ArcRNAs and the formation of nuclear bodies.


Journal

Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
Titre abrégé: Mamm Genome
Pays: United States
ID NLM: 9100916

Informations de publication

Date de publication:
06 2022
Historique:
received: 08 04 2021
accepted: 25 05 2021
pubmed: 5 6 2021
medline: 20 5 2022
entrez: 4 6 2021
Statut: ppublish

Résumé

Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple categories according to their functions and/or molecular properties. Architectual RNAs (arcRNAs) are a group of lncRNAs that serve as architectural components of submicron-scale cellular bodies or nonmembranous organelles, which are composed of specific sets of proteins and nucleic acids involved in particular molecular processes. In this review, we focus on arcRNAs that function in the nucleus, which provide a structural basis for the formation of nuclear bodies, nonmembranous organelles in the cell nucleus. We will summarize the current list of arcRNAs and proteins associated with classic and more recently discovered nuclear bodies and discuss general rules that govern the formation of nuclear bodies, emphasizing weak multivalent interactions mediated by innately flexible biomolecules.

Identifiants

pubmed: 34085114
doi: 10.1007/s00335-021-09881-5
pii: 10.1007/s00335-021-09881-5
doi:

Substances chimiques

RNA, Long Noncoding 0

Types de publication

Journal Article Review Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

382-401

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Références

Abdalla MOA, Yamamoto T, Maehara K, Nogami J, Ohkawa Y, Miura H, Poonperm R, Hiratani I, Nakayama H, Nakao M, Saitoh N (2019) The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis. Nat Commun 10:3778
pubmed: 31439835 pmcid: 6706407 doi: 10.1038/s41467-019-11378-4
Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PW, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, van den Oord J, Nakagawa S, Hirose T, Sablina AA, Lambrechts D, Aerts S, Blanpain C, Marine JC (2016) p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med 22:861–868
pubmed: 27376578 doi: 10.1038/nm.4135
Adriaens C, Rambow F, Bervoets G, Silla T, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S, Jensen TH, Marine JC (2019) The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth. RNA 25:1681–1695
pubmed: 31551298 pmcid: 6859857 doi: 10.1261/rna.071456.119
Ahmed ASI, Dong K, Liu J, Wen T, Yu L, Xu F, Kang X, Osman I, Hu G, Bunting KM, Crethers D, Gao H, Zhang W, Liu Y, Wen K, Agarwal G, Hirose T, Nakagawa S, Vazdarjanova A, Zhou J (2018) Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells. Proc Natl Acad Sci USA 115:E8660–E8667
pubmed: 30139920 pmcid: 6140535
Alberti S, Gladfelter A, Mittag T (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176:419–434
pubmed: 30682370 pmcid: 6445271 doi: 10.1016/j.cell.2018.12.035
Aly MK, Ninomiya K, Adachi S, Natsume T, Hirose T (2019) Two distinct nuclear stress bodies containing different sets of RNA-binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure. Biochem Biophys Res Commun 516:419–423
pubmed: 31227213 doi: 10.1016/j.bbrc.2019.06.061
Andergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL (2019) In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. Elife. https://doi.org/10.7554/eLife.47214
doi: 10.7554/eLife.47214 pubmed: 31738164 pmcid: 6860989
Audas TE, Jacob MD, Lee S (2012) Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. Mol Cell 45:147–157
pubmed: 22284675 doi: 10.1016/j.molcel.2011.12.012
Audas TE, Audas DE, Jacob MD, Ho JJ, Khacho M, Wang M, Perera JK, Gardiner C, Bennett CA, Head T, Kryvenko ON, Jorda M, Daunert S, Malhotra A, Trinkle-Mulcahy L, Gonzalgo ML, Lee S (2016) Adaptation to stressors by systemic protein amyloidogenesis. Dev Cell 39:155–168
pubmed: 27720612 pmcid: 5098424 doi: 10.1016/j.devcel.2016.09.002
Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (2007) Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 318:798–801
pubmed: 17916692 doi: 10.1126/science.1147182
Barr ML, Bertram EG (1949) A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163:676
pubmed: 18120749 doi: 10.1038/163676a0
Barral A, Dejardin J (2020) Telomeric chromatin and TERRA. J Mol Biol 432:4244–4256
pubmed: 32151584 doi: 10.1016/j.jmb.2020.03.003
Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL (2018) A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun 9:1444
pubmed: 29654311 pmcid: 5899154 doi: 10.1038/s41467-018-03614-0
Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP (2014) Considerations when investigating lncRNA function in vivo. Elife 3:e03058
pubmed: 25124674 pmcid: 4132285 doi: 10.7554/eLife.03058
Basu A, Dong B, Krainer AR, Howe CC (1997) The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA- and DNA-binding protein p54nrb/NonO. Mol Cell Biol 17:677–686
pubmed: 9001221 pmcid: 231793 doi: 10.1128/MCB.17.2.677
Bates CM, Bates FS (2017) Block polymers - pure potential. Macromolecules 50:3–22
doi: 10.1021/acs.macromol.6b02355
Beck M, Baumeister W (2016) Cryo-electron tomography: can it reveal the molecular sociology of cells in atomic detail? Trends Cell Biol 26:825–837
pubmed: 27671779 doi: 10.1016/j.tcb.2016.08.006
Benavente R, Rose KM, Reimer G, Hugle-Dorr B, Scheer U (1987) Inhibition of nucleolar reformation after microinjection of antibodies to RNA polymerase I into mitotic cells. J Cell Biol 105:1483–1491
pubmed: 3312231 doi: 10.1083/jcb.105.4.1483
Biamonti G, Vourc’h C (2010) Nuclear stress bodies. Cold Spring Harb Perspect Biol 2:a000695
pubmed: 20516127 pmcid: 2869524 doi: 10.1101/cshperspect.a000695
Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Julicher F, Hyman AA (2009) Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324:1729–1732
pubmed: 19460965 doi: 10.1126/science.1172046
Brockdorff N, Bowness JS, Wei G (2020) Progress toward understanding chromosome silencing by Xist RNA. Genes Dev 34:733–744
pubmed: 32482714 pmcid: 7263139 doi: 10.1101/gad.337196.120
Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA (2012) Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENbeta noncoding RNAs. Proc Natl Acad Sci USA 109:19202–19207
pubmed: 23129630 pmcid: 3511071 doi: 10.1073/pnas.1217338109
Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149:819–831
pubmed: 22541069 pmcid: 3350859 doi: 10.1016/j.cell.2012.03.035
Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, Wang S, Du Z, Hu N, Yu X, Chen J, Wang L, Yang X, He S, Xue Y (2020) RIC-seq for global in situ profiling of RNA-RNA spatial interactions. Nature 582:432–437
pubmed: 32499643 doi: 10.1038/s41586-020-2249-1
Carmo-Fonseca M, Berciano MT, Lafarga M (2010) Orphan nuclear bodies. Cold Spring Harb Perspect Biol 2:a000703
pubmed: 20610547 pmcid: 2926751 doi: 10.1101/cshperspect.a000703
Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW (2016) Comprehensive identification of RNA-binding Domains in human cells. Mol Cell 63:696–710
pubmed: 27453046 pmcid: 5003815 doi: 10.1016/j.molcel.2016.06.029
Cerase A, Armaos A, Neumayer C, Avner P, Guttman M, Tartaglia GG (2019) Phase separation drives X-chromosome inactivation: a hypothesis. Nat Struct Mol Biol 26:331–334
pubmed: 31061525 doi: 10.1038/s41594-019-0223-0
Chen LL, Carmichael GG (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 35:467–478
pubmed: 19716791 pmcid: 2749223 doi: 10.1016/j.molcel.2009.06.027
Chen D, Lei EP (2019) Function and regulation of chromatin insulators in dynamic genome organization. Curr Opin Cell Biol 58:61–68
pubmed: 30875678 pmcid: 6692201 doi: 10.1016/j.ceb.2019.02.001
Chen T, Boisvert FM, Bazett-Jones DP, Richard S (1999) A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cell lines. Mol Biol Cell 10:3015–3033
pubmed: 10473643 pmcid: 25546 doi: 10.1091/mbc.10.9.3015
Chiodi I, Biggiogera M, Denegri M, Corioni M, Weighardt F, Cobianchi F, Riva S, Biamonti G (2000) Structure and dynamics of hnRNP-labelled nuclear bodies induced by stress treatments. J Cell Sci 113(Pt 22):4043–4053
pubmed: 11058091 doi: 10.1242/jcs.113.22.4043
Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY (2018) Promoter of lncRNA Gene PVT1 Is a tumor-suppressor dna boundary element. Cell 173:1398-1412 e1322
pubmed: 29731168 pmcid: 5984165 doi: 10.1016/j.cell.2018.03.068
Choi S, Park C, Kim KE, Kim KK (2017) An in vitro technique to identify the RNA binding-site sequences for RNA-binding proteins. Biotechniques 63:28–33
pubmed: 28701145 doi: 10.2144/000114567
Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY (2015) Systematic discovery of Xist RNA binding proteins. Cell 161:404–416
pubmed: 25843628 pmcid: 4425988 doi: 10.1016/j.cell.2015.03.025
Chujo T, Hirose T (2017) Nuclear bodies built on architectural long noncoding rnas: unifying principles of their construction and function. Mol Cells 40:889–896
pubmed: 29276943 pmcid: 5750707
Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T (2017) Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J 36:1447–1462
pubmed: 28404604 pmcid: 5430218 doi: 10.15252/embj.201695848
Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33:717–726
pubmed: 19217333 pmcid: 2696186 doi: 10.1016/j.molcel.2009.01.026
Daneshvar K, Pondick JV, Kim BM, Zhou C, York SR, Macklin JA, Abualteen A, Tan B, Sigova AA, Marcho C, Tremblay KD, Mager J, Choi MY, Mullen AC (2016) DIGIT is a conserved long noncoding RNA that regulates GSC expression to control definitive endoderm differentiation of embryonic stem cells. Cell Rep 17:353–365
pubmed: 27705785 pmcid: 5120872 doi: 10.1016/j.celrep.2016.09.017
Daneshvar K, Ardehali MB, Klein IA, Hsieh FK, Kratkiewicz AJ, Mahpour A, Cancelliere SOL, Zhou C, Cook BM, Li W, Pondick JV, Gupta SK, Moran SP, Young RA, Kingston RE, Mullen AC (2020) lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Nat Cell Biol 22:1211–1222
pubmed: 32895492 pmcid: 8008247 doi: 10.1038/s41556-020-0572-2
Davis BM, McCurrach ME, Taneja KL, Singer RH, Housman DE (1997) Expansion of a CUG trinucleotide repeat in the 3′ untranslated region of myotonic dystrophy protein kinase transcripts results in nuclear retention of transcripts. Proc Natl Acad Sci USA 94:7388–7393
pubmed: 9207101 pmcid: 23831 doi: 10.1073/pnas.94.14.7388
Ding DQ, Okamasa K, Yamane M, Tsutsumi C, Haraguchi T, Yamamoto M, Hiraoka Y (2012) Meiosis-specific noncoding RNA mediates robust pairing of homologous chromosomes in meiosis. Science 336:732–736
pubmed: 22582262 doi: 10.1126/science.1219518
Ding DQ, Okamasa K, Katou Y, Oya E, Nakayama JI, Chikashige Y, Shirahige K, Haraguchi T, Hiraoka Y (2019) Chromosome-associated RNA-protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe. Nat Commun 10:5598
pubmed: 31811152 pmcid: 6898681 doi: 10.1038/s41467-019-13609-0
Dumbovic G, Biayna J, Banus J, Samuelsson J, Roth A, Diederichs S, Alonso S, Buschbeck M, Perucho M, Forcales SV (2018) A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer. Nucleic Acids Res 46:5504–5524
pubmed: 29912433 pmcid: 6009586 doi: 10.1093/nar/gky263
Eissmann M, Gutschner T, Hammerle M, Gunther S, Caudron-Herger M, Gross M, Schirmacher P, Rippe K, Braun T, Zornig M, Diederichs S (2012) Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol 9:1076–1087
pubmed: 22858678 pmcid: 3551862 doi: 10.4161/rna.21089
Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T (2017) Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci 130:4180–4192
pubmed: 29133588 pmcid: 5769577
Feretzaki M, Pospisilova M, Valador Fernandes R, Lunardi T, Krejci L, Lingner J (2020) RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature 587:303–308
pubmed: 33057192 pmcid: 7116795 doi: 10.1038/s41586-020-2815-6
Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP (2016) Coexisting liquid phases underlie nucleolar subcompartments. Cell 165:1686–1697
pubmed: 27212236 pmcid: 5127388 doi: 10.1016/j.cell.2016.04.047
Fox AH, Lam YW, Leung AK, Lyon CE, Andersen J, Mann M, Lamond AI (2002) Paraspeckles: a novel nuclear domain. Curr Biol 12:13–25
pubmed: 11790299 doi: 10.1016/S0960-9822(01)00632-7
Fox AH, Nakagawa S, Hirose T, Bond CS (2018) Paraspeckles: where long noncoding RNA meets phase separation. Trends Biochem Sci 43:124–135
pubmed: 29289458 doi: 10.1016/j.tibs.2017.12.001
Ghetti A, Pinol-Roma S, Michael WM, Morandi C, Dreyfuss G (1992) hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. Nucleic Acids Res 20:3671–3678
pubmed: 1641332 pmcid: 334017 doi: 10.1093/nar/20.14.3671
Goenka A, Sengupta S, Pandey R, Parihar R, Mohanta GC, Mukerji M, Ganesh S (2016) Human satellite-III non-coding RNAs modulate heat-shock-induced transcriptional repression. J Cell Sci 129:3541–3552
pubmed: 27528402
Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21:198–206
pubmed: 24463464 pmcid: 3950333 doi: 10.1038/nsmb.2764
Hall LL, Byron M, Carone DM, Whitfield TW, Pouliot GP, Fischer A, Jones P, Lawrence JB (2017) Demethylated HSATII DNA and HSATII RNA foci sequester PRC1 and MeCP2 into cancer-specific nuclear bodies. Cell Rep 18:2943–2956
pubmed: 28329686 pmcid: 5429029 doi: 10.1016/j.celrep.2017.02.072
Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M (2006) Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 442:45–50
pubmed: 16823445 doi: 10.1038/nature04881
Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S (2010) The Matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev Cell 19:469–476
pubmed: 20833368 doi: 10.1016/j.devcel.2010.08.006
Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott GJ, Iyer KS, Ho D, Newcombe EA, Hosoki K, Goshima N, Kawaguchi T, Hatters D, Trinkle-Mulcahy L, Hirose T, Bond CS, Fox AH (2015) Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J Cell Biol 210:529–539
pubmed: 26283796 pmcid: 4539981 doi: 10.1083/jcb.201504117
Hirano T, Konoha G, Toda T, Yanagida M (1989) Essential roles of the RNA polymerase I largest subunit and DNA topoisomerases in the formation of fission yeast nucleolus. J Cell Biol 108:243–253
pubmed: 2537310 doi: 10.1083/jcb.108.2.243
Hirose T, Nakagawa S (2016) Clues to long noncoding RNA taxonomy. Biochim Biophys Acta 1859:1–2
pubmed: 26642900 doi: 10.1016/j.bbagrm.2015.11.011
Hirose T, Yamazaki T, Nakagawa S (2019) Molecular anatomy of the architectural NEAT1 noncoding RNA: the domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles. Wiley Interdiscip Rev RNA. 10:e1545
pubmed: 31044562 doi: 10.1002/wrna.1545
Hogan NC, Traverse KL, Sullivan DE, Pardue ML (1994) The nucleus-limited Hsr-omega-n transcript is a polyadenylated RNA with a regulated intranuclear turnover. J Cell Biol 125:21–30
pubmed: 7511142 doi: 10.1083/jcb.125.1.21
Hoki Y, Kimura N, Kanbayashi M, Amakawa Y, Ohhata T, Sasaki H, Sado T (2009) A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development 136:139–146
pubmed: 19036803 doi: 10.1242/dev.026427
Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genom 8:39
doi: 10.1186/1471-2164-8-39
Ilik IA, Malszycki M, Lubke AK, Schade C, Meierhofer D, Aktas T (2020) SON and SRRM2 are essential for nuclear speckle formation. Elife. https://doi.org/10.7554/eLife.60579
doi: 10.7554/eLife.60579 pubmed: 33095160 pmcid: 7671692
Ishiguro T, Sato N, Ueyama M, Fujikake N, Sellier C, Kanegami A, Tokuda E, Zamiri B, Gall-Duncan T, Mirceta M, Furukawa Y, Yokota T, Wada K, Taylor JP, Pearson CE, Charlet-Berguerand N, Mizusawa H, Nagai Y, Ishikawa K (2017) Regulatory role of RNA chaperone TDP 43 for RNA misfolding and repeat associated translation in SCA31. Neuron 94:108-124 e107
pubmed: 28343865 pmcid: 5681996 doi: 10.1016/j.neuron.2017.02.046
Ishikawa K, Durr A, Klopstock T, Muller S, De Toffol B, Vidailhet M, Vighetto A, Marelli C, Wichmann HE, Illig T, Niimi Y, Sato N, Amino T, Stevanin G, Brice A, Mizusawa H (2011) Pentanucleotide repeats at the spinocerebellar ataxia type 31 (SCA31) locus in Caucasians. Neurology 77:1853–1855
pubmed: 22049201 doi: 10.1212/WNL.0b013e3182377e3a
Ishizuka A, Hasegawa Y, Ishida K, Yanaka K, Nakagawa S (2014) Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Genes Cells 19:704–721
pubmed: 25145264 pmcid: 4255692 doi: 10.1111/gtc.12169
Isobe M, Toya H, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S (2020) Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice. RNA 26:251–264
pubmed: 31822595 pmcid: 7025509 doi: 10.1261/rna.072587.119
Jain A, Vale RD (2017) RNA phase transitions in repeat expansion disorders. Nature 546:243–247
pubmed: 28562589 pmcid: 5555642 doi: 10.1038/nature22386
Ji P, Diederichs S, Wang W, Boing S, Metzger R, Schneider PM, Tidow N, Brandt B, Buerger H, Bulk E, Thomas M, Berdel WE, Serve H, Muller-Tidow C (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
pubmed: 12970751 doi: 10.1038/sj.onc.1206928
Jolly C, Usson Y, Morimoto RI (1999) Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc Natl Acad Sci USA 96:6769–6774
pubmed: 10359787 pmcid: 21990 doi: 10.1073/pnas.96.12.6769
Jolly C, Metz A, Govin J, Vigneron M, Turner BM, Khochbin S, Vourc’h C (2004) Stress-induced transcription of satellite III repeats. J Cell Biol 164:25–33
pubmed: 14699086 pmcid: 2171959 doi: 10.1083/jcb.200306104
Kaiser TE, Intine RV, Dundr M (2008) De novo formation of a subnuclear body. Science 322:1713–1717
pubmed: 18948503 doi: 10.1126/science.1165216
Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149:753–767
pubmed: 22579281 pmcid: 6347373 doi: 10.1016/j.cell.2012.04.017
Kawaguchi T, Tanigawa A, Naganuma T, Ohkawa Y, Souquere S, Pierron G, Hirose T (2015) SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies. Proc Natl Acad Sci USA 112:4304–4309
pubmed: 25831520 pmcid: 4394320 doi: 10.1073/pnas.1423819112
Komatsu T, Yokoi S, Fujii K, Mito M, Kimura Y, Iwasaki S, Nakagawa S (2018) UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking. RNA 24:1785–1802
pubmed: 30232101 pmcid: 6239193 doi: 10.1261/rna.067611.118
Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172:393–407
pubmed: 29373828 pmcid: 5978744 doi: 10.1016/j.cell.2018.01.011
Kushawah G, Hernandez-Huertas L, Abugattas-Nunez Del Prado J, Martinez-Morales JR, DeVore ML, Hassan H, Moreno-Sanchez I, Tomas-Gallardo L, Diaz-Moscoso A, Monges DE, Guelfo JR, Theune WC, Brannan EO, Wang W, Corbin TJ, Moran AM, Sanchez Alvarado A, Malaga-Trillo E, Takacs CM, Bazzini AA, Moreno-Mateos MA (2020) CRISPR-Cas13d induces efficient mRNA knockdown in animal embryos. Dev Cell 54:805–817
pubmed: 32768421 doi: 10.1016/j.devcel.2020.07.013
Lakhotia SC (2011) Forty years of the 93D puff of Drosophila melanogaster. J Biosci 36:399–423
pubmed: 21799254 doi: 10.1007/s12038-011-9078-1
Lallemand-Breitenbach V, de Thé H (2010) PML nuclear bodies. Cold Spring Harb Perspect Biol 2:a000661
pubmed: 20452955 pmcid: 2857171 doi: 10.1101/cshperspect.a000661
Lancaster AK, Nutter-Upham A, Lindquist S, King OD (2014) PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. Bioinformatics 30:2501–2502
pubmed: 24825614 pmcid: 4147883 doi: 10.1093/bioinformatics/btu310
Landers CC, Rabeler CA, Ferrari EK, D’Alessandro LR, Kang DD, Malisa J, Bashir SM, Carone DM (2021) Ectopic expression of pericentric HSATII RNA results in nuclear RNA accumulation, MeCP2 recruitment, and cell division defects. Chromosoma 130:75–90
pubmed: 33585981 pmcid: 7889552 doi: 10.1007/s00412-021-00753-0
Langdon EM, Qiu Y, Ghanbari Niaki A, McLaughlin GA, Weidmann CA, Gerbich TM, Smith JA, Crutchley JM, Termini CM, Weeks KM, Myong S, Gladfelter AS (2018) mRNA structure determines specificity of a polyQ-driven phase separation. Science 360:922–927
pubmed: 29650703 pmcid: 6192030 doi: 10.1126/science.aar7432
Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL (2019) The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun 10:5137
pubmed: 31723143 pmcid: 6853988 doi: 10.1038/s41467-019-12970-4
Li L, Chang HY (2014) Physiological roles of long noncoding RNAs: insight from knockout mice. Trends Cell Biol 24:594–602
pubmed: 25022466 pmcid: 4177945 doi: 10.1016/j.tcb.2014.06.003
Loda A, Heard E (2019) Xist RNA in action: past, present, and future. PLoS Genet 15:e1008333
pubmed: 31537017 pmcid: 6752956 doi: 10.1371/journal.pgen.1008333
Lyons JG, Siew K, O’Grady RL (1989) Cellular interactions determining the production of collagenase by a rat mammary carcinoma cell line. Int J Cancer 43:119–125
pubmed: 2536004 doi: 10.1002/ijc.2910430123
Maharana S, Wang J, Papadopoulos DK, Richter D, Pozniakovsky A, Poser I, Bickle M, Rizk S, Guillen-Boixet J, Franzmann TM, Jahnel M, Marrone L, Chang YT, Sterneckert J, Tomancak P, Hyman AA, Alberti S (2018) RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 360(6391):918–921
pubmed: 29650702 pmcid: 6091854 doi: 10.1126/science.aar7366
Mai Y, Eisenberg A (2012) Self-assembly of block copolymers. Chem Soc Rev 41:5969–5985
pubmed: 22776960 doi: 10.1039/c2cs35115c
Mankodi A, Urbinati CR, Yuan QP, Moxley RT, Sansone V, Krym M, Henderson D, Schalling M, Swanson MS, Thornton CA (2001) Muscleblind localizes to nuclear foci of aberrant RNA in myotonic dystrophy types 1 and 2. Hum Mol Genet 10:2165–2170
pubmed: 11590133 doi: 10.1093/hmg/10.19.2165
Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T (2016) The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol 214:45–59
pubmed: 27377249 pmcid: 4932371 doi: 10.1083/jcb.201601024
Marahrens Y, Panning B, Dausman J, Strauss W, Jaenisch R (1997) Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev 11:156–166
pubmed: 9009199 doi: 10.1101/gad.11.2.156
Matera AG, Frey MR, Margelot K, Wolin SL (1995) A perinucleolar compartment contains several RNA polymerase III transcripts as well as the polypyrimidine tract-binding protein, hnRNP I. J Cell Biol 129:1181–1193
pubmed: 7539809 doi: 10.1083/jcb.129.5.1181
McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521:232–236
pubmed: 25915022 pmcid: 4516396 doi: 10.1038/nature14443
McSwiggen DT, Mir M, Darzacq X, Tjian R (2019) Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev 33:1619–1634
pubmed: 31594803 pmcid: 6942051 doi: 10.1101/gad.331520.119
Mei Y, Deng Z, Vladimirova O, Gulve N, Johnson FB, Drosopoulos WC, Schildkraut CL, Lieberman PM (2021) TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity. Sci Rep 11:3509
pubmed: 33568696 pmcid: 7876106 doi: 10.1038/s41598-021-82406-x
Mekhail K, Rivero-Lopez L, Al-Masri A, Brandon C, Khacho M, Lee S (2007) Identification of a common subnuclear localization signal. Mol Biol Cell 18:3966–3977
pubmed: 17652456 pmcid: 1995723 doi: 10.1091/mbc.e07-03-0295
Mello SS, Sinow C, Raj N, Mazur PK, Bieging-Rolett K, Broz DK, Imam JFC, Vogel H, Wood LD, Sage J, Hirose T, Nakagawa S, Rinn J, Attardi LD (2017) Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev 31:1095–1108
pubmed: 28698299 pmcid: 5538433 doi: 10.1101/gad.284661.116
Meszaros B, Erdos G, Dosztanyi Z (2018) IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res 46:W329–W337
pubmed: 29860432 pmcid: 6030935 doi: 10.1093/nar/gky384
Monfort A, Di Minin G, Postlmayr A, Freimann R, Arieti F, Thore S, Wutz A (2015) Identification of Spen as a crucial factor for Xist function through forward genetic screening in haploid embryonic stem cells. Cell Rep 12:554–561
pubmed: 26190100 pmcid: 4530576 doi: 10.1016/j.celrep.2015.06.067
Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T (2012) Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J 31:4020–4034
pubmed: 22960638 pmcid: 3474925 doi: 10.1038/emboj.2012.251
Nakagawa S (2016) Lessons from reverse-genetic studies of lncRNAs. Biochim Biophys Acta 1859:177–183
pubmed: 26117798 doi: 10.1016/j.bbagrm.2015.06.011
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
pubmed: 21444682 pmcid: 3082198 doi: 10.1083/jcb.201011110
Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X, Hirose T, Prasanth KV (2012) Malat1 is not an essential component of nuclear speckles in mice. RNA 18:1487–1499
pubmed: 22718948 pmcid: 3404370 doi: 10.1261/rna.033217.112
Nakagawa S, Shimada M, Yanaka K, Mito M, Arai T, Takahashi E, Fujita Y, Fujimori T, Standaert L, Marine JC, Hirose T (2014) The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice. Development 141:4618–4627
pubmed: 25359727 pmcid: 4302932 doi: 10.1242/dev.110544
Nakagawa S, Yamazaki T, Hirose T (2018) Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu. Open Biol 8:180150
pubmed: 30355755 pmcid: 6223218 doi: 10.1098/rsob.180150
Nemeth A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Peterfia B, Solovei I, Cremer T, Dopazo J, Langst G (2010) Initial genomics of the human nucleolus. PLoS Genet 6:e1000889
pubmed: 20361057 pmcid: 2845662 doi: 10.1371/journal.pgen.1000889
Niimi Y, Takahashi M, Sugawara E, Umeda S, Obayashi M, Sato N, Ishiguro T, Higashi M, Eishi Y, Mizusawa H, Ishikawa K (2013) Abnormal RNA structures (RNA foci) containing a penta-nucleotide repeat (UGGAA)n in the Purkinje cell nucleus is associated with spinocerebellar ataxia type 31 pathogenesis. Neuropathology 33:600–611
pubmed: 23607545 doi: 10.1111/neup.12032
Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T (2020) LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J 39:e102729
pubmed: 31782550 doi: 10.15252/embj.2019102729
Nissan A, Stojadinovic A, Mitrani-Rosenbaum S, Halle D, Grinbaum R, Roistacher M, Bochem A, Dayanc BE, Ritter G, Gomceli I, Bostanci EB, Akoglu M, Chen YT, Old LJ, Gure AO (2012) Colon cancer associated transcript-1: a novel RNA expressed in malignant and pre-malignant human tissues. Int J Cancer 130:1598–1606
pubmed: 21547902 doi: 10.1002/ijc.26170
Nizami Z, Deryusheva S, Gall JG (2010) The Cajal body and histone locus body. Cold Spring Harb Perspect Biol 2:a000653
pubmed: 20504965 pmcid: 2890199 doi: 10.1101/cshperspect.a000653
Ohno S, Kaplan WD, Kinosita R (1959) Formation of the sex chromatin by a single X-chromosome in liver cells of Rattus norvegicus. Exp Cell Res 18:415–418
pubmed: 14428474 doi: 10.1016/0014-4827(59)90031-X
Olivero CE, Martinez-Terroba E, Zimmer J, Liao C, Tesfaye E, Hooshdaran N, Schofield JA, Bendor J, Fang D, Simon MD, Zamudio JR, Dimitrova N (2020) p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell 77:761-774 e768
pubmed: 31973890 pmcid: 7184554 doi: 10.1016/j.molcel.2019.12.014
Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K (2020) A protein assembly mediates Xist localization and gene silencing. Nature 587:145–151
pubmed: 32908311 pmcid: 7644664 doi: 10.1038/s41586-020-2703-0
Pederson T (2011a) The nucleolus. Cold Spring Harb Perspect Biol 3:a000638
pubmed: 21106648 pmcid: 3039934
Pederson T (2011b) The nucleus introduced. Cold Spring Harb Perspect Biol 3:a000521
pubmed: 20660024 pmcid: 3101846
Peng A, Weber SC (2019) Evidence for and against liquid-liquid phase separation in the nucleus. Noncoding RNA 5:50
Pintacuda G, Wei G, Roustan C, Kirmizitas BA, Solcan N, Cerase A, Castello A, Mohammed S, Moindrot B, Nesterova TB, Brockdorff N (2017) hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to establish polycomb-mediated chromosomal silencing. Mol Cell 68:955-969 e910
pubmed: 29220657 pmcid: 5735038 doi: 10.1016/j.molcel.2017.11.013
Pollock C, Huang S (2010) The perinucleolar compartment. Cold Spring Harb Perspect Biol 2:a000679
pubmed: 20182614 pmcid: 2828281 doi: 10.1101/cshperspect.a000679
Prasanth KV, Rajendra TK, Lal AK, Lakhotia SC (2000) Omega speckles—a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr-omega RNA in Drosophila. J Cell Sci 113(Pt 19):3485–3497
pubmed: 10984439 doi: 10.1242/jcs.113.19.3485
Querido E, Gallardo F, Beaudoin M, Menard C, Chartrand P (2011) Stochastic and reversible aggregation of mRNA with expanded CUG-triplet repeats. J Cell Sci 124:1703–1714
pubmed: 21511730 doi: 10.1242/jcs.073270
Ridings-Figueroa R, Stewart ER, Nesterova TB, Coker H, Pintacuda G, Godwin J, Wilson R, Haslam A, Lilley F, Ruigrok R, Bageghni SA, Albadrani G, Mansfield W, Roulson JA, Brockdorff N, Ainscough JFX, Coverley D (2017) The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory. Genes Dev 31:876–888
pubmed: 28546514 pmcid: 5458755 doi: 10.1101/gad.295907.117
Rinn JL, Chang HY (2020) Long noncoding RNAs: molecular modalities to organismal functions. Annu Rev Biochem 89:283–308
pubmed: 32569523 doi: 10.1146/annurev-biochem-062917-012708
Roden C, Gladfelter AS (2021) RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 22:183–195
pubmed: 32632317 doi: 10.1038/s41580-020-0264-6
Rong Z, Hu J, Corey DR, Mootha VV (2019) Quantitative studies of muscleblind proteins and their interaction with TCF4 RNA foci support involvement in the mechanism of Fuchs’ dystrophy. Invest Ophthalmol vis Sci 60:3980–3991
pubmed: 31560764 pmcid: 6779288 doi: 10.1167/iovs.19-27641
Sanders DW, Kedersha N, Lee DSW, Strom AR, Drake V, Riback JA, Bracha D, Eeftens JM, Iwanicki A, Wang A, Wei MT, Whitney G, Lyons SM, Anderson P, Jacobs WM, Ivanov P, Brangwynne CP (2020) Competing protein-RNA interaction networks control multiphase intracellular organization. Cell 181:306-324 e328
pubmed: 32302570 pmcid: 7816278 doi: 10.1016/j.cell.2020.03.050
Sarge KD, Murphy SP, Morimoto RI (1993) Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress. Mol Cell Biol 13:1392–1407
pubmed: 8441385 pmcid: 359449
Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T (2009) MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 106:2525–2530
pubmed: 19188602 pmcid: 2650297 doi: 10.1073/pnas.0807899106
Sato N, Amino T, Kobayashi K, Asakawa S, Ishiguro T, Tsunemi T, Takahashi M, Matsuura T, Flanigan KM, Iwasaki S, Ishino F, Saito Y, Murayama S, Yoshida M, Hashizume Y, Takahashi Y, Tsuji S, Shimizu N, Toda T, Ishikawa K, Mizusawa H (2009) Spinocerebellar ataxia type 31 is associated with “inserted” penta-nucleotide repeats containing (TGGAA)n. Am J Hum Genet 85:544–557
pubmed: 19878914 pmcid: 2775824 doi: 10.1016/j.ajhg.2009.09.019
Schoeftner S, Blasco MA (2008) Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 10:228–236
pubmed: 18157120 doi: 10.1038/ncb1685
Senner CE, Nesterova TB, Norton S, Dewchand H, Godwin J, Mak W, Brockdorff N (2011) Disruption of a conserved region of Xist exon 1 impairs Xist RNA localisation and X-linked gene silencing during random and imprinted X chromosome inactivation. Development 138:1541–1550
pubmed: 21389056 pmcid: 3062423 doi: 10.1242/dev.056812
Shadle SC, Zhong JW, Campbell AE, Conerly ML, Jagannathan S, Wong CJ, Morello TD, van der Maarel SM, Tapscott SJ (2017) DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genet 13:e1006658
pubmed: 28273136 pmcid: 5362247 doi: 10.1371/journal.pgen.1006658
Shadle SC, Bennett SR, Wong CJ, Karreman NA, Campbell AE, van der Maarel SM, Bass BL, Tapscott SJ (2019) DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD. Hum Mol Genet 28:3997–4011
pubmed: 31630170 pmcid: 7342170 doi: 10.1093/hmg/ddz242
Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K (2021) Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat Commun 12:236
pubmed: 33431896 pmcid: 7801683 doi: 10.1038/s41467-020-20487-4
Shichino Y, Yamashita A, Yamamoto M (2014) Meiotic long non-coding meiRNA accumulates as a dot at its genetic locus facilitated by Mmi1 and plays as a decoy to lure Mmi1. Open Biol 4:140022
pubmed: 24920274 pmcid: 4077057 doi: 10.1098/rsob.140022
Shin Y, Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science 357:eaaf4382
pubmed: 28935776 doi: 10.1126/science.aaf4382
Shtivelman E, Henglein B, Groitl P, Lipp M, Bishop JM (1989) Identification of a human transcription unit affected by the variant chromosomal translocations 2;8 and 8;22 of Burkitt lymphoma. Proc Natl Acad Sci USA 86:3257–3260
pubmed: 2470097 pmcid: 287109 doi: 10.1073/pnas.86.9.3257
Souquere S, Beauclair G, Harper F, Fox A, Pierron G (2010) Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies. Mol Biol Cell 21:4020–4027
pubmed: 20881053 pmcid: 2982136 doi: 10.1091/mbc.e10-08-0690
Spector DL, Lamond AI (2011) Nuclear speckles. Cold Spring Harb Perspect Biol 3:a000646
pubmed: 20926517 pmcid: 3039535 doi: 10.1101/cshperspect.a000646
Standaert L, Adriaens C, Radaelli E, Van Keymeulen A, Blanpain C, Hirose T, Nakagawa S, Marine JC (2014) The long noncoding RNA Neat1 is required for mammary gland development and lactation. RNA 20:1844–1849
pubmed: 25316907 pmcid: 4238351 doi: 10.1261/rna.047332.114
Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19:347–359
pubmed: 19106332 pmcid: 2661813 doi: 10.1101/gr.087775.108
Swinnen B, Robberecht W, Van Den Bosch L (2020) RNA toxicity in non-coding repeat expansion disorders. EMBO J 39:e101112
pubmed: 31721251 doi: 10.15252/embj.2018101112
Taneja KL, McCurrach M, Schalling M, Housman D, Singer RH (1995) Foci of trinucleotide repeat transcripts in nuclei of myotonic dystrophy cells and tissues. J Cell Biol 128:995–1002
pubmed: 7896884 doi: 10.1083/jcb.128.6.995
Tang L (2020) Guiding Cas13 for RNA knockdown. Nat Methods 17:461
pubmed: 32371975
Theodoridis PR, Bokros M, Marijan D, Balukoff NC, Wang D, Kirk CC, Budine TD, Goldsmith HD, Wang M, Audas TE, Lee S (2021) Local translation in nuclear condensate amyloid bodies. Proc Natl Acad Sci U S A 118:e2014457118
pubmed: 33568529 pmcid: 7896321 doi: 10.1073/pnas.2014457118
Thoraval D, Asakawa J, Wimmer K, Kuick R, Lamb B, Richardson B, Ambros P, Glover T, Hanash S (1996) Demethylation of repetitive DNA sequences in neuroblastoma. Genes Chromosom Cancer 17:234–244
pubmed: 8946205 doi: 10.1002/(SICI)1098-2264(199612)17:4<234::AID-GCC5>3.0.CO;2-4
Ting DT, Lipson D, Paul S, Brannigan BW, Akhavanfard S, Coffman EJ, Contino G, Deshpande V, Iafrate AJ, Letovsky S, Rivera MN, Bardeesy N, Maheswaran S, Haber DA (2011) Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331:593–596
pubmed: 21233348 pmcid: 3701432 doi: 10.1126/science.1200801
Tomita S, Abdalla MOA, Fujiwara S, Matsumori H, Maehara K, Ohkawa Y, Iwase H, Saitoh N, Nakao M (2015) A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. Nat Commun 6:6966
pubmed: 25923108 doi: 10.1038/ncomms7966
Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938
pubmed: 20797886 pmcid: 4158944 doi: 10.1016/j.molcel.2010.08.011
Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, Ronning P, Reuland B, Guenther K, Beadnell TC, Essig J, Otto GM, O’Sullivan MG, Largaespada DA, Schwertfeger KL, Marahrens Y, Kawakami Y, Bagchi A (2014) PVT1 dependence in cancer with MYC copy-number increase. Nature 512:82–86
pubmed: 25043044 pmcid: 4767149 doi: 10.1038/nature13311
Tycowski KT, Shu MD, Borah S, Shi M, Steitz JA (2012) Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses. Cell Rep 2:26–32
pubmed: 22840393 pmcid: 3430378 doi: 10.1016/j.celrep.2012.05.020
Tycowski KT, Shu MD, Steitz JA (2016) Myriad triple-helix-forming structures in the transposable element RNAs of plants and fungi. Cell Rep 15:1266–1276
pubmed: 27134163 pmcid: 4864102 doi: 10.1016/j.celrep.2016.04.010
Ulitsky I (2016) Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet 17:601–614
pubmed: 27573374 doi: 10.1038/nrg.2016.85
Valgardsdottir R, Chiodi I, Giordano M, Rossi A, Bazzini S, Ghigna C, Riva S, Biamonti G (2008) Transcription of Satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res 36:423–434
pubmed: 18039709 doi: 10.1093/nar/gkm1056
van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI (2010) High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell 21:3735–3748
pubmed: 20826608 pmcid: 2965689 doi: 10.1091/mbc.e10-06-0508
Wang C, Politz JC, Pederson T, Huang S (2003) RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartment. Mol Biol Cell 14:2425–2435
pubmed: 12808040 pmcid: 194890 doi: 10.1091/mbc.e02-12-0818
Wang J, Choi JM, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174:688-699 e616
pubmed: 29961577 pmcid: 6063760 doi: 10.1016/j.cell.2018.06.006
Watanabe Y, Yamamoto M (1994) S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78:487–498
pubmed: 7520368 doi: 10.1016/0092-8674(94)90426-X
West JA, Mito M, Kurosaka S, Takumi T, Tanegashima C, Chujo T, Yanaka K, Kingston RE, Hirose T, Bond C, Fox A, Nakagawa S (2016) Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol 214:817–830
pubmed: 27646274 pmcid: 5037409 doi: 10.1083/jcb.201601071
Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26:2392–2407
pubmed: 23073843 pmcid: 3489998 doi: 10.1101/gad.204438.112
Wu H, Yin QF, Luo Z, Yao RW, Zheng CC, Zhang J, Xiang JF, Yang L, Chen LL (2016) Unusual processing generates SPA LncRNAs that sequester multiple rna binding proteins. Mol Cell 64:534–548
pubmed: 27871485 doi: 10.1016/j.molcel.2016.10.007
Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z, Zhang S, Wang HB, Ge J, Lu X, Yang L, Chen LL (2014) Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 24:513–531
pubmed: 24662484 pmcid: 4011346 doi: 10.1038/cr.2014.35
Xing Y, Johnson CV, Dobner PR, Lawrence JB (1993) Higher level organization of individual gene transcription and RNA splicing. Science 259:1326–1330
pubmed: 8446901 doi: 10.1126/science.8446901
Yamamoto T, Yamazaki T, Hirose T (2021) Triblock copolymer micelle model of spherical paraspeckles. bioRxiv. https://doi.org/10.1101/2020.1111.1101.364190
doi: 10.1101/2020.1111.1101.364190
Yamazaki T, Fujikawa C, Kubota A, Takahashi A, Hirose T (2018a) CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles. Biochem Biophys Res Commun 504:218–224
pubmed: 30180948 doi: 10.1016/j.bbrc.2018.08.158
Yamazaki T, Souquere S, Chujo T, Kobelke S, Chong YS, Fox AH, Bond CS, Nakagawa S, Pierron G, Hirose T (2018b) Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through Phase separation. Mol Cell 70:1038-1053 e1037
pubmed: 29932899 doi: 10.1016/j.molcel.2018.05.019
Yamazaki T, Yamamoto T, Yoshino H, Souquere S, Nakagawa S, Pierron G, Hirose T (2021) Paraspeckles are constructed as block copolymer micelles. EMBO J. https://doi.org/10.15252/embj.2020107270
doi: 10.15252/embj.2020107270 pubmed: 34121201
Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL (2011) Genomewide characterization of non-polyadenylated RNAs. Genome Biol 12:R16
pubmed: 21324177 pmcid: 3188798 doi: 10.1186/gb-2011-12-2-r16
Yang L, Kirby JE, Sunwoo H, Lee JT (2016) Female mice lacking Xist RNA show partial dosage compensation and survive to term. Genes Dev 30:1747–1760
pubmed: 27542829 pmcid: 5002979 doi: 10.1101/gad.281162.116
Yao RW, Xu G, Wang Y, Shan L, Luan PF, Wang Y, Wu M, Yang LZ, Xing YH, Yang L, Chen LL (2019) Nascent pre-rRNA sorting via phase separation drives the assembly of dense fibrillar Components in the human nucleolus. Mol Cell 76:767-783 e711
pubmed: 31540874 doi: 10.1016/j.molcel.2019.08.014
Yap K, Mukhina S, Zhang G, Tan JSC, Ong HS, Makeyev EV (2018) A short tandem repeat-enriched RNA Assembles a nuclear compartment to control alternative splicing and promote cell survival. Mol Cell 72:525–540
pubmed: 30318443 pmcid: 6224606 doi: 10.1016/j.molcel.2018.08.041
Yin QF, Yang L, Zhang Y, Xiang JF, Wu YW, Carmichael GG, Chen LL (2012) Long noncoding RNAs with snoRNA ends. Mol Cell 48:219–230
pubmed: 22959273 doi: 10.1016/j.molcel.2012.07.033
Zhang B, Arun G, Mao YS, Lazar Z, Hung G, Bhattacharjee G, Xiao X, Booth CJ, Wu J, Zhang C, Spector DL (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
pubmed: 22840402 pmcid: 3408587 doi: 10.1016/j.celrep.2012.06.003

Auteurs

Shinichi Nakagawa (S)

RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan. nakagawas@pharm.hokudai.ac.jp.

Tomohiro Yamazaki (T)

Laboratory of RNA Biofunction, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.

Taro Mannen (T)

College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.

Tetsuro Hirose (T)

Laboratory of RNA Biofunction, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.

Articles similaires

Humans Pulmonary Disease, Chronic Obstructive RNA, Long Noncoding Male Female
Humans Small Cell Lung Carcinoma RNA, Long Noncoding Sulfonamides Animals
Humans Female Ovarian Neoplasms Cell Proliferation RNA, Long Noncoding
Humans Temozolomide RNA, Long Noncoding Glioblastoma Drug Resistance, Neoplasm

Classifications MeSH