Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery
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Title
Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery
Authors
Keywords
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Journal
NATURE REVIEWS MOLECULAR CELL BIOLOGY
Volume 21, Issue 3, Pages 123-136
Publisher
Springer Science and Business Media LLC
Online
2020-02-04
DOI
10.1038/s41580-019-0209-0
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Note: Only part of the references are listed.- Biology of RNA Surveillance in Development and Disease
- (2019) Brice Laffleur et al. TRENDS IN CELL BIOLOGY
- The RNA exosome nuclease complex regulates human embryonic stem cell differentiation
- (2019) Cedric Belair et al. JOURNAL OF CELL BIOLOGY
- EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks
- (2019) Judit Domingo-Prim et al. Nature Communications
- The Integrator complex cleaves nascent mRNAs to attenuate transcription
- (2019) Deirdre C. Tatomer et al. GENES & DEVELOPMENT
- ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation
- (2019) Dustin L. Gable et al. GENES & DEVELOPMENT
- R-Loops Promote Antisense Transcription across the Mammalian Genome
- (2019) Sue Mei Tan-Wong et al. MOLECULAR CELL
- A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2
- (2019) William Garland et al. Cell Reports
- Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown
- (2018) Hachung Chung et al. CELL
- Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex
- (2018) Eva-Maria Weick et al. CELL
- Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs
- (2018) Katsutoshi Imamura et al. EMBO JOURNAL
- Nuclear lncRNA stabilization in the host response to bacterial infection
- (2018) Mathias Munschauer et al. EMBO JOURNAL
- Nuclear mRNA Surveillance Mechanisms: Function and Links to Human Disease
- (2018) Pragyan Singh et al. JOURNAL OF MOLECULAR BIOLOGY
- RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination
- (2018) Claudia Ribeiro de Almeida et al. MOLECULAR CELL
- Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation
- (2018) Tomohiro Yamazaki et al. MOLECULAR CELL
- MiCEE is a ncRNA-protein complex that mediates epigenetic silencing and nucleolar organization
- (2018) Indrabahadur Singh et al. NATURE GENETICS
- Structural basis for MTR4–ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex
- (2018) M. Rhyan Puno et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage
- (2018) Agnese Cristini et al. Cell Reports
- The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts
- (2018) Toomas Silla et al. Cell Reports
- Nuclear RNA surveillance complexes silence HIV-1 transcription
- (2018) Xavier Contreras et al. PLoS Pathogens
- RNase H2 Loss in Murine Astrocytes Results in Cellular Defects Reminiscent of Nucleic Acid-Mediated Autoinflammation
- (2018) Kareen Bartsch et al. Frontiers in Immunology
- The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes
- (2018) Juan Chen et al. CELL RESEARCH
- The RNA exosome contributes to gene expression regulation during stem cell differentiation
- (2018) Marta Lloret-Llinares et al. NUCLEIC ACIDS RESEARCH
- Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence
- (2018) Takayuki Nojima et al. MOLECULAR CELL
- Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors
- (2017) John C. Zinder et al. GENES & DEVELOPMENT
- Absence of RNase H2 triggers generation of immunogenic micronuclei removed by autophagy
- (2017) Kareen Bartsch et al. HUMAN MOLECULAR GENETICS
- Perturbations in the Replication Program Contribute to Genomic Instability in Cancer
- (2017) Britny Blumenfeld et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- R-Loop Depletion by Over-expressed RNase H1 in Mouse B Cells Increases Activation-Induced Deaminase Access to the Transcribed Strand without Altering Frequency of Isotype Switching
- (2017) Robert W. Maul et al. JOURNAL OF MOLECULAR BIOLOGY
- R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters
- (2017) Liang Chen et al. MOLECULAR CELL
- Dynamic landscape and regulation of RNA editing in mammals
- (2017) Meng How Tan et al. NATURE
- Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks
- (2017) Flavia Michelini et al. NATURE CELL BIOLOGY
- Biomolecular condensates: organizers of cellular biochemistry
- (2017) Salman F. Banani et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- DNA–RNA hybrids: the risks of DNA breakage during transcription
- (2017) Andrés Aguilera et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- The RNA exosome and RNA exosome-linked disease
- (2017) Derrick J. Morton et al. RNA
- Liquid phase condensation in cell physiology and disease
- (2017) Yongdae Shin et al. SCIENCE
- Attacked from All Sides: RNA Decay in Antiviral Defense
- (2017) Jerome Molleston et al. Viruses-Basel
- DNA–RNA hybrids: the risks of DNA breakage during transcription
- (2017) Andrés Aguilera et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation
- (2017) Sreerama Chaitanya Sridhara et al. Cell Reports
- Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies
- (2016) June-Koo Lee et al. Annual Review of Pathology-Mechanisms of Disease
- Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells
- (2016) Sai Luo et al. Cell Stem Cell
- Ribonuclease H2 mutations induce a cGAS/STING‐dependent innate immune response
- (2016) Karen J Mackenzie et al. EMBO JOURNAL
- A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation
- (2016) Jerome M. Molleston et al. GENES & DEVELOPMENT
- Biogenesis and Transcriptional Regulation of Long Noncoding RNAs in the Human Immune System
- (2016) Charles F. Spurlock et al. JOURNAL OF IMMUNOLOGY
- Mutations inEXOSC2are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt
- (2016) Nataliya Di Donato et al. JOURNAL OF MEDICAL GENETICS
- DNA Replication—A Matter of Fidelity
- (2016) Rais A. Ganai et al. MOLECULAR CELL
- Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts
- (2016) Nicola Meola et al. MOLECULAR CELL
- The regulation and functions of the nuclear RNA exosome complex
- (2016) Cornelia Kilchert et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut
- (2016) N. J. Proudfoot SCIENCE
- XRN2 Links Transcription Termination to DNA Damage and Replication Stress
- (2016) Julio C. Morales et al. PLoS Genetics
- Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA
- (2015) Simin Zheng et al. CELL
- RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity
- (2015) Evangelos Pefanis et al. CELL
- Long noncoding RNAs in innate immunity
- (2015) Yuan Zhang et al. Cellular & Molecular Immunology
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- (2015) Hemanth Tummala et al. JOURNAL OF CLINICAL INVESTIGATION
- Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition
- (2015) Nova Fong et al. MOLECULAR CELL
- Integrator mediates the biogenesis of enhancer RNAs
- (2015) Fan Lai et al. NATURE
- Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening
- (2015) Bridget D Stuart et al. NATURE GENETICS
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- (2015) Daniel Holoch et al. NATURE REVIEWS GENETICS
- Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing
- (2015) Venkata R. Chalamcharla et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself
- (2015) B. J. Liddicoat et al. SCIENCE
- The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis
- (2015) Michal Lubas et al. Cell Reports
- The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability
- (2014) Stephan Hamperl et al. DNA REPAIR
- Widespread contribution of transposable elements to the innovation of gene regulatory networks
- (2014) Vasavi Sundaram et al. GENOME RESEARCH
- Defective removal of ribonucleotides from DNA promotes systemic autoimmunity
- (2014) Claudia Günther et al. JOURNAL OF CLINICAL INVESTIGATION
- Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability
- (2014) Julie Sollier et al. MOLECULAR CELL
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- Noncoding RNA transcription targets AID to divergently transcribed loci in B cells
- (2014) Evangelos Pefanis et al. NATURE
- Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
- (2014) Alexandre Fort et al. NATURE GENETICS
- The SKIV2L RNA exosome limits activation of the RIG-I-like receptors
- (2014) Sterling C Eckard et al. NATURE IMMUNOLOGY
- EXOSC3 mutations in pontocerebellar hypoplasia type 1: novel mutations and genotype-phenotype correlations
- (2014) Veerle RC Eggens et al. Orphanet Journal of Rare Diseases
- Transcription and Recombination: When RNA Meets DNA
- (2014) A. Aguilera et al. Cold Spring Harbor Perspectives in Biology
- EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia
- (2014) Veronika Boczonadi et al. Nature Communications
- A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs
- (2013) Alex Charles Tuck et al. CELL
- Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers
- (2013) Ulf Andersson Ørom et al. CELL
- Long Noncoding RNAs: Cellular Address Codes in Development and Disease
- (2013) Pedro J. Batista et al. CELL
- Aicardi-Goutières syndrome: a model disease for systemic autoimmunity
- (2013) M. A. Lee-Kirsch et al. CLINICAL AND EXPERIMENTAL IMMUNOLOGY
- A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage
- (2013) P. Richard et al. GENES & DEVELOPMENT
- E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells
- (2013) J. Sun et al. GENES & DEVELOPMENT
- Aicardi–Goutières syndrome: clues from the RNase H2 knock-out mouse
- (2013) Björn Rabe JOURNAL OF MOLECULAR MEDICINE-JMM
- EXOSC3 mutations in isolated cerebellar hypoplasia and spinal anterior horn involvement
- (2013) Roberta Biancheri et al. JOURNAL OF NEUROLOGY
- A Lytic Viral Long Noncoding RNA Modulates the Function of a Latent Protein
- (2013) M. Campbell et al. JOURNAL OF VIROLOGY
- Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
- (2013) Fan Lai et al. NATURE
- Endogenous retroviruses function as species-specific enhancer elements in the placenta
- (2013) Edward B Chuong et al. NATURE GENETICS
- Long non-coding RNAs: new players in cell differentiation and development
- (2013) Alessandro Fatica et al. NATURE REVIEWS GENETICS
- Pontocerebellar hypoplasia type 1: Clinical spectrum and relevance of EXOSC3 mutations
- (2013) S. Rudnik-Schoneborn et al. NEUROLOGY
- Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
- (2013) A. A. Sigova et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing
- (2013) Olivier J. Becherel et al. PLoS Genetics
- Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII
- (2012) Alexandre Wagschal et al. CELL
- Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development
- (2012) Martin A.M. Reijns et al. CELL
- Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes
- (2012) Amaya Alzu et al. CELL
- Co-transcriptional degradation of aberrant pre-mRNA by Xrn2
- (2012) Lee Davidson et al. EMBO JOURNAL
- Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- (2012) H. Tani et al. GENOME RESEARCH
- Genome-wide analysis of long noncoding RNA stability
- (2012) M. B. Clark et al. GENOME RESEARCH
- Senataxin, Defective in the Neurodegenerative Disorder Ataxia with Oculomotor Apraxia 2, Lies at the Interface of Transcription and the DNA Damage Response
- (2012) O. Yuce et al. MOLECULAR AND CELLULAR BIOLOGY
- RNA Polymerase II Collision Interrupts Convergent Transcription
- (2012) David J. Hobson et al. MOLECULAR CELL
- R Loops: From Transcription Byproducts to Threats to Genome Stability
- (2012) Andrés Aguilera et al. MOLECULAR CELL
- RNAi triggered by specialized machinery silences developmental genes and retrotransposons
- (2012) Soichiro Yamanaka et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Spatial partitioning of the regulatory landscape of the X-inactivation centre
- (2012) Elphège P. Nora et al. NATURE
- Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation
- (2012) Farzaneh Modarresi et al. NATURE BIOTECHNOLOGY
- Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration
- (2012) Jijun Wan et al. NATURE GENETICS
- Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature
- (2012) Gillian I Rice et al. NATURE GENETICS
- Transcription as a source of genome instability
- (2012) Nayun Kim et al. NATURE REVIEWS GENETICS
- Regulation of cytoplasmic mRNA decay
- (2012) Daniel R. Schoenberg et al. NATURE REVIEWS GENETICS
- Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing
- (2012) P. A. Latos et al. SCIENCE
- Nuclear noncoding RNA surveillance: is the end in sight?
- (2012) Sandra L. Wolin et al. TRENDS IN GENETICS
- G-quadruplexes in RNA biology
- (2012) Stefania Millevoi et al. Wiley Interdisciplinary Reviews-RNA
- The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates
- (2011) Uttiya Basu et al. CELL
- Divergent transcription: A new feature of active promoters
- (2011) Amy C. Seila et al. CELL CYCLE
- Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes
- (2011) Prasun Chakraborty et al. DNA REPAIR
- RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability
- (2011) Lamia Wahba et al. MOLECULAR CELL
- Molecular Mechanisms of Long Noncoding RNAs
- (2011) Kevin C. Wang et al. MOLECULAR CELL
- Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination
- (2011) Konstantina Skourti-Stathaki et al. MOLECULAR CELL
- Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex
- (2011) Michal Lubas et al. MOLECULAR CELL
- Initial genome sequencing and analysis of multiple myeloma
- (2011) Michael A. Chapman et al. NATURE
- CTCF-mediated functional chromatin interactome in pluripotent cells
- (2011) Lusy Handoko et al. NATURE GENETICS
- Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin
- (2011) Francisca E Reyes-Turcu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Clr4/Suv39 and RNA Quality Control Factors Cooperate to Trigger RNAi and Suppress Antisense RNA
- (2011) K. Zhang et al. SCIENCE
- The Lytic Transcriptome of Kaposi's Sarcoma-Associated Herpesvirus Reveals Extensive Transcription of Noncoding Regions, Including Regions Antisense to Important Genes
- (2010) S. Chandriani et al. JOURNAL OF VIROLOGY
- An antisense RNA that governs the expression kinetics of a multifunctional virulence gene
- (2010) Eun-Jin Lee et al. MOLECULAR MICROBIOLOGY
- Mediator and cohesin connect gene expression and chromatin architecture
- (2010) Michael H. Kagey et al. NATURE
- RNA helicases at work: binding and rearranging
- (2010) Eckhard Jankowsky TRENDS IN BIOCHEMICAL SCIENCES
- Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein Binds and Protects a Nuclear Noncoding RNA from Cellular RNA Decay Pathways
- (2010) Brooke B. Sahin et al. PLoS Pathogens
- Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation
- (2009) Amila Suraweera et al. HUMAN MOLECULAR GENETICS
- G Clustering Is Important for the Initiation of Transcription-Induced R-Loops In Vitro, whereas High G Density without Clustering Is Sufficient Thereafter
- (2009) D. Roy et al. MOLECULAR AND CELLULAR BIOLOGY
- Competition between the RNA Transcript and the Nontemplate DNA Strand during R-Loop Formation In Vitro: a Nick Can Serve as a Strong R-Loop Initiation Site
- (2009) D. Roy et al. MOLECULAR AND CELLULAR BIOLOGY
- An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles
- (2009) Christine M. Clemson et al. MOLECULAR CELL
- Small silencing RNAs: an expanding universe
- (2009) Megha Ghildiyal et al. NATURE REVIEWS GENETICS
- Biogenesis of small RNAs in animals
- (2009) V. Narry Kim et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
- (2009) J. Sheik Mohamed et al. RNA
- G-quadruplex structures: in vivo evidence and function
- (2009) Hans J. Lipps et al. TRENDS IN CELL BIOLOGY
- Global Transcription in Pluripotent Embryonic Stem Cells
- (2008) Sol Efroni et al. Cell Stem Cell
- Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1
- (2008) I. Chernyakov et al. GENES & DEVELOPMENT
- Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
- (2008) M. E. Dinger et al. GENOME RESEARCH
- Genome instability: a mechanistic view of its causes and consequences
- (2008) Andrés Aguilera et al. NATURE REVIEWS GENETICS
- The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin
- (2008) T. Nagano et al. SCIENCE
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