Abstract
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.
Highlights
The great majority of mammalian genome sequences are transcribed, at least occasionally, a phenomenon known as pervasive transcription [1,2,3,4]
Assuming that these sets of long intergenic non-coding RNA (lincRNA) are random samples from human and mouse lincRNomes, comparison of the Genome analysis of humans and other mammals reveals a surprisingly small number of protein-coding genes, only slightly over 20,000
About two third of the lincRNA genes appear to be conserved between human and mouse, implying thousands of conserved but still uncharacterized functions
Summary
The great majority of mammalian genome sequences are transcribed, at least occasionally, a phenomenon known as pervasive transcription [1,2,3,4]. Tiling array analyses of several human chromosomes have shown that over 90% of the bases are transcribed in at least one cell type [1,5,6,7,8]. Some of the lincRNAs have been shown to perform various regulatory roles but the majority remain functionally uncharacterized [7,12,13,14,15,16,17]. The fraction of the genome allotted to lincRNAs remains unknown
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