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Significance of lncRNA abundance to function

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Abstract

Long noncoding RNAs (lncRNAs) have emerged as regulators of diverse cellular processes. Although the vast majority of lncRNAs are expressed at lower levels compared to messenger RNAs (mRNAs), many lncRNAs play a central role in the regulation of cellular homeostasis and gene expression. With the advancement of next generation sequencing technologies, recent studies illustrate the diversity of lncRNA function. This diversity can be due to differences in their mechanisms of action, spatio-temporal expression, and/or abundance, all of which can vary depending on the particular cell type or tissue. Here, we discuss how the abundance of lncRNAs is an important feature that is often linked to their functions, and why it is crucial to quantitate lncRNA abundance, its local concentration within a cell or a tissue or the dynamic changes in expression levels during cell cycle progression or upon environmental stimuli, to shed light on their physiological roles.

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References

  • Ahnert SE, Fink TM, Zinovyev A (2008) How much non-coding DNA do eukaryotes require? J Theor Biol 252:587–592

    Article  CAS  PubMed  Google Scholar 

  • Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, Olson EN (2015) A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160:595–606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson KM, Anderson DM, McAnally JR, Shelton JM, Bassel-Duby R, Olson EN (2016) Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development. Nature 539:433–436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arun G, Diermeier S, Akerman M, Chang KC, Wilkinson JE, Hearn S, Kim Y, MacLeod AR, Krainer AR, Norton L, Brogi E, Egeblad M, Spector DL (2016) Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 30:34–51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Autuoro JM, Pirnie SP, Carmichael GG (2014) Long noncoding RNAs in imprinting and X chromosome inactivation. Biomolecules 4:76–100

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bosson AD, Zamudio JR, Sharp PA (2014) Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell 56:347–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915–1927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A (2015) Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol 16:20

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL, Jenkins LM, Shabalina SA, Mo M, Dasso M, Yang Y, Wakefield LM, Zhu Y, Frier SM, Moriarity BS, Prasanth KV, Perez-Pinera P, Lal A (2017) Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3. Elife. https://doi.org/10.7554/eLife.23244

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X (2015) RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Denzler R, Agarwal V, Stefano J, Bartel DP, Stoffel M (2014) Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell 54:766–776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Derrien T, Guigo R, Johnson R (2011) The long non-coding RNAs: A new (P)layer in the “dark matter.” Front Genet 2:107

    PubMed  Google Scholar 

  • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T (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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elguindy MM, Mendell JT (2021) NORAD-induced Pumilio phase separation is required for genome stability. Nature 595:303–308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eliscovich C, Shenoy SM, Singer RH (2017) Imaging mRNA and protein interactions within neurons. Proc Natl Acad Sci USA 114:E1875–E1884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Engreitz JM, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES (2014) RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell 159:188–199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES (2016) Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539:452–455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Engreitz JM, Ollikainen N, Guttman M (2016) Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 17:756–770

    Article  CAS  PubMed  Google Scholar 

  • Fatica A, Bozzoni I (2014) Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet 15:7–21

    Article  CAS  PubMed  Google Scholar 

  • Gil N, Ulitsky I (2020) Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 21:102–117

    Article  CAS  PubMed  Google Scholar 

  • Grelet S, Link LA, Howley B, Obellianne C, Palanisamy V, Gangaraju VK, Diehl JA, Howe PH (2017) A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression. Nat Cell Biol 19:1105–1115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9:e1003569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA (2017) A phase separation model for transcriptional control. Cell 169:13–23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langerod A, Borresen-Dale AL, Kim SK, van de Vijver M, Sukumar S, Whitfield ML, Kellis M, Xiong Y, Wong DJ, Chang HY (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43:621–629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanduri C (2016) Long noncoding RNAs: Lessons from genomic imprinting. Biochim Biophys Acta 1859:102–111

    Article  CAS  PubMed  Google Scholar 

  • Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ (2015) Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell 16:88–101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim KM, Noh JH, Abdelmohsen K, Gorospe M (2017) Mitochondrial noncoding RNA transport. BMB Rep 50:164–174

    Article  PubMed  PubMed Central  Google Scholar 

  • Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172:393–407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing C (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  CAS  PubMed  Google Scholar 

  • Latos PA, Pauler FM, Koerner MV, Senergin HB, Hudson QJ, Stocsits RR, Allhoff W, Stricker SH, Klement RM, Warczok KE, Aumayr K, Pasierbek P, Barlow DP (2012) Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338:1469–1472

    Article  CAS  PubMed  Google Scholar 

  • Lee S, Kopp F, Chang TC, Sataluri A, Chen B, Sivakumar S, Yu H, Xie Y, Mendell JT (2016) Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164:69–80

    Article  CAS  PubMed  Google Scholar 

  • Li J, Liu C (2019) Coding or noncoding, the converging concepts of RNAs. Front Genet 10:496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li XL, Subramanian M, Jones MF, Chaudhary R, Singh DK, Zong X, Gryder B, Sindri S, Mo M, Schetter A, Wen X, Parvathaneni S, Kazandjian D, Jenkins LM, Tang W, Elloumi F, Martindale JL, Huarte M, Zhu Y, Robles AI, Frier SM, Rigo F, Cam M, Ambs S, Sharma S, Harris CC, Dasso M, Prasanth KV, Lal A (2017) Long noncoding RNA PURPL suppresses basal p53 levels and promotes tumorigenicity in colorectal cancer. Cell Rep 20:2408–2423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Meng X, Wei C, Zhou Y, Chen H, Huang H, Chen M (2018) Dissecting LncRNA roles in renal cell carcinoma metastasis and characterizing genomic heterogeneity by single-cell RNA-seq. Mol Cancer Res 16:1879–1888

    Article  CAS  PubMed  Google Scholar 

  • Li XL, Pongor L, Tang W, Das S, Muys BR, Jones MF, Lazar SB, Dangelmaier EA, Hartford CC, Grammatikakis I, Hao Q, Sun Q, Schetter A, Martindale JL, Tang B, Jenkins LM, Robles AI, Walker RL, Ambs S, Chari R, Shabalina SA, Gorospe M, Hussain SP, Harris CC, Meltzer PS, Prasanth KV, Aladjem MI, Andresson T, Lal A (2020) A small protein encoded by a putative lncRNA regulates apoptosis and tumorigenicity in human colorectal cancer cells. Elife. https://doi.org/10.7554/eLife.53734

    Article  PubMed  PubMed Central  Google Scholar 

  • Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, Chao JA, Park HY, de Turris V, Lopez-Jones M, Singer RH (2011) A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods 8:165–170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA (2016) Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol 17:67

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Makarewich CA, Baskin KK, Munir AZ, Bezprozvannaya S, Sharma G, Khemtong C, Shah AM, McAnally JR, Malloy CR, Szweda LI, Bassel-Duby R, Olson EN (2018) MOXI is a mitochondrial micropeptide that enhances fatty acid beta-oxidation. Cell Rep 23:3701–3709

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McDonel P, Guttman M (2019) Approaches for understanding the mechanisms of long noncoding RNA regulation of gene expression. Cold Spring Harb Perspect Biol. https://doi.org/10.1101/cshperspect.a032151

    Article  PubMed  PubMed Central  Google Scholar 

  • Mele M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL (2017) Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res 27:27–37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moffitt JR, Hao J, Bambah-Mukku D, Lu T, Dulac C, Zhuang X (2016) High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. Proc Natl Acad Sci USA 113:14456–14461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N, Collin O, Basyuk E, Bertrand E, Darzacq X, Zimmer C (2013) FISH-quant: automatic counting of transcripts in 3D FISH images. Nat Methods 10:277–278

    Article  CAS  PubMed  Google Scholar 

  • Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U (2017) Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol 24:86–96

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Noh JH, Kim KM, Abdelmohsen K, Yoon JH, Panda AC, Munk R, Kim J, Curtis J, Moad CA, Wohler CM, Indig FE, de Paula W, Dudekula DB, De S, Piao Y, Yang X, Martindale JL, de Cabo R, Gorospe M (2016) HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNA RMRP. Genes Dev 30:1224–1239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Puvvula PK, Desetty RD, Pineau P, Marchio A, Moon A, Dejean A, Bischof O (2014) Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit. Nat Commun 5:5323

    Article  PubMed  Google Scholar 

  • Quan PL, Sauzade M, Brouzes E (2018) dPCR: a technology review. Sensors. https://doi.org/10.3390/s18041271

    Article  PubMed  PubMed Central  Google Scholar 

  • Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA (2013) Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12:616–628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sahakyan A, Yang Y, Plath K (2018) The role of Xist in X-chromosome dosage compensation. Trends Cell Biol 28:999–1013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146:353–358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schertzer MD, Braceros KCA, Starmer J, Cherney RE, Lee DM, Salazar G, Justice M, Bischoff SR, Cowley DO, Ariel P, Zylka MJ, Dowen JM, Magnuson T, Calabrese JM (2019) lncRNA-induced spread of polycomb controlled by genome architecture, RNA abundance, and CpG island DNA. Mol Cell 75:523-537 e510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schertzer MD, Murvin MM, Calabrese JM (2020) Using RNA Sequencing and spike-in RNAs to measure intracellular abundance of lncRNAs and mRNAs. Bio Protoc. https://doi.org/10.21769/bioprotoc.3772

    Article  PubMed  PubMed Central  Google Scholar 

  • Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M, Proudfoot NJ (2017) Distinctive patterns of transcription and RNA processing for human lincRNAs. Mol Cell 65:25–38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY (2016) An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet 48:1370–1376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T (2015) A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep 16:1520–1534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spector DL, Lamond AI (2011) Nuclear speckles. Cold Spring Harb Perspect Biol. https://doi.org/10.1101/cshperspect.a000646

    Article  PubMed  PubMed Central  Google Scholar 

  • Statello L, Guo CJ, Chen LL, Huarte M (2021) Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol 22:96–118

    Article  CAS  PubMed  Google Scholar 

  • Tichon A, Gil N, Lubelsky Y, Havkin Solomon T, Lemze D, Itzkovitz S, Stern-Ginossar N, Ulitsky I (2016) A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nat Commun 7:12209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tutucci E, Livingston NM, Singer RH, Wu B (2018) Imaging mRNA In Vivo, from birth to death. Annu Rev Biophys 47:85–106

    Article  CAS  PubMed  Google Scholar 

  • Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP (2014) The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J 33:296–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120–124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE (2014) The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell 55:791–802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R, Qiao J, Tang F (2013) Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 20:1131–1139

    Article  CAS  PubMed  Google Scholar 

  • Yang F, Yi F, Han X, Du Q, Liang Z (2013) MALAT-1 interacts with hnRNP C in cell cycle regulation. FEBS Lett 587:3175–3181

    Article  CAS  PubMed  Google Scholar 

  • Yao RW, Wang Y, Chen LL (2019) Cellular functions of long noncoding RNAs. Nat Cell Biol 21:542–551

    Article  CAS  PubMed  Google Scholar 

  • Yildirim O, Izgu EC, Damle M, Chalei V, Ji F, Sadreyev RI, Szostak JW, Kingston RE (2020) S-phase enriched non-coding RNAs regulate gene expression and cell cycle progression. Cell Rep 31:107629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou J, Xu J, Zhang L, Liu S, Ma Y, Wen X, Hao J, Li Z, Ni Y, Li X, Zhou F, Li Q, Wang F, Wang X, Si Y, Zhang P, Liu C, Bartolomei M, Tang F, Liu B, Yu J, Lan Y (2019) Combined Single-cell profiling of lncRNAs and functional screening reveals that H19 Is pivotal for embryonic hematopoietic stem cell development. Cell Stem Cell 24:285-298 e285

    Article  CAS  PubMed  Google Scholar 

  • Ziegler C, Kretz M (2017) The more the merrier-complexity in long non-coding RNA loci. Front Endocrinol 8:90

    Article  Google Scholar 

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This research was funded by the Intramural research program of the Center for Cancer Research, National Cancer Institute, National Institutes of Health.

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  1. Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Ioannis Grammatikakis & Ashish Lal

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  1. Ioannis Grammatikakis
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Grammatikakis, I., Lal, A. Significance of lncRNA abundance to function. Mamm Genome 33, 271–280 (2022). https://doi.org/10.1007/s00335-021-09901-4

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