The identification and functional annotation of RNA structures conserved in vertebrates. Academic Article uri icon

Overview

abstract

  • Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.

authors

  • Seemann, Stefan E
  • Mirza, Aashiq H.
  • Hansen, Claus
  • Bang-Berthelsen, Claus H
  • Garde, Christian
  • Christensen-Dalsgaard, Mikkel
  • Torarinsson, Elfar
  • Yao, Zizhen
  • Workman, Christopher T
  • Pociot, Flemming
  • Nielsen, Henrik
  • Tommerup, Niels
  • Ruzzo, Walter L
  • Gorodkin, Jan

publication date

  • May 9, 2017

Research

keywords

  • Gene Expression Regulation
  • Nucleic Acid Conformation
  • RNA
  • Regulatory Elements, Transcriptional
  • Vertebrates

Identity

PubMed Central ID

  • PMC5538553

Scopus Document Identifier

  • 85024840196

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/btx114

PubMed ID

  • 28487280

Additional Document Info

volume

  • 27

issue

  • 8