Detailed secondary structure models of invertebrate 7SK RNAs

RNA Biol. 2018 Feb 1;15(2):158-164. doi: 10.1080/15476286.2017.1412913. Epub 2017 Dec 21.

Abstract

The 7SK RNA is a small nuclear RNA that is involved in the regulation of Pol-II transcription. It is very well conserved in vertebrates, but shows extensive variations in both sequence and structure across invertebrates. A systematic homology search extended the collection of 7SK genes in both Arthropods and Lophotrochozoa making use of the large number of recently published invertebrate genomes. The extended data set made it possible to infer complete consensus structures for invertebrate 7SK RNAs. These show that not only the well-conserved 5'- and 3'- domains but all the interior Stem A domain is universally conserved. In contrast, Stem B region exhibits substantial structural variation and does not adhere to a common structural model beyond phylum level.

Keywords: 7SK RNA; RNA secondary structure; homology search; non-coding RNA; pol-III transcripts; sequence covariation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Conserved Sequence
  • Evolution, Molecular
  • Invertebrates / chemistry
  • Invertebrates / genetics*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Small Cytoplasmic / chemistry*
  • RNA, Small Cytoplasmic / genetics*
  • Sequence Homology, Nucleic Acid
  • Signal Recognition Particle / chemistry*
  • Signal Recognition Particle / genetics*

Substances

  • 7SL RNA
  • RNA, Small Cytoplasmic
  • Signal Recognition Particle

Grants and funding

Ali M. Yazbeck was funded by a doctoral stipend of the National Council for Scientific Research of Lebanon, Lebanon (CNRS-L). Machine readable data accompanying this article are available at http://www.bioinf.uni-leipzig.de/publications/supplements/17-013