes.Nature reviews. Genetics · 2020Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOnly a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs.
resultsWe systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality.
conclusionsWe estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.