Mechanisms of long noncoding RNA function in development and disease
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Okazaki Y, Furuno M, Kasukawa T et al (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563–573. doi: 10.1038/nature01266
Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 489:101–108. doi: 10.1038/nature11233
Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789. doi: 10.1101/gr.132159.111
Cabili MN, Trapnell C, Goff L et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915–1927. doi: 10.1101/gad.17446611
Guo X, Gao L, Wang Y et al (2015) Advances in long noncoding RNAs: identification, structure prediction and function annotation. Brief Funct Genomics. doi: 10.1093/bfgp/elv022
Harrow J, Frankish A, Gonzalez JM et al (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22:1760–1774. doi: 10.1101/gr.135350.111
Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802. doi: 10.1016/j.cell.2011.10.002
Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM (2014) Long non-coding RNAs as a source of new peptides. elife 3:e03523. doi: 10.7554/eLife.03523
Guttman M, Russell P, Ingolia NT et al (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154:240–251. doi: 10.1016/j.cell.2013.06.009
Bánfai B, Jia H, Khatun J et al (2012) Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 22:1646–1657. doi: 10.1101/gr.134767.111
Bazzini AA, Johnstone TG, Christiano R et al (2014) Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. doi: 10.1002/embj.201488411
Frith MC, Forrest AR, Nourbakhsh E et al (2006) The abundance of short proteins in the mammalian proteome. PLoS Genet 2:e52. doi: 10.1371/journal.pgen.0020052
Anderson DM, Anderson KM, Chang C-L et al (2015) A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160:595–606. doi: 10.1016/j.cell.2015.01.009
Pauli A, Norris ML, Valen E et al (2014) Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343:1248636. doi: 10.1126/science.1248636
Yan Y, Cooper C, Hamedani MK et al (2015) The steroid receptor RNA activator protein (SRAP) controls cancer cell migration/motility. FEBS Lett 589:4010–4018. doi: 10.1016/j.febslet.2015.11.007
Rupaimoole R, Lee J, Haemmerle M et al (2015) Long noncoding RNA ceruloplasmin promotes cancer growth by altering glycolysis. Cell Rep 13:2395–2402. doi: 10.1016/j.celrep.2015.11.047
Novikova IV, Hennelly SP, Tung C-S, Sanbonmatsu KY (2013) Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol 425:3731–3746. doi: 10.1016/j.jmb.2013.02.030
Weeks KM (2015) Review toward all RNA structures, concisely. Biopolymers 103:438–448. doi: 10.1002/bip.22601
Smola MJ, Rice GM, Busan S et al (2015) Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc 10:1643–1669. doi: 10.1038/nprot.2015.103
Spitale RC, Flynn RA, Zhang QC et al (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature. doi: 10.1038/nature14263
Guttman M, Amit I, Garber M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227. doi: 10.1038/nature07672
Sun M, Gadad SS, Kim D-S, Kraus WL (2015) Discovery, annotation, and functional analysis of long noncoding RNAs controlling Cell-cycle gene expression and proliferation in breast cancer cells. Mol Cell. doi: 10.1016/j.molcel.2015.06.023
Marques AC, Hughes J, Graham B et al (2013) Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol 14:R131. doi: 10.1186/gb-2013-14-11-r131
ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. doi: 10.1038/nature11247
Iyer MK, Niknafs YS, Malik R et al (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47:199–208. doi: 10.1038/ng.3192
Hansen TB, Jensen TI, Clausen BH et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384–388. doi: 10.1038/nature11993
Memczak S, Jens M, Elefsinioti A et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338. doi: 10.1038/nature11928
Werner MS, Ruthenburg AJ (2015) Nuclear fractionation reveals thousands of chromatin-tethered noncoding RNAs adjacent to active genes. Cell Rep 12:1089–1098. doi: 10.1016/j.celrep.2015.07.033
Herman RC, Williams JG, Penman S (1976) Message and non-message sequences adjacent to poly(A) in steady state heterogeneous nuclear RNA of HeLa cells. Cell 7:429–437
Yue F, Cheng Y, Breschi A et al (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515:355–364. doi: 10.1038/nature13992
Haerty W, Ponting CP (2015) Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. RNA 21:333–346. doi: 10.1261/rna.047324.114
Nitsche A, Rose D, Fasold M et al (2015) Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. RNA 21:801–812. doi: 10.1261/rna.046342.114
Ulitsky I, Shkumatava A, Jan CH et al (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147:1537–1550. doi: 10.1016/j.cell.2011.11.055
Necsulea A, Soumillon M, Warnefors M et al (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505:635–640. doi: 10.1038/nature12943
Diederichs S (2014) The four dimensions of noncoding RNA conservation. Trends Genet 30:121–123. doi: 10.1016/j.tig.2014.01.004
Mercer TR, Dinger ME, Sunkin SM et al (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 105:716–721. doi: 10.1073/pnas.0706729105
Goff LA, Groff AF, Sauvageau M et al (2015) Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 112:6855–6862. doi: 10.1073/pnas.1411263112
Grote P, Herrmann BG (2015) Long noncoding RNAs in organogenesis: making the difference. Trends Genet 31:329–335. doi: 10.1016/j.tig.2015.02.002
Plath K, Fang J, Mlynarczyk-Evans SK et al (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135. doi: 10.1126/science.1084274
da Rocha ST, Boeva V, Escamilla-Del-Arenal M et al (2014) Jarid2 Is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome. Mol Cell 53:301–316. doi: 10.1016/j.molcel.2014.01.002
Zhao J, Sun BK, Erwin JA et al (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322:750–756. doi: 10.1126/science.1163045
Rinn JL, Kertesz M, Wang JK et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323. doi: 10.1016/j.cell.2007.05.022
Li L, Liu B, Wapinski OL et al (2013) Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep 5:3–12. doi: 10.1016/j.celrep.2013.09.003
Schorderet P, Duboule D (2011) Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet 7:e1002071. doi: 10.1371/journal.pgen.1002071
Klattenhoff CA, Scheuermann JC, Surface LE et al (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152:570–583. doi: 10.1016/j.cell.2013.01.003
Grote P, Herrmann BG (2013) The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol 10:1579–1585. doi: 10.4161/rna.26165
Grote P, Wittler L, Hendrix D et al (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24:206–214. doi: 10.1016/j.devcel.2012.12.012
Marín-Béjar O, Marchese FP, Athie A et al (2013) Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol 14:R104. doi: 10.1186/gb-2013-14-9-r104
Brockdorff N (2013) Noncoding RNA and Polycomb recruitment. RNA 19:429–442. doi: 10.1261/rna.037598.112
Khalil AM, Guttman M, Huarte M et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106:11667–11672. doi: 10.1073/pnas.0904715106
Guttman M, Donaghey J, Carey BW et al (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295–300. doi: 10.1038/nature10398
Zhao J, Ohsumi TK, Kung JT et al (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939–953. doi: 10.1016/j.molcel.2010.12.011
Schmitz K-M, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264–2269. doi: 10.1101/gad.590910
O’Leary VB, Ovsepian SV, Carrascosa LG et al (2015) PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation in response to low-dose irradiation. Cell Rep 11:474–485. doi: 10.1016/j.celrep.2015.03.043
Mondal T, Subhash S, Vaid R et al (2015) MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Comms 6:7743. doi: 10.1038/ncomms8743
Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–1307. doi: 10.1016/j.cell.2013.02.012
Hu X, Feng Y, Zhang D et al (2014) A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell 26:344–357. doi: 10.1016/j.ccr.2014.07.009
Pasmant E, Laurendeau I, Héron D et al (2007) Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res 67:3963–3969. doi: 10.1158/0008-5472.CAN-06-2004
Yap KL, Li S, Muñoz-Cabello AM et al (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38:662–674. doi: 10.1016/j.molcel.2010.03.021
Trievel RC, Shilatifard A (2009) WDR5, a complexed protein. Nat Struct Mol Biol 16:678–680. doi: 10.1038/nsmb0709-678
Yang YW, Flynn RA, Chen Y et al (2014) Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. elife 3:e02046. doi: 10.7554/eLife.02046
Wang KC, Yang YW, Liu B et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120–124. doi: 10.1038/nature09819
Gomez JA, Wapinski OL, Yang YW et al (2013) The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell 152:743–754. doi: 10.1016/j.cell.2013.01.015
Di Ruscio A, Ebralidze AK, Benoukraf T et al (2013) DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 503:371–376. doi: 10.1038/nature12598
Arab K, Park YJ, Lindroth AM et al (2014) Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol Cell. doi: 10.1016/j.molcel.2014.06.031
Hamazaki N, Uesaka M, Nakashima K et al (2015) Gene activation-associated long noncoding RNAs function in mouse preimplantation development. Development 142:910–920. doi: 10.1242/dev.116996
Prensner JR, Iyer MK, Sahu A et al (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 45:1392–1398. doi: 10.1038/ng.2771
Han P, Li W, Lin C-H et al (2014) A long noncoding RNA protects the heart from pathological hypertrophy. Nature 514:102–106. doi: 10.1038/nature13596
Bond AM, Vangompel MJW, Sametsky EA et al (2009) Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci 12:1020–1027. doi: 10.1038/nn.2371
Cajigas I, Leib DE, Cochrane J et al (2015) Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition. Development 142:2641–2652. doi: 10.1242/dev.126318
Minajigi A, Froberg JE, Wei C et al (2015) A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 349:aab2276. doi: 10.1126/science.aab2276
Wang Y, He L, Du Y et al (2015) The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling. Cell Stem Cell 16:413–425. doi: 10.1016/j.stem.2015.03.003
Kaneko S, Bonasio R, Saldaña-Meyer R et al (2013) Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol Cell. doi: 10.1016/j.molcel.2013.11.012
Merry CR, Forrest ME, Sabers JN et al (2015) DNMT1-associated long non-coding RNAs regulate global gene expression and DNA methylation in colon cancer. Hum Mol Genet. doi: 10.1093/hmg/ddv343
Davidovich C, Wang X, Cifuentes-Rojas C et al (2015) Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA. Mol Cell. doi: 10.1016/j.molcel.2014.12.017
Jiang W, Liu Y, Liu R et al (2015) The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression. Cell Rep 11:137–148. doi: 10.1016/j.celrep.2015.03.008
Kurian L, Aguirre A, Sancho-Martinez I et al (2015) Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. Circulation 131:1278–1290. doi: 10.1161/CIRCULATIONAHA.114.013303
Ng S-Y, Bogu GK, Soh BS, Stanton LW (2013) The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis. Mol Cell 51:349–359. doi: 10.1016/j.molcel.2013.07.017
Rapicavoli NA, Qu K, Zhang J et al (2013) A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. elife 2:e00762. doi: 10.7554/eLife.00762
Krawczyk M, Emerson BM (2014) p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes. elife 3:e01776
Wang P, Xue Y, Han Y et al (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344:310–313. doi: 10.1126/science.1251456
Xing Z, Lin A, Li C et al (2014) lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 159:1110–1125. doi: 10.1016/j.cell.2014.10.013
Kung JT, Kesner B, An JY et al (2015) Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol Cell. doi: 10.1016/j.molcel.2014.12.006
Sun S, Del Rosario BC, Szanto A et al (2013) Jpx RNA activates Xist by evicting CTCF. Cell 153:1537–1551. doi: 10.1016/j.cell.2013.05.028
Kim T-K, Hemberg M, Gray JM et al (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465:182–187. doi: 10.1038/nature09033
Koch F, Fenouil R, Gut M et al (2011) Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 18:956–963. doi: 10.1038/nsmb.2085
Natoli G, Andrau J-C (2012) Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 46:1–19. doi: 10.1146/annurev-genet-110711-155459
Collis P, Antoniou M, Grosveld F (1990) Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression. EMBO J 9:233–240
Ashe HL, Monks J, Wijgerde M et al (1997) Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev 11:2494–2509
Orom UA, Shiekhattar R (2011) Long non-coding RNAs and enhancers. Curr Opin Genet Dev 21:194–198. doi: 10.1016/j.gde.2011.01.020
Andersson R, Gebhard C, Miguel-Escalada I et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507:455–461. doi: 10.1038/nature12787
Ounzain S, Pezzuto I, Micheletti R et al (2014) Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease. J Mol Cell Cardiol 76:55–70. doi: 10.1016/j.yjmcc.2014.08.009
Orom UA, Derrien T, Beringer M et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46–58. doi: 10.1016/j.cell.2010.09.001
Li W, Notani D, Ma Q et al (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516–520. doi: 10.1038/nature12210
Lai F, Orom UA, Cesaroni M et al (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494:497–501. doi: 10.1038/nature11884
Schaukowitch K, Joo J-Y, Liu X et al (2014) Enhancer RNA facilitates NELF release from immediate early genes. Mol Cell 56:29–42. doi: 10.1016/j.molcel.2014.08.023
Mousavi K, Zare H, Dell’orso S et al (2013) eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51:606–617. doi: 10.1016/j.molcel.2013.07.022
Yin Y, Yan P, Lu J et al (2015) Opposing roles for the lncRNA haunt and its genomic locus in regulating HOXA Gene activation during embryonic stem cell differentiation. Cell Stem Cell 16:504–516. doi: 10.1016/j.stem.2015.03.007
Maamar H, Cabili MN, Rinn J, Raj A (2013) linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev 27:1260–1271. doi: 10.1101/gad.217018.113
Welsh IC, Kwak H, Chen FL et al (2015) Chromatin architecture of the Pitx2 locus requires CTCF- and Pitx2-dependent asymmetry that mirrors embryonic gut laterality. Cell Rep. doi: 10.1016/j.celrep.2015.08.075
Yang L, Lin C, Jin C et al (2013) lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 500:598–602. doi: 10.1038/nature12451
Yang F, Deng X, Ma W et al (2015) The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 16:52. doi: 10.1186/s13059-015-0618-0
Hacisuleyman E, Goff LA, Trapnell C et al (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21:198–206. doi: 10.1038/nsmb.2764
Bergmann JH, Li J, Eckersley-Maslin MA et al (2015) Regulation of the ESC transcriptome by nuclear long non-coding RNAs. Genome Res 25:1336–1346. doi: 10.1101/gr.189027.114
Ramos AD, Andersen RE, Liu SJ et al (2015) The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell 16:439–447. doi: 10.1016/j.stem.2015.02.007
Lin N, Chang K-Y, Li Z et al (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 53:1005–1019. doi: 10.1016/j.molcel.2014.01.021
Aprea J, Prenninger S, Dori M et al (2013) Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J 32:3145–3160. doi: 10.1038/emboj.2013.245
Barry G, Briggs JA, Vanichkina DP et al (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 19:486–494. doi: 10.1038/mp.2013.45
Tripathi V, Ellis JD, Shen Z et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938. doi: 10.1016/j.molcel.2010.08.011
Eißmann M, Gutschner T, Hämmerle M et al (2012) Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol 9:1076–1087. doi: 10.4161/rna.21089
Lee S, Kopp F, Chang T-C et al (2015) Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell. doi: 10.1016/j.cell.2015.12.017
Chen CY, Sarnow P (1995) Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 268:415–417. doi: 10.1126/science.7536344
Yan L, Yang M, Guo H et al (2013) Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 20:1131–1139. doi: 10.1038/nsmb.2660
Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990) The product of the H19 gene may function as an RNA. Mol Cell Biol 10:28–36
Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351:153–155. doi: 10.1038/351153a0
Leighton PA, Ingram RS, Eggenschwiler J et al (1995) Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375:34–39. doi: 10.1038/375034a0
Dey BK, Pfeifer K, Dutta A (2014) The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev 28:491–501. doi: 10.1101/gad.234419.113
Latos PA, Pauler FM, Koerner MV et al (2012) Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338:1469–1472. doi: 10.1126/science.1228110
Kanduri C (2016) Long noncoding RNAs: lessons from genomic imprinting. Biochim Biophys Acta 1859:102–111. doi: 10.1016/j.bbagrm.2015.05.006
Penny GD, Kay GF, Sheardown SA et al (1996) Requirement for Xist in X chromosome inactivation. Nature 379:131–137. doi: 10.1038/379131a0
Marahrens Y, Panning B, Dausman J et al (1997) Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev 11:156–166
Zhou Y, Cheunsuchon P, Nakayama Y et al (2010) Activation of paternally expressed genes and perinatal death caused by deletion of the Gtl2 gene. Development 137:2643–2652. doi: 10.1242/dev.045724
Sauvageau M, Goff LA, Lodato S et al (2013) Multiple knockout mouse models reveal lincRNAs are required for life and brain development. elife 2:e01749. doi: 10.7554/eLife.01749
Nakagawa S, Naganuma T, Shioi G, Hirose T (2011) Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol 193:31–39. doi: 10.1083/jcb.201011110
Oliver PL, Chodroff RA, Gosal A et al (2015) Disruption of Visc-2, a brain-expressed conserved long noncoding RNA, does not elicit an overt anatomical or behavioral phenotype. Cereb Cortex 25:3572–3585. doi: 10.1093/cercor/bhu196
Li L, Chang HY (2014) Physiological roles of long noncoding RNAs: insight from knockout mice. Trends Cell Biol. doi: 10.1016/j.tcb.2014.06.003
Nakagawa S, Shimada M, Yanaka K et al (2014) The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice. Development. doi: 10.1242/dev.110544
Herriges MJ, Swarr DT, Morley MP et al (2014) Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev 28:1363–1379. doi: 10.1101/gad.238782.114
Ng S-Y, Johnson R, Stanton LW (2012) Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J 31:522–533. doi: 10.1038/emboj.2011.459
Ramos AD, Diaz A, Nellore A et al (2013) Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12:616–628. doi: 10.1016/j.stem.2013.03.003
Chalei V, Sansom SN, Kong L et al (2014) The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. elife 3:e04530. doi: 10.7554/eLife.04530
Chan AS, Thorner PS, Squire JA, Zielenska M (2002) Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between rhabdomyosarcoma subtypes. Oncogene 21:3029–3037. doi: 10.1038/sj.onc.1205460
Uhde CW, Vives J, Jaeger I, Li M (2010) Rmst is a novel marker for the mouse ventral mesencephalic floor plate and the anterior dorsal midline cells. PLoS One 5:e8641. doi: 10.1371/journal.pone.0008641
Wheeler E, Huang N, Bochukova EG et al (2013) Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. Nat Genet 45:513–517. doi: 10.1038/ng.2607
Blackshaw S, Harpavat S, Trimarchi J et al (2004) Genomic analysis of mouse retinal development. PLoS Biol 2:E247. doi: 10.1371/journal.pbio.0020247
Krol J, Krol I, Alvarez CPP et al (2015) A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture. Nat Comms 6:7305. doi: 10.1038/ncomms8305
Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10:49. doi: 10.1186/1471-213X-10-49
Sone M, Hayashi T, Tarui H et al (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120:2498–2506. doi: 10.1242/jcs.009357
Kretz M, Webster DE, Flockhart RJ et al (2012) Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev 26:338–343. doi: 10.1101/gad.182121.111
Zhu L, Xu P-C (2013) Downregulated LncRNA-ANCR promotes osteoblast differentiation by targeting EZH2 and regulating Runx2 expression. Biochem Biophys Res Commun 432:612–617. doi: 10.1016/j.bbrc.2013.02.036
Lopez-Pajares V, Qu K, Zhang J et al (2015) A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell 32:693–706. doi: 10.1016/j.devcel.2015.01.028
Kretz M, Siprashvili Z, Chu C et al (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231–235. doi: 10.1038/nature11661
Ji P, Diederichs S, Wang W et al (2003) MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22:8031–8041. doi: 10.1038/sj.onc.1206928
Srikantan V, Zou Z, Petrovics G et al (2000) PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc Natl Acad Sci USA 97:12216–12221. doi: 10.1073/pnas.97.22.12216
Brunner AL, Beck AH, Edris B et al (2012) Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol 13:R75. doi: 10.1186/gb-2012-13-8-r75
Yan X, Hu Z, Feng Y et al (2015) Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell 28:529–540. doi: 10.1016/j.ccell.2015.09.006
Du Z, Fei T, Verhaak RGW et al (2013) Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol 20:908–913. doi: 10.1038/nsmb.2591
Pandey GK, Mitra S, Subhash S et al (2014) The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell 26:722–737. doi: 10.1016/j.ccell.2014.09.014
Gutschner T, Hämmerle M, Eißmann M et al (2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res 73:1180–1189. doi: 10.1158/0008-5472.CAN-12-2850
Xue S, Li Q-W, Che J-P et al (2015) Decreased expression of long non-coding RNA NBAT-1 is associated with poor prognosis in patients with clear cell renal cell carcinoma. Int J Clin Exp Pathol 8:3765–3774
Trimarchi T, Bilal E, Ntziachristos P et al (2014) Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell 158:593–606. doi: 10.1016/j.cell.2014.05.049
Gupta RA, Shah N, Wang KC et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076. doi: 10.1038/nature08975
Liu B, Sun L, Liu Q et al (2015) A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. Cancer Cell 27:370–381. doi: 10.1016/j.ccell.2015.02.004
Dijkstra JM, Alexander DB (2015) The “NF-κB interacting long noncoding RNA” (NKILA) transcript is antisense to cancer-associated gene PMEPA1. F1000Res 4:96. doi: 10.12688/f1000research.6400.1
Arun G, Diermeier S, Akerman M et al (2015) Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 30:34–51. doi: 10.1101/gad.270959.115
Nakagawa S, Ip JY, Shioi G et al (2012) Malat1 is not an essential component of nuclear speckles in mice. RNA 18:1487–1499. doi: 10.1261/rna.033217.112
Zhang B, Arun G, Mao YS et al (2012) The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2:111–123. doi: 10.1016/j.celrep.2012.06.003
Karreth FA, Reschke M, Ruocco A et al (2015) The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. doi: 10.1016/j.cell.2015.02.043
Gil J, Peters G (2006) Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. Nat Rev Mol Cell Biol 7:667–677. doi: 10.1038/nrm1987
Wan G, Mathur R, Hu X et al (2013) Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway. Cell Signal 25:1086–1095. doi: 10.1016/j.cellsig.2013.02.006
Montes M, Nielsen MM, Maglieri G et al (2015) The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence. Nat Comms 6:6967. doi: 10.1038/ncomms7967
Kumar PP, Emechebe U, Smith R et al (2014) Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex. elife. doi: 10.7554/eLife.02805
Huarte M, Guttman M, Feldser D et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409–419. doi: 10.1016/j.cell.2010.06.040
Sánchez Y, Segura V, Marín-Béjar O et al (2014) Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. Nat Comms 5:5812. doi: 10.1038/ncomms6812
Dimitrova N, Zamudio JR, Jong RM et al (2014) LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol Cell 54:777–790. doi: 10.1016/j.molcel.2014.04.025
Wu G, Cai J, Han Y et al (2014) LincRNA-p21 regulates neointima formation, vascular smooth muscle cell proliferation, apoptosis, and atherosclerosis by enhancing p53 activity. Circulation 130:1452–1465. doi: 10.1161/CIRCULATIONAHA.114.011675
Ishii N, Ozaki K, Sato H et al (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 51:1087–1099. doi: 10.1007/s10038-006-0070-9
Broadbent HM, Peden JF, Lorkowski S et al (2008) Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet 17:806–814. doi: 10.1093/hmg/ddm352
Visel A, Zhu Y, May D et al (2010) Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464:409–412. doi: 10.1038/nature08801
Matkovich SJ, Edwards JR, Grossenheider TC et al (2014) Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs. Proc Natl Acad Sci USA 111:12264–12269. doi: 10.1073/pnas.1410622111
Ounzain S, Micheletti R, Beckmann T et al (2015) Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 36:353–368a. doi: 10.1093/eurheartj/ehu180
Ounzain S, Micheletti R, Arnan C et al (2015) CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis. J Mol Cell Cardiol. doi: 10.1016/j.yjmcc.2015.09.016
Kumarswamy R, Bauters C, Volkmann I et al (2014) Circulating long noncoding RNA, LIPCAR, predicts survival in patients with heart failure. Circ Res 114:1569–1575. doi: 10.1161/CIRCRESAHA.114.303915
Bassett AR, Akhtar A, Barlow DP et al (2014) Considerations when investigating lncRNA function in vivo. elife 3:e03058
Janowski BA, Huffman KE, Schwartz JC et al (2005) Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat Chem Biol 1:216–222. doi: 10.1038/nchembio725
Goff LA, Rinn JL (2015) Linking RNA biology to lncRNAs. Genome Res 25:1456–1465. doi: 10.1101/gr.191122.115
Stadtfeld M, Apostolou E, Ferrari F, et al. (2012) Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet 44:398–405, S1–S2. doi:10.1038/ng.1110
Zhang X, Lian Z, Padden C et al (2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113:2526–2534. doi: 10.1182/blood-2008-06-162164
Delpretti S, Montavon T, Leleu M et al (2013) Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep. doi: 10.1016/j.celrep.2013.09.002
Gong C, Li Z, Ramanujan K et al (2015) A long non-coding RNA, LncMyoD, regulates skeletal muscle differentiation by blocking IMP2-mediated mRNA translation. Dev Cell 34:181–191. doi: 10.1016/j.devcel.2015.05.009
Prensner JR, Sahu A, Iyer MK et al (2014) The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer. Oncotarget 5:1434–1438
McHugh CA, Chen C-K, Chow A et al (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521:232–236. doi: 10.1038/nature14443