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Title: Identification and characterization of a class of MALAT1 -like genomic loci

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. Furthermore, 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.

Authors:
 [1];  [2];  [2];  [3];  [4];  [5];  [2];  [6];  [7];  [5];  [6];  [2]
  1. Cold Spring Harbor Lab., Cold Spring Harbor, NY (United States); Univ. of Rochester, Rochester, NY (United States)
  2. Cold Spring Harbor Lab., Cold Spring Harbor, NY (United States)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Howard Hughes Medical Institute, Ashburn, VA (United States); U.S. National Library of Medicine, Bethesda, MD (United States)
  5. Harvard Univ., Cambridge, MA (United States)
  6. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  7. Univ. of North Carolina, Charlotte, NC (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1364397
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Cell Reports
Additional Journal Information:
Journal Volume: 19; Journal Issue: 8; Journal ID: ISSN 2211-1247
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; long noncoding RNA; MALAT1; tRNA-like; triple helix; piRNA; PIWI; testis; evolution; lizard; Anolis carolinesis

Citation Formats

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., and Spector, David L.. Identification and characterization of a class of MALAT1 -like genomic loci. United States: N. p., 2017. Web. doi:10.1016/J.CELREP.2017.05.006.
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.. Identification and characterization of a class of MALAT1 -like genomic loci. United States. doi:10.1016/J.CELREP.2017.05.006.
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., and Spector, David L.. Tue . "Identification and characterization of a class of MALAT1 -like genomic loci". United States. doi:10.1016/J.CELREP.2017.05.006. https://www.osti.gov/servlets/purl/1364397.
@article{osti_1364397,
title = {Identification and characterization of a class of MALAT1 -like genomic loci},
author = {Zhang, Bin and Mao, Yuntao S. and Diermeier, Sarah D. and Novikova, Irina V. and Nawrocki, Eric P. and Jones, Tom A. and Lazar, Zsolt and Tung, Chang -Shung and Luo, Weijun and Eddy, Sean R. and Sanbonmatsu, Karissa Y. and Spector, David L.},
abstractNote = {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. Furthermore, 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.},
doi = {10.1016/J.CELREP.2017.05.006},
journal = {Cell Reports},
number = 8,
volume = 19,
place = {United States},
year = {Tue May 23 00:00:00 EDT 2017},
month = {Tue May 23 00:00:00 EDT 2017}
}

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