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

Journal Article · · Cell Reports
 [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)
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.
Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1364397
Journal Information:
Cell Reports, Journal Name: Cell Reports Journal Issue: 8 Vol. 19; ISSN 2211-1247
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (63)

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε book January 2010
MALAT1 — a paradigm for long noncoding RNA function in cancer journal March 2013
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs journal June 2007
3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA journal November 2008
Long Noncoding RNAs with Enhancer-like Function in Human Cells journal October 2010
ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs journal November 2011
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution journal December 2011
Long Noncoding RNAs: Cellular Address Codes in Development and Disease journal March 2013
lincRNAs: Genomics, Evolution, and Mechanisms journal July 2013
Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement journal July 2014
RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites journal September 2014
On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme journal February 2015
Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins journal January 2016
The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult journal July 2012
Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi journal May 2016
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities journal May 2010
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation journal September 2010
The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites journal September 2014
Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain journal January 2012
Role of tRNA-like structures in controlling plant virus replication journal February 2009
piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism journal August 2012
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression journal August 2010
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs journal December 2002
A novel class of small RNAs bind to MILI protein in mouse testes journal June 2006
A germline-specific class of small RNAs binds mammalian Piwi proteins journal June 2006
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals journal February 2009
Landscape of transcription in human cells journal September 2012
Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs journal December 2010
Nucleation of nuclear bodies by RNA journal January 2011
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis journal August 2009
Genome-wide transcription and the implications for genomic organization journal May 2007
All-atom homology model of the Escherichia coli 30S ribosomal subunit journal September 2002
Structure of the SAM-II riboswitch bound to S-adenosylmethionine journal January 2008
Triple-helix structure in telomerase RNA contributes to catalysis journal May 2008
Promiscuous RNA binding by Polycomb repressive complex 2 journal September 2013
Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix journal June 2014
MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer journal September 2003
Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN  noncoding RNAs journal November 2012
Structural determinants for ligand capture by a class II preQ 1 riboswitch journal January 2014
Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA journal November 2016
The 3'-terminal end (NCCA) of tRNA determines the structure and stability of the aminoacyl acceptor stem. journal July 1993
STAR: ultrafast universal RNA-seq aligner journal October 2012
Infernal 1.1: 100-fold faster RNA homology searches journal September 2013
A novel class of small RNAs in mouse spermatogenic cells journal June 2006
A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails journal October 2012
Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss journal December 2015
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression journal September 2012
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis journal November 2011
GENCODE: The reference human genome annotation for The ENCODE Project journal September 2012
Small RNA Silencing Pathways in Germ and Stem Cells journal January 2008
Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity journal September 2004
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays journal December 2004
Characterization of the piRNA Complex from Rat Testes journal July 2006
Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix journal November 2010
Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus journal May 2011
tRNAs Marked with CCACCA Are Targeted for Degradation journal November 2011
Genome Regulation by Long Noncoding RNAs journal July 2012
The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells journal December 2012
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains journal February 2007
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome journal January 2009
Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes journal January 2010
Malat1 is not an essential component of nuclear speckles in mice journal June 2012
Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development journal August 2012

Cited By (12)

Molecular anatomy of the architectural NEAT1 noncoding RNA: The domains, interactors, and biogenesis pathway required to build phase‐separated nuclear paraspeckles journal May 2019
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution journal January 2020
Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors journal February 2020
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates journal October 2018
A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis journal March 2018
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering journal December 2019
Challenges and perspectives for structural biology of lncRNAs—the example of the Xist lncRNA A-repeats journal July 2019
Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering posted_content October 2019
Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: An in silico analysis posted_content April 2019
Long Non-coding RNAs as Communicators and Mediators Between the Tumor Microenvironment and Cancer Cells journal August 2019
Identifying Structural Domains and Conserved Regions in the Long Non-Coding RNA lncTCF7 journal September 2019
Secondary Structural Model of Human MALAT1 Reveals Multiple Structure–Function Relationships journal November 2019

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