Regulatory long non-coding RNA and its functions

The discovery of large numbers of long non-coding RNAs (lncRNAs) has been driven by genome-wide transcriptional analyses. Compared to small ncRNAs, lncRNAs have been shown to harbor biological activities, but the functions of the great majority of lncRNAs are not known. There is growing evidence that lncRNAs can regulate gene expression at epigenetic, transcription, and post-transcription levels and widely take part in various physiological and pathological processes, such as participating in cell development, immunity, oncogenesis, clinical disease processes, etc. Here, the current research efforts on the function of lncRNA in recent years were summarized.

[1]  E. Dees,et al.  The product of the H19 gene may function as an RNA , 1990, Molecular and cellular biology.

[2]  Carolyn J. Brown,et al.  A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome , 1991, Nature.

[3]  J. Brosius,et al.  Primary structure, neural-specific expression, and dendritic location of human BC200 RNA , 1993, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[4]  V. Erdmann,et al.  The product of the imprinted H19 gene is an oncofetal RNA. , 1997, Molecular pathology : MP.

[5]  J. Brosius,et al.  Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice , 2004, Behavioural Brain Research.

[6]  S. Batalov,et al.  A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT , 2005, Science.

[7]  J. Sample,et al.  Protection from Interferon-Induced Apoptosis by Epstein-Barr Virus Small RNAs Is Not Mediated by Inhibition of PKR , 2005, Journal of Virology.

[8]  G. Hannon,et al.  Control of translation and mRNA degradation by miRNAs and siRNAs. , 2006, Genes & development.

[9]  E. Heard,et al.  A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. , 2006, Genes & development.

[10]  Brian S. Clark,et al.  The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. , 2006, Genes & development.

[11]  G. Wilkinson,et al.  Complex I Binding by a Virally Encoded RNA Regulates Mitochondria-Induced Cell Death , 2007, Science.

[12]  M. Kuroda,et al.  Noncoding RNAs and Intranuclear Positioning in Monoallelic Gene Expression , 2007, Cell.

[13]  Jing Zhao,et al.  Activation of p53 by MEG3 Non-coding RNA* , 2007, Journal of Biological Chemistry.

[14]  P. Stadler,et al.  RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription , 2007, Science.

[15]  G. Hannon,et al.  The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race , 2007, Science.

[16]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[17]  John R. Young,et al.  Non-coding RNAs revealed during identification of genes involved in chicken immune responses , 2008, Immunogenetics.

[18]  K. Kinzler,et al.  The Antisense Transcriptomes of Human Cells , 2008, Science.

[19]  C. Wahlestedt,et al.  A Novel RNA Transcript with Antiapoptotic Function Is Silenced in Fragile X Syndrome , 2008, PloS one.

[20]  David I. Smith,et al.  Long, abundantly expressed non-coding transcripts are altered in cancer. , 2008, Human molecular genetics.

[21]  A. Feinberg,et al.  Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA , 2008, Nature.

[22]  Satyanarayan Rao,et al.  A novel noncoding RNA processed by Drosha is restricted to nucleus in mouse. , 2008, RNA.

[23]  C. S. Sullivan.  New roles for large and small viral RNAs in evading host defences , 2008, Nature Reviews Genetics.

[24]  J. Komorowski,et al.  Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. , 2008, Molecular cell.

[25]  A. G. de Herreros,et al.  A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. , 2008, Genes & development.

[26]  Celso A. Espinoza,et al.  Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. , 2008, Molecular cell.

[27]  T. Morgan,et al.  Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase , 2008, Nature Medicine.

[28]  Y. Kuroiwa,et al.  RNA-binding Protein TLS Is a Major Nuclear Aggregate-interacting Protein in Huntingtin Exon 1 with Expanded Polyglutamine-expressing Cells* , 2008, Journal of Biological Chemistry.

[29]  C. Glass,et al.  Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription , 2008, Nature.

[30]  M. Mourtada-Maarabouni,et al.  GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer , 2009, Oncogene.

[31]  Tim R. Mercer,et al.  LONG NONCODING RNAs: INSIGHTS INTO FUNCTION , 2009 .

[32]  C. Ponting,et al.  Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness , 2009, Genome Biology.

[33]  K. Ohta,et al.  Cascade transcription of mRNA-type long non-coding RNAs (mlonRNAs) and local chromatin remodeling , 2009, Epigenetics.

[34]  D. Spector,et al.  Long noncoding RNAs: functional surprises from the RNA world. , 2009, Genes & development.

[35]  M. Laan,et al.  Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression , 2009, BMC Molecular Biology.

[36]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

[37]  K. Morris.  Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells , 2009, Epigenetics.

[38]  C. Ponting,et al.  Evolution and Functions of Long Noncoding RNAs , 2009, Cell.

[39]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[40]  P. Sorensen,et al.  The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA , 2010, BMC Biology.

[41]  David I. Smith,et al.  Identification of long stress-induced non-coding transcripts that have altered expression in cancer. , 2010, Genomics.

[42]  Stephen A. Stanhope,et al.  A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. , 2010, Blood.

[43]  C. Kanduri,et al.  Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1 , 2010, Development.

[44]  M. Groudine,et al.  Enhancers: the abundance and function of regulatory sequences beyond promoters. , 2010, Developmental biology.

[45]  P. Harrison,et al.  Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs , 2010, PloS one.

[46]  A. Gabory,et al.  The H19 locus: Role of an imprinted non‐coding RNA in growth and development , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[47]  J. Rinn,et al.  Large non-coding RNAs: missing links in cancer? , 2010, Human molecular genetics.

[48]  Yong Huang,et al.  Biological functions of microRNAs: a review , 2011, Journal of Physiology and Biochemistry.

[49]  T. Derrien,et al.  Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.

[50]  Lisa E. Gralinski,et al.  Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling , 2010, mBio.

[51]  J. Mattick,et al.  Long non-coding RNAs in nervous system function and disease , 2010, Brain Research.

[52]  Howard Y. Chang,et al.  Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis , 2010, Nature.

[53]  J. Rinn,et al.  Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells , 2010, Nature Genetics.

[54]  K. Shibata,et al.  Oxytocin stimulates expression of a noncoding RNA tumor marker in a human neuroblastoma cell line. , 2010, Life sciences.

[55]  Toshiro K. Ohsumi,et al.  Genome-wide identification of polycomb-associated RNAs by RIP-seq. , 2010, Molecular cell.

[56]  J. Rinn,et al.  A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.

[57]  Shuhan Sun,et al.  Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans , 2011, Hepatology.

[58]  Yusuke Nakamura,et al.  Association of a novel long non‐coding RNA in 8q24 with prostate cancer susceptibility , 2011, Cancer science.

[59]  J. Mattick,et al.  The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. , 2011, Cancer research.

[60]  Howard Y. Chang,et al.  A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression , 2011, Nature.

[61]  H. Ishimoto,et al.  A Conserved Long Noncoding RNA Affects Sleep Behavior in Drosophila , 2011, Genetics.

[62]  Carolyn J. Brown,et al.  The functional role of long non-coding RNA in human carcinomas , 2011, Molecular Cancer.

[63]  Shuli Kang,et al.  Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network , 2011, Nucleic acids research.

[64]  John T. Wei,et al.  Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression , 2011, Nature Biotechnology.

[65]  A. Chinnaiyan,et al.  The emergence of lncRNAs in cancer biology. , 2011, Cancer discovery.

[66]  P. Sorensen,et al.  A possible role for long non-coding RNA in modulating signaling pathways. , 2011, Medical hypotheses.

[67]  J. Rinn,et al.  lincRNAs act in the circuitry controlling pluripotency and differentiation , 2011, Nature.