Journal Articles

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

June 01, 2017

Bin Zhang, Yuntao S. Mao, Sarah D. Diermeier, Irina V. Novikova, Eric P. Nawrocki, Tom A. Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R. Eddy (2017). Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Reports 19(8).

Author Affiliations

1 Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
2 Department of Pathology and Laboratory Medicine, Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
3 Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
4 Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, MS K710 Los Alamos, NM 87545, USA
5 Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA 20147, USA
6 National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
7 Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
8 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, US

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.

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