A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes
Abstract Background Only 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. R...
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doaj-c338ea8b9a234874a4221ba4638d39ab2020-11-24T21:44:34ZengBMCGenome Biology1474-760X2017-08-0118111510.1186/s13059-017-1293-0A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genesHadas Hezroni0Rotem Ben-Tov Perry1Zohar Meir2Gali Housman3Yoav Lubelsky4Igor Ulitsky5Department of Biological Regulation, Weizmann Institute of ScienceDepartment of Biological Regulation, Weizmann Institute of ScienceDepartment of Biological Regulation, Weizmann Institute of ScienceDepartment of Biological Regulation, Weizmann Institute of ScienceDepartment of Biological Regulation, Weizmann Institute of ScienceDepartment of Biological Regulation, Weizmann Institute of ScienceAbstract Background Only 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. Results We 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. Conclusions We 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.http://link.springer.com/article/10.1186/s13059-017-1293-0Long noncoding RNAsEvolutionPseudogenesTranslational regulationuORFsX inactivation |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hadas Hezroni Rotem Ben-Tov Perry Zohar Meir Gali Housman Yoav Lubelsky Igor Ulitsky |
spellingShingle |
Hadas Hezroni Rotem Ben-Tov Perry Zohar Meir Gali Housman Yoav Lubelsky Igor Ulitsky A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes Genome Biology Long noncoding RNAs Evolution Pseudogenes Translational regulation uORFs X inactivation |
author_facet |
Hadas Hezroni Rotem Ben-Tov Perry Zohar Meir Gali Housman Yoav Lubelsky Igor Ulitsky |
author_sort |
Hadas Hezroni |
title |
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes |
title_short |
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes |
title_full |
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes |
title_fullStr |
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes |
title_full_unstemmed |
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes |
title_sort |
subset of conserved mammalian long non-coding rnas are fossils of ancestral protein-coding genes |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2017-08-01 |
description |
Abstract Background Only 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. Results We 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. Conclusions We 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. |
topic |
Long noncoding RNAs Evolution Pseudogenes Translational regulation uORFs X inactivation |
url |
http://link.springer.com/article/10.1186/s13059-017-1293-0 |
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