The vast, conserved mammalian lincRNome.

We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimen...

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Autores principales:	David Managadze, Alexander E Lobkovsky, Yuri I Wolf, Svetlana A Shabalina, Igor B Rogozin, Eugene V Koonin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/6518004c0c3e445898824a702985df50
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spelling	oai:doaj.org-article:6518004c0c3e445898824a702985df502021-11-18T05:52:25ZThe vast, conserved mammalian lincRNome.1553-734X1553-735810.1371/journal.pcbi.1002917https://doaj.org/article/6518004c0c3e445898824a702985df502013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23468607/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized.David ManagadzeAlexander E LobkovskyYuri I WolfSvetlana A ShabalinaIgor B RogozinEugene V KooninPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 2, p e1002917 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 David Managadze Alexander E Lobkovsky Yuri I Wolf Svetlana A Shabalina Igor B Rogozin Eugene V Koonin The vast, conserved mammalian lincRNome.
description	We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized.
format	article
author	David Managadze Alexander E Lobkovsky Yuri I Wolf Svetlana A Shabalina Igor B Rogozin Eugene V Koonin
author_facet	David Managadze Alexander E Lobkovsky Yuri I Wolf Svetlana A Shabalina Igor B Rogozin Eugene V Koonin
author_sort	David Managadze
title	The vast, conserved mammalian lincRNome.
title_short	The vast, conserved mammalian lincRNome.
title_full	The vast, conserved mammalian lincRNome.
title_fullStr	The vast, conserved mammalian lincRNome.
title_full_unstemmed	The vast, conserved mammalian lincRNome.
title_sort	vast, conserved mammalian lincrnome.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/6518004c0c3e445898824a702985df50
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The vast, conserved mammalian lincRNome.

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