Apr 29, 2016

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

BioRxiv : the Preprint Server for Biology
Paulo P AmaralTony Kouzarides

Abstract

The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider positional conservation across mammalian genomes as an indicator of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human genomes that are preserved in genomic position relative to orthologous coding genes. The identified positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are co-expressed in a tissue-specific manner. Strikingly, over half of all positionally conserved RNAs in this set are linked to distinct chromatin organization structures, overlapping the binding sites for the CTCF chromatin organizer and located at chromatin loop anchor points and borders of topologically associating domains (TADs). These t opological a nchor p oint (tap)RNAs possess conserved sequence domains that are enriched in potential recognition motifs for Zinc Finger proteins. Characterization of these non-coding RNAs and their associated coding genes shows that they are functionally connect...Continue Reading

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Mentioned in this Paper

Zinc Fingers
Conserved Sequence
Chromatin Loop
Genome
Genes
Taps protein, mouse
RNA, Untranslated
CTCF
Definition
CCCTC-binding factor

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