Identification and Characterization of a Class of MALAT1-like Genomic Loci

Cell Rep. 2017 May 23;19(8):1723-1738. doi: 10.1016/j.celrep.2017.05.006.

Abstract

The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module. MALAT1-like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). MALAT1-like loci also produce multiple small RNA species, including PIWI-interacting RNAs (piRNAs), from the antisense strand. The 3' ends of tancRNAs serve as potential targets for the PIWI-piRNA complex. Thus, we have identified an evolutionarily conserved class of long noncoding RNAs (lncRNAs) with similar structural constraints, post-transcriptional processing, and subcellular localization and a distinct function in spermatocytes.

Keywords: Anolis carolinesis; MALAT1; PIWI; evolution; lizard; long noncoding RNA; piRNA; tRNA-like; testis; triple helix.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Cell Nucleus / metabolism
  • Genetic Loci*
  • Genome, Human*
  • Humans
  • Lizards / genetics
  • Male
  • Nucleic Acid Conformation
  • Organ Specificity / genetics
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / genetics*
  • RNA, Small Interfering / genetics
  • Spermatocytes / metabolism

Substances

  • RNA, Long Noncoding
  • RNA, Small Interfering