151
Views
0
CrossRef citations to date
0
Altmetric
Special Report

The Regulation of Mammalian mRNA Transcription by lncRNAs: Recent Discoveries and Current Concepts

&
Pages 95-102 | Published online: 15 Feb 2013

References

  • Koziol MJ , RinnJL. RNA traffic control of chromatin complexes. Curr. Opin. Genet. Dev.20(2) , 142–148 (2010).
  • Wang KC , ChangHY. Molecular mechanisms of long noncoding RNAs. Mol. Cell43(6) , 904–914 (2011).
  • Cabianca DS , CasaV, BodegaB et al. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4) , 819–831 (2012).
  • Yu W , GiusD, OnyangoP et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175) , 202–206 (2008).
  • Gupta RA , ShahN, WangKC et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291) , 1071–1076 (2010).
  • Huarte M , GuttmanM, FeldserD et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142(3) , 409–419 (2010).
  • Kogo R , ShimamuraT, MimoriK et al. Long non-coding RNA HOTAIR regulates Polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71(20) , 6320–6326 (2011).
  • Morris KV , SantosoS, TurnerAM, PastoriC, HawkinsPG. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet.4(11) , e1000258 (2008).
  • Kotake Y , NakagawaT, KitagawaK et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30(16) , 1956–1962 (2011).
  • Yap KL , LiS, Munoz-CabelloAM et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38(5) , 662–674 (2010).
  • Jeon Y , SarmaK, LeeJT. New and Xisting regulatory mechanisms of X chromosome inactivation. Curr. Opin. Genet. Dev.22(2) , 62–71 (2012).
  • Mohammad F , MondalT, KanduriC. Epigenetics of imprinted long noncoding RNAs. Epigenetics4(5) , 277–286 (2009).
  • Mohammad F , MondalT, GusevaN, PandeyGK, KanduriC. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development137(15) , 2493–2499 (2010).
  • Wang KC , YangYW, LiuB et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341) , 120–124 (2011).
  • Rinn JL , KerteszM, WangJK et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7) , 1311–1323 (2007).
  • Tsai MC , ManorO, WanY et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992) , 689–693 (2010).
  • Schorderet P , DubouleD. Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet.7(5) , e1002071 (2011).
  • Guttman M , DonagheyJ, CareyBW et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364) , 295–300 (2011).
  • Ng SY , JohnsonR, StantonLW. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J.31(3) , 522–533 (2012).
  • Hawkins PG , MorrisKV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription1(3) , 165–175 (2010).
  • Kino T , HurtDE, IchijoT, NaderN, ChrousosGP. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal.3(107) , ra8 (2010).
  • Hung T , WangY, LinMF et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 43(7) , 621–629 (2011).
  • Lanz RB , McKennaNJ, OnateSA et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97(1) , 17–27 (1999).
  • Foulds CE , TsimelzonA, LongW et al. Research resource: expression profiling reveals unexpected targets and functions of the human steroid receptor RNA activator (SRA) gene. Mol. Endocrinol. 24(5) , 1090–1105 (2010).
  • Caretti G , SchiltzRL, DilworthFJ et al. The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Genes Dev. 11(4) , 547–560 (2006).
  • Yao H , BrickK, EvrardY, XiaoT, Camerini-OteroRD, FelsenfeldG. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev.24(22) , 2543–2555 (2010).
  • Hatchell EC , ColleySM, BeveridgeDJ et al. SLIRP, a small SRA binding protein, is a nuclear receptor corepressor. Mol. Cell 22(5) , 657–668 (2006).
  • Shi Y , DownesM, XieW et al. Sharp, an inducible cofactor that integrates nuclear receptor repression and activation. Genes Dev. 15(9) , 1140–1151 (2001).
  • D‘Orso I , FrankelAD. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat. Struct. Mol. Biol.17(7) , 815–821 (2010).
  • Sobhian B , LaguetteN, YatimA et al. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol. Cell 38(3) , 439–451 (2010).
  • Mariner PD , WaltersRD, EspinozaCA et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 29(4) , 499–509 (2008).
  • Yakovchuk P , GoodrichJA, KugelJF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc. Natl Acad. Sci. USA106(14) , 5569–5574 (2009).
  • Yakovchuk P , GoodrichJA, KugelJF. B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription2(1) , 45–49 (2011).
  • Nagano T , MitchellJA, SanzLA et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322(5908) , 1717–1720 (2008).
  • Carter D , ChakalovaL, OsborneCS, DaiYF, FraserP. Long-range chromatin regulatory interactions in vivo. Nat. Genet.32(4) , 623–626 (2002).
  • Pandey RR , MondalT, MohammadF et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32(2) , 232–246 (2008).
  • Simon MD , WangCI, KharchenkoPV et al. The genomic binding sites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108(51) , 20497–20507 (2011).
  • Chu C , QuK, ZhongFL, ArtandiSE, ChangHY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell44(4) , 667–678 (2011).
  • Zappulla DC , CechTR. Yeast telomerase RNA: a flexible scaffold for protein subunits. Proc. Natl Acad. Sci. USA101(27) , 10024–10029 (2004).
  • Zappulla DC , CechTR. RNA as a flexible scaffold for proteins: yeast telomerase and beyond. Cold Spring Harb. Symp. Quant. Biol.71 , 217–224 (2006).
  • Rapicavoli NA , PothEM, ZhuH, BlackshawS. The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev.6 , 32 (2011).
  • He N , JahchanNS, HongE et al. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol. Cell 29(5) , 588–599 (2008).
  • Colley SM , LeedmanPJ. Steroid receptor RNA activator – a nuclear receptor coregulator with multiple partners: insights and challenges. Biochimie93(11) , 1966–1972 (2011).
  • Mao YS , ZhangB, SpectorDL. Biogenesis and function of nuclear bodies. Trends Genet.27(8) , 295–306 (2011).
  • Mohammad F , PandeyRR, NaganoT et al. Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol. Cell. Biol. 28(11) , 3713–3728 (2008).
  • Hutchinson JN , EnsmingerAW, ClemsonCM, LynchCR, LawrenceJB, ChessA. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics8 , 39 (2007).
  • Ji P , DiederichsS, WangW et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22(39) , 8031–8041 (2003).
  • Lin R , MaedaS, LiuC, KarinM, EdgingtonTS. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene26(6) , 851–858 (2007).
  • Tano K , MizunoR, OkadaT et al. MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS Lett. 584(22) , 4575–4580 (2010).
  • Yang L , LinC, LiuW et al. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147(4) , 773–788 (2011).
  • Tripathi V , EllisJD, ShenZ et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39(6) , 925–938 (2010).
  • Eissmann M , GutschnerT, HammerleM et al. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 9(8) , 1076–1087 (2012).
  • Nakagawa S , IpJY, ShioiG et al. Malat1 is not an essential component of nuclear speckles in mice. RNA 18(8) , 1487–1499 (2012).
  • Zhang B , ArunG, MaoYS et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2(1) , 111–123 (2012).
  • Bond CS , FoxAH. Paraspeckles: nuclear bodies built on long noncoding RNA. J. Cell Biol.186(5) , 637–644 (2009).
  • Clemson CM , HutchinsonJN, SaraSA et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33(6) , 717–726 (2009).
  • Chen LL , CarmichaelGG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell35(4) , 467–478 (2009).
  • Sasaki YT , IdeueT, SanoM, MituyamaT, HiroseT. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl Acad. Sci. USA106(8) , 2525–2530 (2009).
  • Sunwoo H , DingerME, WiluszJE, AmaralPP, MattickJS, SpectorDL. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res.19(3) , 347–359 (2009).
  • Mao YS , SunwooH, ZhangB, SpectorDL. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat. Cell Biol.13(1) , 95–101 (2011).
  • Nakagawa S , NaganumaT, ShioiG, HiroseT. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J. Cell Biol.193(1) , 31–39 (2011).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.