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

Zhang, Bin, Mao, Yuntao S., Diermeier, Sarah D., Novikova, Irina V., Nawrocki, Eric P., Jones, Tom A., Lazar, Zsolt, Tung, Chang-Shung, Luo, Weijun, Eddy, Sean R., Sanbonmatsu, Karissa Y., Spector, David L. (2017) Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Reports, 19 (8). pp. 1723-1738. ISSN 2211-1247

URL: https://www.ncbi.nlm.nih.gov/pubmed/28538188
DOI: 10.1016/j.celrep.2017.05.006

Abstract

Summary 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.

Item Type: Paper
Uncontrolled Keywords: long noncoding RNA MALAT1 tRNA-like triple helix piRNA PIWI testis evolution lizard Anolis carolinesis
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > Piwi protein
evolution
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > long non-coding RNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > piRNA
CSHL Authors:
Communities: CSHL labs > Spector lab
Depositing User: Matt Covey
Date Deposited: 24 May 2017 20:15
Last Modified: 07 Sep 2017 13:50
Related URLs:
Dataset ID:
URI: http://repository.cshl.edu/id/eprint/34805

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