Cellular functions of long noncoding RNAs
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[1] A. Lamond,et al. Nuclear speckles. , 2011, Cold Spring Harbor perspectives in biology.
[2] Maria Carmo-Fonseca,et al. Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs , 2017, Molecular cell.
[3] S. Konermann,et al. Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors , 2018, Cell.
[4] E. Lander,et al. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood , 2017, Nature.
[5] N. Brockdorff,et al. The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. , 2010, Developmental cell.
[6] John M. Shelton,et al. A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance , 2015, Cell.
[7] P. Pandolfi,et al. A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.
[8] N. Goshima,et al. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL , 2016, The Journal of cell biology.
[9] H. Le Hir,et al. Transcriptome-wide identification of RNA binding sites by CLIP-seq. , 2013, Methods.
[10] C. Glass,et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription , 2013, Nature.
[11] A. Inga,et al. The Ribonucleic Complex HuR-MALAT1 Represses CD133 Expression and Suppresses Epithelial-Mesenchymal Transition in Breast Cancer. , 2016, Cancer research.
[12] Jeannie T. Lee,et al. Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1) , 2017, Proceedings of the National Academy of Sciences.
[13] R. Margueron,et al. PRC2 is dispensable for HOTAIR‐mediated transcriptional repression , 2017, The EMBO journal.
[14] F. Hou,et al. Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex , 2014, British Journal of Cancer.
[15] J. Mendell,et al. Functional Classification and Experimental Dissection of Long Noncoding RNAs , 2018, Cell.
[16] Ye Xu,et al. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus , 2015, Genes & development.
[17] Junhui Ge,et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus , 2014, Cell Research.
[18] Celso A. Espinoza,et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. , 2008, Molecular cell.
[19] S. Itzkovitz,et al. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells , 2015, Nature Communications.
[20] Tsung-Cheng Chang,et al. Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins , 2016, Cell.
[21] V. Medina,et al. Histamine H4 receptor: insights into a potential therapeutic target in breast cancer. , 2015, Frontiers in bioscience.
[22] J. Rinn,et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution , 2015, Genome Biology.
[23] Ling-Ling Chen,et al. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria , 2018, Nature Cell Biology.
[24] Keegan D. Korthauer,et al. High‐throughput identification of RNA nuclear enrichment sequences , 2017, bioRxiv.
[25] Kotb Abdelmohsen,et al. LincRNA-p21 suppresses target mRNA translation. , 2012, Molecular cell.
[26] Celso A. Espinoza,et al. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis , 2004, Nature Structural &Molecular Biology.
[27] Jeannie T. Lee,et al. Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. , 2015, Science.
[28] Howard Y. Chang,et al. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.
[29] Takahide Yokoi,et al. NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies , 2014, Molecular biology of the cell.
[30] E. Ashley,et al. A long non-coding RNA protects the heart from pathological hypertrophy , 2014, Nature.
[31] A. Fox,et al. Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies , 2010, Molecular biology of the cell.
[32] Christopher J. Cronin,et al. Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH , 2018, Cell.
[33] David G. Knowles,et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.
[34] L. Maquat,et al. lncRNAs transactivate Staufen1-mediated mRNA decay by duplexing with 3'UTRs via Alu elements , 2010, Nature.
[35] Jesse M. Engreitz,et al. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood , 2017, Nature.
[36] Howard Y. Chang,et al. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. , 2013, Cell reports.
[37] Stephen C. Cannon,et al. A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle , 2016, Science.
[38] Charles Gawad,et al. Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types , 2012, PloS one.
[39] Jernej Ule,et al. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes , 2012, Genome Biology.
[40] John N. Hutchinson,et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. , 2009, Molecular cell.
[41] Jeannie T. Lee,et al. The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells , 2015, Proceedings of the National Academy of Sciences.
[42] M. Esteller,et al. Head-to-head antisense transcription and R-loop formation promotes transcriptional activation , 2015, Proceedings of the National Academy of Sciences.
[43] Justin Demmerle,et al. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy , 2014, Proceedings of the National Academy of Sciences.
[44] M. Atchison,et al. Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X , 2016, Proceedings of the National Academy of Sciences.
[45] K. Prasanth,et al. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. , 2017, Trends in genetics : TIG.
[46] Shinichi Nakagawa,et al. Malat1 is not an essential component of nuclear speckles in mice. , 2012, RNA.
[47] J. Rinn,et al. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs , 2016, bioRxiv.
[48] K. Rippe,et al. Alu element‐containing RNAs maintain nucleolar structure and function , 2015, The EMBO journal.
[49] Luc DesGroseillers,et al. Mammalian Staufen1 Recruits Upf1 to Specific mRNA 3′UTRs so as to Elicit mRNA Decay , 2005, Cell.
[50] Howard Y. Chang,et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.
[51] Yutaka Suzuki,et al. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. , 2014, Molecular cell.
[52] E. Lander,et al. The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome , 2013, Science.
[53] C. Bond,et al. Paraspeckles: nuclear bodies built on long noncoding RNA , 2009, The Journal of cell biology.
[54] E. Lander,et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing , 2016, Nature.
[55] Jeannie T. Lee,et al. Comment on “Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing” , 2017, Science.
[56] D. Spector,et al. Direct Visualization of the Co-transcriptional Assembly of a Nuclear Body by Noncoding RNAs , 2010, Nature Cell Biology.
[57] D. Barlow,et al. Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.
[58] S. Dimmeler,et al. Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth , 2014, Circulation Research.
[59] J. Kjems,et al. Natural RNA circles function as efficient microRNA sponges , 2013, Nature.
[60] S. Nakagawa,et al. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice , 2011, The Journal of cell biology.
[61] Chaolin Zhang,et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. , 2012, Cell reports.
[62] A. Krainer,et al. Abstract PR11: Differentiation of mammary tumors and reduction in metastasis upon Malat1 LncRNA loss , 2016 .
[63] Aviv Regev,et al. RNA targeting with CRISPR–Cas13 , 2017, Nature.
[64] G. Carmichael,et al. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. , 2009, Molecular cell.
[65] H. Benyamini,et al. Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation. , 2017, Cancer research.
[66] Qiangfeng Cliff Zhang,et al. Systematic Discovery of Xist RNA Binding Proteins , 2015, Cell.
[67] Howard Y. Chang,et al. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element , 2018, Cell.
[68] C. Azzalin,et al. Telomeric Repeat–Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends , 2007, Science.
[69] Gene W. Yeo,et al. NEAT1 Scaffolds RNA Binding Proteins and the Microprocessor to Globally Enhance Pri-miRNA Processing , 2017, Nature Structural &Molecular Biology.
[70] Michael J. Sweredoski,et al. The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3 , 2015, Nature.
[71] Qiang Zhou,et al. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription , 2001, Nature.
[72] P. Pandolfi,et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.
[73] A. Fox,et al. Nuclear bodies: news insights into structure and function. , 2017, Current opinion in cell biology.
[74] Christopher J. Krueger,et al. A molecular beacon-based approach for live-cell imaging of RNA transcripts with minimal target engineering at the single-molecule level , 2017, Scientific Reports.
[75] B. Blencowe,et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. , 2010, Molecular cell.
[76] Andrea J. Kriz,et al. Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X. , 2019, Molecular cell.
[77] J. Lawrence,et al. XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.
[78] Shinichi Nakagawa,et al. The long noncoding RNA Neat1 is required for mammary gland development and lactation , 2014, RNA.
[79] T. Cech,et al. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. , 2015, Molecular cell.
[80] L. Steinmetz,et al. Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality , 2013, Nature Structural &Molecular Biology.
[81] Jeannie T. Lee,et al. Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.
[82] N. Brockdorff,et al. PCGF3/5–PRC1 initiates Polycomb recruitment in X chromosome inactivation , 2017, Science.
[83] David L. Spector,et al. 3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA , 2008, Cell.
[84] Xiaoyi Cao,et al. Systematic Mapping of RNA-Chromatin Interactions In Vivo , 2017, Current Biology.
[85] F. Pauler,et al. Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing , 2012, Science.
[86] W. Olivas,et al. Roles of Puf proteins in mRNA degradation and translation , 2011, Wiley interdisciplinary reviews. RNA.
[87] T. Mituyama,et al. MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles , 2009, Proceedings of the National Academy of Sciences.
[88] Jennifer A. Doudna,et al. Programmable RNA Tracking in Live Cells with CRISPR/Cas9 , 2016, Cell.
[89] Ling-Ling Chen,et al. SLERT Regulates DDX21 Rings Associated with Pol I Transcription , 2017, Cell.
[90] P. Jolivet,et al. Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle , 2017, Cell.
[91] Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. , 2015, Science.
[92] Gene W. Yeo,et al. Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP) , 2016, Nature Methods.
[93] T. Hirose,et al. Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies. , 2016, Biochimica et biophysica acta.
[94] R. McCarthy,et al. LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56. , 2016, Molecular cell.
[95] F. Niazi,et al. A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA , 2014, Molecular and Cellular Biology.
[96] J. Steitz,et al. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. , 2004, RNA.
[97] J. Shepherd,et al. Cycle. , 2020, The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry.
[98] Sharon R Grossman,et al. RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites , 2014, Cell.
[99] J. Lawrence,et al. XIST RNA and architecture of the inactive X chromosome: implications for the repeat genome. , 2010, Cold Spring Harbor symposia on quantitative biology.
[100] Jeannie T. Lee,et al. The X chromosome in space , 2017, Nature Reviews Genetics.
[101] Shanshan Zhu,et al. Circular intronic long noncoding RNAs. , 2013, Molecular cell.
[102] S. Aerts,et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity , 2016, Nature Medicine.
[103] Piero Carninci,et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat , 2012, Nature.
[104] Paulo P. Amaral,et al. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. , 2009, Genome research.
[105] J. Franc,et al. Circadian RNA expression elicited by 3’-UTR IRAlu-paraspeckle associated elements , 2016, eLife.
[106] C. Bond,et al. Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation. , 2018, Molecular cell.
[107] G. Carmichael,et al. Alu element‐mediated gene silencing , 2008, The EMBO journal.
[108] Phillip A Sharp,et al. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. , 2014, Molecular cell.
[109] A. Pombo,et al. Three-dimensional genome architecture: players and mechanisms , 2015, Nature Reviews Molecular Cell Biology.
[110] M. Rosenfeld,et al. Enhancers as non-coding RNA transcription units: recent insights and future perspectives , 2016, Nature Reviews Genetics.
[111] S. Batalov,et al. Antisense Transcription in the Mammalian Transcriptome , 2005, Science.
[112] J. Rinn,et al. Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs , 2015, PloS one.
[113] G. Kreiman,et al. Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.
[114] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[115] E. Lander,et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability , 2018, Nature.
[116] John N. Hutchinson,et al. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains , 2007, BMC Genomics.
[117] Yuehua Wu,et al. Long noncoding RNAs with snoRNA ends. , 2012, Molecular cell.
[118] Sebastian D. Mackowiak,et al. Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.
[119] X. Zhuang,et al. Spatially resolved, highly multiplexed RNA profiling in single cells , 2015, Science.
[120] J. Rinn,et al. Neat1 is a p53-inducible lincRNA essential for transformation suppression , 2017, Genes & development.
[121] David P. Bartel,et al. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain , 2018, Cell.
[122] Jeannie T. Lee,et al. Perinucleolar Targeting of the Inactive X during S Phase: Evidence for a Role in the Maintenance of Silencing , 2007, Cell.
[123] J. Rinn,et al. An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance , 2018, Cell.
[124] I. Ulitsky,et al. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells , 2017, Nature.
[125] C. Ghigna,et al. Transcription of Satellite III non-coding RNAs is a general stress response in human cells , 2007, Nucleic Acids Research.
[126] D. Duboule,et al. Hotair Is Dispensible for Mouse Development , 2016, PLoS genetics.
[127] H. Yao,et al. A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. , 2015, Cancer cell.
[128] S. Diederichs,et al. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. , 2011, Genome research.
[129] N. Goshima,et al. Alternative 3′‐end processing of long noncoding RNA initiates construction of nuclear paraspeckles , 2012, The EMBO journal.
[130] A. Harvey,et al. Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles , 2017, RNA.
[131] Xuetao Cao,et al. The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation , 2014, Science.
[132] David R. Kelley,et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre , 2014, Nature Structural &Molecular Biology.
[133] R. Kingston,et al. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization , 2016, The Journal of cell biology.
[134] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[135] D. Largaespada,et al. PVT1 dependence in cancer with MYC copy-number increase , 2014, Nature.
[136] Sarah K. Bowman,et al. High-resolution Xist binding maps reveal 2-step spreading during X-inactivation , 2013, Nature.
[137] Michael Y Tolstorukov,et al. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. , 2014, Molecular cell.
[138] Howard Y. Chang,et al. NONCODING RNA: CRISPRi‐based genome‐scale identification of functional long noncoding RNA loci in human cells , 2017 .
[139] I. Grummt,et al. LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure. , 2015, Molecular cell.
[140] Michael Q. Zhang,et al. Regulating Gene Expression through RNA Nuclear Retention , 2005, Cell.
[141] Maite Huarte,et al. A Long Noncoding RNA Regulates Sister Chromatid Cohesion. , 2016, Molecular cell.
[142] John M. Shelton,et al. Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development , 2016, Nature.
[143] Eiki Takahashi,et al. The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice , 2014, Development.
[144] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[145] Jun Zhang,et al. Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. , 2016, Molecular cell.
[146] Howard Y. Chang,et al. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing , 2014, Nature.
[147] R. Lehmann,et al. The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. , 1997, RNA.
[148] Noah Ollikainen,et al. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing , 2016, Science.
[149] Nicholas T Ingolia,et al. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. , 2014, Cell reports.
[150] J. Lawrence,et al. Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes , 2014, Cell.
[151] Vikram Agarwal,et al. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. , 2014, Molecular cell.
[152] R. Pappu,et al. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution , 2017, Journal of Cell Science.