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:
-
- Cold Spring Harbor Lab., Cold Spring Harbor, NY (United States); Univ. of Rochester, Rochester, NY (United States)
- Cold Spring Harbor Lab., Cold Spring Harbor, NY (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Howard Hughes Medical Institute, Ashburn, VA (United States); U.S. National Library of Medicine, Bethesda, MD (United States)
- Harvard Univ., Cambridge, MA (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Univ. of North Carolina, Charlotte, NC (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1364397
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- 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. https://doi.org/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. https://doi.org/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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