Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

被引：315

作者：

Ponjavic, Jasmina ^{[1
]}

Oliver, Peter L. ^{[1
]}

Lunter, Gerton ^{[1
]}

Ponting, Chris P. ^{[1
]}

机构：

[1] Univ Oxford, MRC, Funct Genom Unit, Dept Physiol Anat & Genet, Oxford, England

来源：

PLOS GENETICS | 2009年 / 5卷 / 08期

关键词：

POLYMERASE-II; WIDE ANALYSIS; MOUSE; IDENTIFICATION; EXPRESSION; GENES; VERTEBRATE; SEQUENCES; PROMOTER; ELEMENTS;

D O I：

10.1371/journal.pgen.1000617

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary constraint, a hallmark of functionality. Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures. Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development. This led us to the hypothesis that spatiotemporal co-expression of ncRNAs and nearby protein-coding genes represents a general phenomenon, a prediction that was confirmed subsequently by in situ hybridisation in developing and adult mouse brain. We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

引用

页数：14

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