Gene regulation by long non-coding RNAs and its biological functions

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216

Genome engineering using the CRISPR-Cas9 system

Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

Salmena, L., Poliseno, L., Tay, Y., Kats, L., & Pandolfi, P. P. (2011) · Cell · doi:10.1016/j.cell.2011.07.014 · Cited by 7,262

Biomolecular condensates: organizers of cellular biochemistry

Banani, S. F., Lee, H. O., Hyman, A. A., & Rosen, M. K. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.7 · Cited by 6,058

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expressionPreprint

Derrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,135

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016

Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246

Functional Classification and Experimental Dissection of Long Noncoding RNAs

Kopp, F. B., & Mendell, J. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.011 · Cited by 3,574

Long non-coding RNAs: new players in cell differentiation and development

Fatica, A., & Bozzoni, I. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3606 · Cited by 2,980

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., Tramontano, A., & Bozzoni, I. (2011) · Cell · doi:10.1016/j.cell.2011.09.028 · Cited by 2,554

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450

RNA targeting with CRISPR–Cas13

Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine, V., Cox, D. B. T., Kellner, M. J., Regev, A., et al. (2017) · Nature · doi:10.1038/nature24049 · Cited by 2,093

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.06.040 · Cited by 2,053

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 2,005

Long Noncoding RNAs with Enhancer-like Function in Human Cells

Ørom, U. A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.001 · Cited by 1,721

An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles

Clemson, C. M., Hutchinson, J. N., Sara, S. A., Ensminger, A. W., Fox, A. H., Chess, A., & Lawrence, J. B. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.026 · Cited by 1,445

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

Yap, K. L., Li, S., Muñoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., Gil, J., Walsh, M. J., & Zhou, M.-M. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.021 · Cited by 1,391

Telomeric Repeat–Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends

Azzalin, C. M., Reichenbach, P., Khoriauli, L., Giulotto, E., & Lingner, J. (2007) · Science · doi:10.1126/science.1147182 · Cited by 1,379

RNA-guided gene activation by CRISPR-Cas9-based transcription factors

Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2600 · Cited by 1,328

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

Gong, C., & Maquat, L. E. (2011) · Nature · doi:10.1038/nature09701 · Cited by 1,294

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.027 · Cited by 1,293

RNAi-Mediated Targeting of Heterochromatin by the RITS Complex

Verdel, A., Jia, S., Gerber, S. A., Sugiyama, T., Gygi, S. P., Grewal, S. I. S., & Moazed, D. (2004) · Science · doi:10.1126/science.1093686 · Cited by 1,268

Local regulation of gene expression by lncRNA promoters, transcription and splicing

Engreitz, J. M., Haines, J. E., Perez, E. M., Munson, G., Chen, J., Kane, M., McDonel, P. E., Guttman, M., & Lander, E. S. (2016) · Nature · doi:10.1038/nature20149 · Cited by 1,253

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

Pandey, R. R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini‐DiNardo, D., & Kanduri, C. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.08.022 · Cited by 1,192

Alternative polyadenylation of mRNA precursors

Tian, B., & Manley, J. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.116 · Cited by 1,179

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

Hung, T., Wang, Y., Lin, M. F., Koegel, A. K., Kotake, Y., Grant, G. D., Horlings, H. M., Shah, N., Umbricht, C. B., Wang, P., et al. (2011) · Nature Genetics · doi:10.1038/ng.848 · Cited by 1,165

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

McHugh, C. A., Chen, C., Chow, A. Y., Surka, C., Tran, C., McDonel, P. E., Pandya‐Jones, A., Blanco, M. R., Burghard, C. P., Moradian, A., et al. (2015) · Nature · doi:10.1038/nature14443 · Cited by 1,139

The non-coding Air RNA is required for silencing autosomal imprinted genes

Sleutels, F., Zwart, R., & Barlow, D. P. (2002) · Nature · doi:10.1038/415810a · Cited by 1,096

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A. Y., Merkurjev, D., Zhang, J., Ohgi, K., Song, X., et al. (2013) · Nature · doi:10.1038/nature12210 · Cited by 1,049

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

Prensner, J. R., Iyer, M. K., Balbin, O. A., Dhanasekaran, S. M., Cao, Q., Brenner, J. C., Laxman, B., Asangani, I. A., Grasso, C. S., Kominsky, H. D., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1914 · Cited by 1,037

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

Carrieri, C., Cimatti, L., Biagioli, M., Beugnet, A., Zucchelli, S., Fedele, S., Pesce, E., Ferrer, I., Collavin, L., Santoro, C., et al. (2012) · Nature · doi:10.1038/nature11508 · Cited by 1,032

A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains

Hutchinson, J. N., Ensminger, A. W., Clemson, C., Lynch, C. R., Lawrence, J. B., & Chess, A. J. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-39 · Cited by 1,017

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

Engreitz, J., Pandya‐Jones, A., McDonel, P. E., Shishkin, A., Sirokman, K., Surka, C., Kadri, S., Xing, J. C., Goren, A., Lander, E. S., et al. (2013) · Science · doi:10.1126/science.1237973 · Cited by 1,008

An atlas of human long non-coding RNAs with accurate 5′ ends

Hon, C.-C., Ramilowski, J. A., Harshbarger, J., Bertin, N., Rackham, O. J. L., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T. M., Severin, J., et al. (2017) · Nature · doi:10.1038/nature21374 · Cited by 1,007

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

Grote, P., Wittler, L., Hendrix, D. A., Koch, F., Währisch, S., Beisaw, A., Macura, K., Bläß, G., Kellis, M., Werber, M., et al. (2013) · Developmental Cell · doi:10.1016/j.devcel.2012.12.012 · Cited by 977

Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth

Michalik, K., You, X. A., Manavski, Y., Doddaballapur, A., Zörnig, M., Braun, T. W., John, D., Ponomareva, Y., Chen, W., Uchida, S., et al. (2014) · Circulation Research · doi:10.1161/circresaha.114.303265 · Cited by 941

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934

Divergent Transcription from Active Promoters

Seila, A. C., Calabrese, J. M., Levine, S. S., Yeo, G. W.-M., Rahl, P. B., Flynn, R. A., Young, R. A., & Sharp, P. A. (2008) · Science · doi:10.1126/science.1162253 · Cited by 930

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz, M., Siprashvili, Z., Chu, C., Webster, D., Zehnder, A., Qu, K., Lee, C. S., Flockhart, R., Groff, A., Chow, J. M., et al. (2012) · Nature · doi:10.1038/nature11661 · Cited by 920

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

Liu, B., Sun, L., Liu, Q., Gong, C., Yao, Y., Lv, X., Lin, L., Yao, H., Su, F., Li, D., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.02.004 · Cited by 906

The Human Mitochondrial Transcriptome

Mercer, T. R., Neph, S., Dinger, M. E., Crawford, J., Smith, M. A., Shearwood, A.-M. J., Haugen, E., Bracken, C. P., Rackham, O., Stamatoyannopoulos, J. A., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.051 · Cited by 905

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

Lee, S., Kopp, F. B., Chang, T.-C., Sataluri, A., Chen, B., Sivakumar, S., Yu, H., Xie, Y., & Mendell, J. T. (2015) · Cell · doi:10.1016/j.cell.2015.12.017 · Cited by 892

Evaluation of 2‘-modified oligonucleotides containing 2‘-deoxy gaps as antisense inhibitors of gene expression

Monia, B. P., Lesnik, E. A., Gonzalez, C., Lima, W. F., McGee, D. P. C., Guinosso, C. J., Kawasaki, A. M., Cook, P. D., & Freier, S. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85268-7 · Cited by 779

Principles for targeting RNA with drug-like small molecules

Warner, K. D., Hajdin, C. E., & Weeks, K. M. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.93 · Cited by 762

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

Xiang, J., Yin, Q.-F., Chen, T., Zhang, Y., Zhang, X.-O., Wu, Z., Zhang, S., Wang, H., Ge, J., Lu, X., et al. (2014) · Cell Research · doi:10.1038/cr.2014.35 · Cited by 744

PVT1 dependence in cancer with MYC copy-number increase

Tseng, Y., Moriarity, B. S., Gong, W., Akiyama, R., Tiwari, A., Kawakami, H., Ronning, P., REULAND, B. D., Guenther, K. L., Beadnell, T. C., et al. (2014) · Nature · doi:10.1038/nature13311 · Cited by 743

Regulation of gene expression by cis-acting long non-coding RNAs

Gil, N., & Ulitsky, I. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0184-5 · Cited by 736

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

Denzler, R., Agarwal, V., Stefano, J., Bartel, D. P., & Stoffel, M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.045 · Cited by 734

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

Wilusz, J. E., Freier, S. M., & Spector, D. L. (2008) · Cell · doi:10.1016/j.cell.2008.10.012 · Cited by 729

Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript

Martianov, I., Ramadass, A., Barros, A. S., Chow, N., & Akoulitchev, A. V. (2007) · Nature · doi:10.1038/nature05519 · Cited by 728

MEG3 noncoding RNA: a tumor suppressor

Zhou, Y., Zhang, X., & Klibanski, A. (2012) · Journal of Molecular Endocrinology · doi:10.1530/jme-12-0008 · Cited by 724

Gene regulation in the immune system by long noncoding RNAs

Chen, Y. G., Satpathy, A. T., & Chang, H. Y. (2017) · Nature Immunology · doi:10.1038/ni.3771 · Cited by 694

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Sauvageau, M., Goff, L. A., Lodato, S., Bonev, B., Groff, A. F., Gerhardinger, C., Sanchez-Gomez, D. B., Hacisuleyman, E., Li, E. V., Spence, M. C., et al. (2013) · eLife · doi:10.7554/elife.01749 · Cited by 691

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

Hezroni, H., Koppstein, D., Schwartz, M. G., Avrutin, A., Bartel, D. P., & Ulitsky, I. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.023 · Cited by 677

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

Lee, J. T., & Bartolomei, M. S. (2013) · Cell · doi:10.1016/j.cell.2013.02.016 · Cited by 674

MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspecklesPreprint

Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P., Mattick, J. S., & Spector, D. L. (2008) · Genome Research · doi:10.1101/gr.087775.108 · Cited by 672

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Mondal, T., Subhash, S., Vaid, R., Enroth, S., Uday, S., Reinius, B., Mitra, S., Mohammed, A., James, A. R., Hoberg, E., et al. (2015) · Nature Communications · doi:10.1038/ncomms8743 · Cited by 665

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

Yang, L., Lin, C., Jin, C., Yang, J. C., Tanasă, B., Li, W., Merkurjev, D., Ohgi, K. A., Meng, D., Zhang, J., et al. (2013) · Nature · doi:10.1038/nature12451 · Cited by 665

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

Lu, Z., Zhang, Q. C., Lee, B., Flynn, R. A., Smith, M. A., Robinson, J. T., Davidovich, C., Gooding, A. R., Goodrich, K. J., Mattick, J. S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.028 · Cited by 647

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman, E., Goff, L. A., Trapnell, C., Williams, A., Henao‐Mejia, J., Sun, L., McClanahan, P. D., Hendrickson, D. G., Sauvageau, M., Kelley, D. R., et al. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2764 · Cited by 644

Towards a complete map of the human long non-coding RNA transcriptome

Uszczyńska-Ratajczak, B., Lagarde, J., Frankish, A., Guigó, R., & Johnson, R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0017-y · Cited by 637

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer

Chakravarty, D., Sboner, A., Nair, S. S., Γιαννοπούλου, Ε., Li, R., Hennig, S., Mosquera, J. M., Pauwels, J. E., Park, K., Kossaï, M., et al. (2014) · Nature Communications · doi:10.1038/ncomms6383 · Cited by 624

ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs

Yang, L., Lin, C., Liu, W., Zhang, J., Ohgi, K. A., Grinstein, J. D., Dorrestein, P. C., & Rosenfeld, M. G. (2011) · Cell · doi:10.1016/j.cell.2011.08.054 · Cited by 612

CCAT2 , a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancerPreprint

Ling, H. Y., Spizzo, R., Atlasi, Y., Nicoloso, M. S., Shimizu, M., Redis, R. S., Nishida, N., Gafà, R., Song, J. H., Guo, Z., et al. (2013) · Genome Research · doi:10.1101/gr.152942.112 · Cited by 605

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

Sasaki, Y., Ideue, T., Sano, M., Mitsuyama, T., & Hirose, T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807899106 · Cited by 604

Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA lossPreprint

Arun, G., Diermeier, S. D., Akerman, M., Chang, K.-C., Wilkinson, J. E., Hearn, S., Kim, Y., MacLeod, A. R., Krainer, A. R., Norton, L., et al. (2015) · Genes & Development · doi:10.1101/gad.270959.115 · Cited by 603

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

Yamazaki, T., Souquère, S., Chujo, T., Kobelke, S., Chong, Y. S., Fox, A. H., Bond, C. S., Nakagawa, S., Pierron, G., & Hirose, T. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.019 · Cited by 598

Melanoma addiction to the long non-coding RNA SAMMSON

Leucci, E., Vendramin, R., Spinazzi, M., Laurette, P., Fiers, M. W. E. J., Wouters, J., Radaelli, E., Eyckerman, S., Leonelli, C., Vanderheyden, K., et al. (2016) · Nature · doi:10.1038/nature17161 · Cited by 593

Antisense Oligonucleotides: An Emerging Area in Drug Discovery and Development

Dhuri, K., Bechtold, C., Quijano, E., Pham, H. T. T., Gupta, A., Vikram, A., & Bahal, R. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9062004 · Cited by 586

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

Fang, S., Zhang, L., Guo, J., Niu, Y., Wu, Y., Li, H., Zhao, L., Li, X., Teng, X., Sun, X., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1107 · Cited by 563

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

Melo, C. A., Drost, J., Wijchers, P. J., van de Werken, H., de Wit, E., Vrielink, J. A. F. O., Elkon, R., Melo, S. A., Léveillé, N., Kalluri, R., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.11.021 · Cited by 544

Regulatory R-loops as facilitators of gene expression and genome stability

Niehrs, C., & Luke, B. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0206-3 · Cited by 543

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

Latos, P. A., Pauler, F. M., Koerner, M. V., Senergin, B. H., Hudson, Q. J., Stocsits, R. R., Allhoff, W., Stricker, S. H., Klement, R. M., Warczok, K. E., et al. (2012) · Science · doi:10.1126/science.1228110 · Cited by 542

TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres

Deng, Z., Norseen, J., Wiedmer, A., Riethman, H. C., & Lieberman, P. M. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.025 · Cited by 542

exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes

Li, S., Li, Y., Chen, B., Zhao, J., Yu, S., Tang, Y., Zheng, Q., Li, Y., Wang, P., He, X., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx891 · Cited by 542

Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice

Yildirim, E., Kirby, J. E., Brown, D. E., Mercier, F., Sadreyev, R. I., Scadden, D. T., & Lee, J. T. (2013) · Cell · doi:10.1016/j.cell.2013.01.034 · Cited by 532

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

Engreitz, J., Sirokman, K., McDonel, P. E., Shishkin, A. A., Surka, C., Russell, P. H., Grossman, S. R., Chow, A. Y., Guttman, M., & Lander, E. S. (2014) · Cell · doi:10.1016/j.cell.2014.08.018 · Cited by 514

Modular Recognition of RNA by a Human Pumilio-Homology Domain

Wang, X., McLachlan, J., Zamore, P. D., & Hall, T. M. T. (2002) · Cell · doi:10.1016/s0092-8674(02)00873-5 · Cited by 507

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genesPreprint

Schmitz, K., Mayer, C., Postepska‐Igielska, A., & Grummt, I. (2010) · Genes & Development · doi:10.1101/gad.590910 · Cited by 506

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

Jeon, Y., & Lee, J. T. (2011) · Cell · doi:10.1016/j.cell.2011.06.026 · Cited by 498

Transcription factor trapping by RNA in gene regulatory elements

Sigova, A. A., Abraham, B. J., Ji, X., Molinie, B., Hannett, N. M., Guo, Y. E., Jangi, M., Giallourakis, C. C., Sharp, P. A., & Young, R. A. (2015) · Science · doi:10.1126/science.aad3346 · Cited by 492

A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tailsPreprint

Wilusz, J. E., JnBaptiste, C. K., Lu, L. Y., Kuhn, C., Joshua‐Tor, L., & Sharp, P. A. (2012) · Genes & Development · doi:10.1101/gad.204438.112 · Cited by 487

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaens, C., Standaert, L., Barra, J., Latil, M., Verfaillie, A., Kalev, P., Boeckx, B., Wijnhoven, P. W. G., Radaelli, E., Vermi, W., et al. (2016) · Nature Medicine · doi:10.1038/nm.4135 · Cited by 481

Evidence for natural antisense transcript-mediated inhibition of microRNA function

Faghihi, M. A., Zhang, M., Huang, J., Modarresi, F., Van der Brug, M. P., Nalls, M. A., Cookson, M. R., St-Laurent, G., & Wahlestedt, C. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r56 · Cited by 473

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

Wang, Z., Yang, B., Zhang, M., Guo, W., Wu, Z., Wang, Y., Jia, L., Li, S., Johnson, R., Demchok, J. A., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.006 · Cited by 473

Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition

Bosson, A., Zamudio, J. R., & Sharp, P. A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.09.018 · Cited by 471

Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization

Csorba, T., Questa, J. I., Sun, Q., & Dean, C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419030111 · Cited by 470

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

Arora, R., Lee, Y., Wischnewski, H., Brun, C. M., Schwarz, T., & Azzalin, C. M. (2014) · Nature Communications · doi:10.1038/ncomms6220 · Cited by 468

Long Noncoding RNAs with snoRNA Ends

Yin, Q.-F., Yang, L. C., Zhang, Y., Xiang, J., Wu, Y., Carmichael, G., & Chen, L. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.07.033 · Cited by 464

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

Cho, S. W., Xu, J., Sun, R., Mumbach, M. R., Carter, A. C., Chen, Y. G., Yost, K. E., Kim, J., He, J., Nevins, S. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.068 · Cited by 459

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

Briggs, J., Wolvetang, E. J., Mattick, J. S., Rinn, J. L., & Barry, G. (2015) · Neuron · doi:10.1016/j.neuron.2015.09.045 · Cited by 456

A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation

Atianand, M., Hu, W., Satpathy, A. T., Shen, Y., Ricci, E. P., Alvarez‐Dominguez, J. R., Bhatta, A., Schattgen, S., McGowan, J. D., Blin, J., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.075 · Cited by 446

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova, N., Zamudio, J. R., Jong, R. M., Soukup, D., Resnick, R., Sarma, K., Ward, A. J., Raj, A., Lee, J. T., Sharp, P. A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.025 · Cited by 445

NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death

Huang, D., Chen, J., Yang, L., Ouyang, Q., Li, J., Lao, L., Zhao, J., Liu, J., Lu, Y., Xing, Y., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0207-y · Cited by 445

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

Vos, S. M., Farnung, L., Boehning, M., Wigge, C., Linden, A., Urlaub, H., & Cramer, P. (2018) · Nature · doi:10.1038/s41586-018-0440-4 · Cited by 432

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

Trimarchi, T., Bilal, E., Ntziachristos, P., Fabbri, G., Dalla‐Favera, R., Tsirigos, A., & Aifantis, I. (2014) · Cell · doi:10.1016/j.cell.2014.05.049 · Cited by 426

Structural organization of the inactive X chromosome in the mouse

Giorgetti, L., Lajoie, B. R., Carter, A. C., Attia, M., Zhan, Y., Xu, J., Chen, C. J., Kaplan, N., Chang, H. Y., Heard, É., et al. (2016) · Nature · doi:10.1038/nature18589 · Cited by 410

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

Luo, S., Lu, J. Y., Liu, L., Yin, Y., Chen, C., Han, X., Wu, B., Xu, R., Liu, W., Yan, P., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.01.024 · Cited by 407

Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks

Holdt, L. M., Hoffmann, S., Sass, K., Langenberger, D., Scholz, M., Krohn, K., Finstermeier, K., Stahringer, A., Wilfert, W., Beutner, F., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003588 · Cited by 397

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

Sun, Q., Csorba, T., Skourti-Stathaki, K., et al. (2013) · Science · doi:10.1126/science.1234848 · Cited by 393

Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

Michelini, F., Pitchiaya, S., Vitelli, V., Sharma, S., Gioia, U., Pessina, F., Cabrini, M., Wang, Y., Capozzo, I., Iannelli, F., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3643 · Cited by 392

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Munschauer, M., Nguyen, C. T., Sirokman, K., Hartigan, C. R., Hogstrom, L. J., Engreitz, J., Ulirsch, J. C., Fulco, C. P., Subramanian, V., Chen, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0453-z · Cited by 386

The Diversity of Long Noncoding RNAs and Their Generation

Wu, H., Yang, L. C., & Chen, L. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.004 · Cited by 386

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

Wutz, A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3035 · Cited by 361

A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression

Grelet, S., Link, L. A., Howley, B. V., Obellianne, C., Palanisamy, V., Gangaraju, V. K., Diehl, J. A., & Howe, P. H. (2017) · Nature Cell Biology · doi:10.1038/ncb3595 · Cited by 357

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

Pintacuda, G., Wei, G., Roustan, C., Kirmizitas, B. A., Solcan, N., Cerase, A., Castelló, A., Mohammed, S., Moindrot, B., Nesterova, T. B., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.013 · Cited by 356

TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA

Flynn, R. L., Centore, R. C., O’Sullivan, R. J., Rai, R., Tse, A., Songyang, Z., Chang, S. S., Karlseder, J., & Zou, L. (2011) · Nature · doi:10.1038/nature09772 · Cited by 355

Translating Dosage Compensation to Trisomy 21

Jiang, J., Jing, Y.-C., Cost, G., Chiang, J.-C., Kolpa, H. J., Cotton, A. M., Carone, D. M., Carone, B. R., Shivak, D. A., Guschin, D., et al. (2013) · Nature · doi:10.1038/nature12394 · Cited by 349

GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability

Hu, W. L., Jin, L., Xu, A., Wang, Y. F., Thorne, R. F., Zhang, X. D., & Wu, M. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0066-7 · Cited by 346

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

Lubelsky, Y., & Ulitsky, I. (2018) · Nature · doi:10.1038/nature25757 · Cited by 342

Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

West, J. A., Mito, M., Kurosaka, S., Takumi, T., Tanegashima, C., Chujo, T., Yanaka, K., Kingston, R. E., Hirose, T., Bond, C. S., et al. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201601071 · Cited by 338

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

Anderson, K. M., Anderson, D. M., McAnally, J., Shelton, J. M., Bassel‐Duby, R., & Olson, E. N. (2016) · Nature · doi:10.1038/nature20128 · Cited by 334

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

Postepska‐Igielska, A., Blank-Giwojna, A., Gasri-Plotnitsky, L., Schmitt, N., Dold, A., Ginsberg, D., & Grummt, I. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.001 · Cited by 331

HOTAIR Forms an Intricate and Modular Secondary Structure

Somarowthu, S., Łęgiewicz, M., Chillón, I., Marcia, M., Liu, F., & Pyle, A. M. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.03.006 · Cited by 326

Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

Isoda, T., Moore, A. J., He, Z., Chandra, V. K., Aida, M., Denholtz, M., van Hamburg, J. P., Fisch, K. M., Chang, A. N., Fahl, S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.001 · Cited by 323

Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence

Balk, B., Maicher, A., Dees, M., Klermund, J., Luke-Glaser, S., Bender, K., & Luke, B. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2662 · Cited by 322

Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation

Malakar, P., Shilo, A., Mogilevsky, A., Stein, I., Pikarsky, E., Nevo, Y., Benyamini, H., Elgavish, S., Zong, X., Prasanth, K. V., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-16-1508 · Cited by 322

Splicing regulation by long noncoding RNAs

Romero-Barrios, N., Legascue, M. F., Benhamed, M., Ariel, F., & Crespi, M. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky095 · Cited by 319

Transcript-RNA-templated DNA recombination and repair

Keskin, H., Shen, Y., Huang, F., Patel, M., Yang, T., Ashley, K., Mazin, A. V., & Storici, F. (2014) · Nature · doi:10.1038/nature13682 · Cited by 316

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

Rackham, O., Shearwood, A.-M. J., Mercer, T. R., Davies, S. M. K., Mattick, J. S., & Filipovska, A. (2011) · RNA · doi:10.1261/rna.029405.111 · Cited by 316

GADD45A binds R-loops and recruits TET1 to CpG island promoters

Arab, K., Karaulanov, E., Musheev, M. U., Trnka, P., Schäfer, A., Grummt, I., & Niehrs, C. (2018) · Nature Genetics · doi:10.1038/s41588-018-0306-6 · Cited by 315

Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

Guo, C., Ma, X.-K., Xing, Y., Zheng, C.-C., Xu, Y.-F., Shan, L., Zhang, J., Wang, S., Wang, Y., Carmichael, G., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.006 · Cited by 315

Stress-induced transcription of satellite III repeats

Jolly, C., Metz, A., Govin, J., Vigneron, M., Turner, B. M., Khochbin, S., & Vourc’h, C. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200306104 · Cited by 314

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

Cai, Z., Cao, C., Ji, L., Ye, R., Wang, D., Xia, C., Wang, S., Du, Z., Hu, N., Yu, X., et al. (2020) · Nature · doi:10.1038/s41586-020-2249-1 · Cited by 310

GRID-seq reveals the global RNA–chromatin interactome

Li, X., Zhou, B., Chen, L., Gou, L., Li, H., & Fu, X. (2017) · Nature Biotechnology · doi:10.1038/nbt.3968 · Cited by 304

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

Yin, Y., Yan, P., Lu, J. Y., Song, G., Zhu, Y., Li, Z., Zhao, Y. C., Shen, B., Huang, X., Zhu, H., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.03.007 · Cited by 303

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

Fanucchi, S., Fok, E. T., Dalla, E., Shibayama, Y., Börner, K., Chang, E. Y., Stoychev, S., Imakaev, M., Grimm, D., Wang, K., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0298-2 · Cited by 303

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Fei, J., Jadaliha, M., Harmon, T. S., Li, I. T. S., Hua, B., Hao, Q., Holehouse, A. S., Reyer, M., Sun, Q., Freier, S. M., et al. (2017) · Journal of Cell Science · doi:10.1242/jcs.206854 · Cited by 300

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

Saldaña-Meyer, R., Rodriguez-Hernaez, J., Escobar, T. M., Nishana, M., Jácome-López, K., Nora, E. P., Bruneau, B. G., Tsirigos, A., Furlan-Magaril, M., Skok, J. A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.015 · Cited by 299

Long Noncoding RNA TARID Directs Demethylation and Activation of the Tumor Suppressor TCF21 via GADD45A

Arab, K., Park, Y. J., Lindroth, A. M., Schäfer, A., Oakes, C. C., Weichenhan, D., Lukanova, A., Lundin, E., Risch, A., Meister, M. A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.031 · Cited by 297

The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

Kotzin, J. J., Spencer, S. P., McCright, S. J., Kumar, D. B. U., Collet, M. A., Mowel, W. K., Elliott, E. N., Uyar, A., Makiya, M. A., Dunagin, M. C., et al. (2016) · Nature · doi:10.1038/nature19346 · Cited by 296

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

Schlackow, M., Nojima, T., Gomes, T., Dhir, A., Carmo‐Fonseca, M., & Proudfoot, N. J. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.11.029 · Cited by 295

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

Ariel, F., Lucero, L. E., Christ, A., Mammarella, M. F., Jégu, T., Veluchamy, A., Mariappan, K. G., Latrasse, D., Blein, T., Liu, C., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.015 · Cited by 291

Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1

Mohammad, F., Mondal, T., Guseva, N., Pandey, G. K., & Kanduri, C. (2010) · Development · doi:10.1242/dev.048181 · Cited by 290

Functional characterization of the TERRA transcriptome at damaged telomeres

Porro, A., Feuerhahn, S., Delafontaine, J., Riethman, H. C., Rougemont, J., & Lingner, J. (2014) · Nature Communications · doi:10.1038/ncomms6379 · Cited by 289

Genome-wide characterization of mammalian promoters with distal enhancer functions

Dao, L. T. M., Galindo-Albarrán, A. O., Castro-Mondragon, J. A., Andrieu-Soler, C., Medina-Rivera, A., Souaid, C., Charbonnier, G., Griffon, A., Vanhille, L., Stephen, T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3884 · Cited by 281

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAsPreprint

Melé, M., Mattioli, K., Mallard, W., Shechner, D. M., Gerhardinger, C., & Rinn, J. L. (2016) · Genome Research · doi:10.1101/gr.214205.116 · Cited by 275

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

Rosenberg, A. B., Patwardhan, R. P., Shendure, J., & Seelig, G. (2015) · Cell · doi:10.1016/j.cell.2015.09.054 · Cited by 265

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

Lagarde, J., Uszczyńska-Ratajczak, B., Carbonell, S., Pérez-Lluch, S., Abad, A., Davis, C., Gingeras, T., Frankish, A., Harrow, J., Guigó, R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3988 · Cited by 265

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

Novikova, I. V., Hennelly, S. P., & Sanbonmatsu, K. Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks071 · Cited by 264

Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA

Audas, T. E., Jacob, M. D., & Lee, S. B. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.012 · Cited by 263

Functional classification of long non-coding RNAs by k-mer content

Kirk, J. M., Kim, S. O., Inoue, K., Smola, M. J., Lee, D. M., Schertzer, M. D., Wooten, J. S., Baker, A. R., Sprague, D., Collins, D. W., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0207-8 · Cited by 261

The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice

Nakagawa, S., Shimada, M., Yanaka, K., Mito, M., Arai, T., Takahashi, E., Fujita, Y., Fujimori, T., Standaert, L., Marine, J., et al. (2014) · Development · doi:10.1242/dev.110544 · Cited by 260

RNA-DNA Triplex Formation by Long Noncoding RNAs

Li, Y., Syed, J., & Sugiyama, H. (2016) · Cell chemical biology · doi:10.1016/j.chembiol.2016.09.011 · Cited by 259

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

Peng, X., Gralinski, L. E., Armour, C. D., Ferris, M. T., Thomas, M. J., Proll, S. C., Bradel-Tretheway, B., Korth, M. J., Castle, J. C., Biery, M. C., et al. (2010) · mBio · doi:10.1128/mbio.00206-10 · Cited by 256

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

Yang, F., Deng, X., Ma, W., Berletch, J. B., Rabaia, N. A., Wei, G., Moore, J. M., Filippova, G. N., Xu, J., Liu, Y., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0618-0 · Cited by 255

Unlinking an lncRNA from Its Associated cis Element

Paralkar, V. R., Taborda, C., Huang, P., Yao, Y., Kossenkov, A. V., Prasad, R., Luan, J. Y., Davies, J. O. J., Hughes, J. R., Hardison, R. C., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.029 · Cited by 253

Long Non-coding RNA NEAT1: A Novel Target for Diagnosis and Therapy in Human Tumors

Dong, P., Xiong, Y., Yue, J., Hanley, S. J. B., Kobayashi, N., Todo, Y., & Watari, H. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00471 · Cited by 250

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56

Jain, A. K., Xi, Y., McCarthy, R. L., Allton, K. L., Akdemir, K. C., Patel, L. R., Aronow, B. J., Lin, C., Li, W., Yang, L., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.039 · Cited by 249

The role of transcription in shaping the spatial organization of the genome

van Steensel, B., & Furlong, E. E. M. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0114-6 · Cited by 247

A long noncoding RNA associated with susceptibility to celiac disease

Castellanos–Rubio, A., Fernández‐Jiménez, N., Kratchmarov, R., Luo, X., Bhagat, G., Green, P. H. R., Schneider, R. J., Kiledjian, M., Bilbao, J. R., & Ghosh, S. (2016) · Science · doi:10.1126/science.aad0467 · Cited by 245

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

Pérez‐Piñera, P., Ousterout, D. G., Brunger, J. M., Farin, A. M., Glass, K. A., Guilak, F., Crawford, G. E., Hartemink, A. J., & Gersbach, C. A. (2013) · Nature Methods · doi:10.1038/nmeth.2361 · Cited by 242

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fita, J., Rahim, A. B., Guigó, R., Vardy, L. A., & Johnson, R. (2016) · RNA · doi:10.1261/rna.053561.115 · Cited by 242

An inducible long noncoding RNA amplifies DNA damage signaling

Schmitt, A. M., Garcia, J. T., Hung, T., Flynn, R. A., Shen, Y., Qu, K., Payumo, A. Y., Peres-da-Silva, A., Brož, D. K., Baum, R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3673 · Cited by 242

Identification of RNA-binding proteins in exosomes capable of interacting with different types of RNA: RBP-facilitated transport of RNAs into exosomes

Statello, L., Maugeri, M., Garre, E., Nawaz, M., Wahlgren, J., Papadimitriou, A., Lundqvist, C., Lindfors, L., Collén, A., Sunnerhagen, P., et al. (2018) · PLOS ONE · doi:10.1371/journal.pone.0195969 · Cited by 242

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boqué-Sastre, R., Soler, M., Oliveira-Mateos, C., Portela, A., Moutinho, C., Sayols, S., Villanueva, A., Esteller, M., & Guil, S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421197112 · Cited by 240

Negative regulation of the interferon response by an interferon-induced long non-coding RNA

Kambara, H., Niazi, F., Kostadinova, L., Moonka, D., Siegel, C., Post, A. B., Carnero, E., Barriocanal, M., Fortes, P., Anthony, D. D., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku713 · Cited by 237

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

Li, J., Landan, G., Pomerantz, M. M., Jaschek, R., Herman, P. K., Reich, D., Yan, C., Khalid, O. S., Kantoff, P. W., Oh, W. K., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000597 · Cited by 235

PARTICLE, a Triplex-Forming Long ncRNA, Regulates Locus-Specific Methylation in Response to Low-Dose Irradiation

O’Leary, V. B., Ovsepian, S. V., Carrascosa, L. G., Buske, F. A., Radulović, V., Niyazi, M., Moertl, S., Trau, M., Atkinson, M. J., & Anastasov, N. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.043 · Cited by 232

HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNARMRPPreprint

Noh, J. H., Kim, K. M., Abdelmohsen, K., Yoon, J., Panda, A. C., Munk, R. B., Kim, J., Curtis, J., Moad, C. A., Wöhler, C., et al. (2016) · Genes & Development · doi:10.1101/gad.276022.115 · Cited by 232

Single-cell transcriptome sequencing: recent advances and remaining challenges

Liu, S., & Trapnell, C. (2016) · F1000Research · doi:10.12688/f1000research.7223.1 · Cited by 230

U1 snRNP regulates chromatin retention of noncoding RNAs

Yin, Y., Lu, J., Zhang, X., Shao, W., Xu, Y., Li, P., Hong, Y., Cui, L., Shan, G., Tian, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2105-3 · Cited by 229

Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening

Esposito, R., Bosch, N., Lanzós, A., Polidori, T., Pulido-Quetglas, C., & Johnson, R. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.01.019 · Cited by 223

The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

Marín-Béjar, O., Mas, A. M., González, J., Martínez, D., Athie, A., Morales, X., Galduroz, M., Raimondi, I., Grossi, E., Guo, S., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1331-y · Cited by 223

The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation

Beckedorff, F., Ayupe, A. C., Crocci-Souza, R., Amaral, M. S., Nakaya, H. I., Soltys, D. T., Menck, C. F. M., Reis, E. M. R., & Verjovski‐Almeida, S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003705 · Cited by 221

ANRIL: A lncRNA at the CDKN2A/B Locus With Roles in Cancer and Metabolic Disease

Kong, Y., Hsieh, C.-H., & Alonso, L. C. (2018) · Frontiers in Endocrinology · doi:10.3389/fendo.2018.00405 · Cited by 216

Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

Uroda, T., Anastasakou, E., Rossi, A., Teulon, J., Pellequer, J., Annibale, P., Pessey, O., Inga, A., Chillón, I., & Marcia, M. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.025 · Cited by 204

Long noncoding RNA XIST expedites metastasis and modulates epithelial–mesenchymal transition in colorectal cancer

Chen, D.-L., Chen, L.-Z., Lu, Y., Zhang, D.-S., Zeng, Z.-L., Pan, Z.-Z., Huang, P., Wang, F.-H., Li, Y., Ju, H., et al. (2017) · Cell Death and Disease · doi:10.1038/cddis.2017.421 · Cited by 197

HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice

Luo, H., Zhu, G., Xu, J., Lai, Q., Yan, B., Guo, Y., Fung, T. K., Zeisig, B. B., Cui, Y., Zha, J., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.10.011 · Cited by 195

A protein assembly mediates Xist localization and gene silencing

Pandya‐Jones, A., Markaki, Y., Serizay, J., Chitiashvili, T., Mancia, W., Damianov, A., Chronis, C., Papp, B., Chen, C., McKee, R., et al. (2020) · Nature · doi:10.1038/s41586-020-2703-0 · Cited by 195

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

Sánchez, Y., Segura, V., Marín-Béjar, O., Athie, A., Marchese, F. P., González, J., Bujanda, L., Guo, S., Matheu, A., & Huarte, M. (2014) · Nature Communications · doi:10.1038/ncomms6812 · Cited by 194

Stress-induced Nuclear Bodies Are Sites of Accumulation of Pre-mRNA Processing Factors

Denegri, M., Chiodi, I., Corioni, M., Cobianchi, F., Riva, S., & Biamonti, G. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.11.3502 · Cited by 193

Rapid evolutionary turnover underlies conserved lncRNA–genome interactionsPreprint

Quinn, J. J., Zhang, Q. C., Georgiev, P., Ilik, İ., Akhtar, A., & Chang, H. Y. (2016) · Genes & Development · doi:10.1101/gad.272187.115 · Cited by 190

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., PCAWG Drivers and Functional Interpretation Group, Abascal, F., Amin, S. B., Bader, G. D., et al. (2020) · Communications Biology · doi:10.1038/s42003-019-0741-7 · Cited by 189

PRC2 is dispensable for HOTAIR‐mediated transcriptional repression

Portoso, M., Ragazzini, R., Brenčič, Ž., Moiani, A., Michaud, A., Vassilev, I., Wassef, M. A., Servant, N., Sargueil, B., & Margueron, R. (2017) · The EMBO Journal · doi:10.15252/embj.201695335 · Cited by 187

Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5

Kim, T., Cui, R., Jeon, Y.-J., Lee, J. H., Lee, J., Sim, H., Park, J. K., Fadda, P., Tili, E., Nakanishi, H., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400350111 · Cited by 186

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

Nojima, T., Tellier, M., Foxwell, J., de Almeida, C. R., Tan‐Wong, S. M., Dhir, S., Dujardin, G., Dhir, A., Murphy, S., & Proudfoot, N. J. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.011 · Cited by 181

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers

Gao, Y., Wang, P., Wang, Y., Ma, X., Zhi, H., Zhou, D., Li, X., Fang, Y., Shen, W., Xu, Y., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1096 · Cited by 180

Detection of RNA–DNA binding sites in long noncoding RNAs

Kuo, C., Hänzelmann, S., Cetin, N. S., Frank, S., Zajzon, B., Derks, J.-P., Akhade, V. S., Ahuja, G., Kanduri, C., Grummt, I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz037 · Cited by 180

Long Non-Coding RNAs Control Hematopoietic Stem Cell Function

Luo, M., Jeong, M., Sun, D., Park, H. J., Rodriguez, B. A. T., Xia, Z., Yang, L., Zhang, X., Sheng, K., Darlington, G., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.02.002 · Cited by 179

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

Marques, A. C., Hughes, J. R., Graham, B., Kowalczyk, M. S., Higgs, D. R., & Ponting, C. P. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r131 · Cited by 178

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

Colognori, D., Sunwoo, H., Kriz, A. J., Wang, C., & Lee, J. T. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.015 · Cited by 177

LncRNA‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

Ninomiya, K., Adachi, S., Natsume, T., Iwakiri, J., Terai, G., Asai, K., & Hirose, T. (2019) · The EMBO Journal · doi:10.15252/embj.2019102729 · Cited by 171

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Bonetti, A., Agostini, F., Suzuki, A. M., Hashimoto, K., Pascarella, G., Gimenez, J., Roos, L., Nash, A. J., Ghilotti, M., Cameron, C. J. F., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14337-6 · Cited by 168

Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

Chakraborty, A., Tapryal, N., Venkova, T., Horikoshi, N., PANDITA, R. K., Sarker, A. H., Sarkar, P. S., Pandita, T. K., & Hazra, T. K. (2016) · Nature Communications · doi:10.1038/ncomms13049 · Cited by 166

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

Bell, J. C., Jukam, D., Teran, N. A., Risca, V. I., Smith, O. K., Johnson, W. L., Skotheim, J. M., Greenleaf, W. J., & Straight, A. F. (2018) · eLife · doi:10.7554/elife.27024 · Cited by 166

R-Loops Promote Antisense Transcription across the Mammalian Genome

Tan‐Wong, S. M., Dhir, S., & Proudfoot, N. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.002 · Cited by 164

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Hawkes, E., Hennelly, S. P., Novikova, I. V., Irwin, J. A., Dean, C., & Sanbonmatsu, K. Y. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.08.045 · Cited by 163

Mitotic Transcription Installs Sgo1 at Centromeres to Coordinate Chromosome Segregation

Liu, H., Qu, Q., Warrington, R. T., Rice, A. M., Cheng, N., & Yu, H. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.018 · Cited by 162

A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival

Yap, K., Mukhina, S., Zhang, G., Tan, J. S. C., Ong, H. S., & Makeyev, E. V. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.08.041 · Cited by 162

When Long Noncoding Becomes Protein Coding

Hartford, C. C. R., & Lal, A. (2020) · Molecular and Cellular Biology · doi:10.1128/mcb.00528-19 · Cited by 160

Roles of Puf proteins in mRNA degradation and translation

Miller, M. A., & Olivas, W. M. (2010) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.69 · Cited by 159

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

Wu, H., Yin, Q.-F., Luo, Z., Yao, R.-W., Zheng, C.-C., Zhang, J., Xiang, J., Yang, L. C., & Chen, L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.007 · Cited by 159

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

Lin, Y., Schmidt, B. F., Bruchez, M. P., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky046 · Cited by 159

Role of MYC-Regulated Long Noncoding RNAs in Cell Cycle Regulation and Tumorigenesis

Kim, T., Jeon, Y.-J., Cui, R., Lee, J.-H., Peng, Y., Kim, S.-H., Tili, E., Alder, H., & Croce, C. M. (2015) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/dju505 · Cited by 153

Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex

Zuckerman, B. M., Ron, M., Mikl, M., Segal, E., & Ulitsky, I. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.05.013 · Cited by 153

TERRA recruitment of polycomb to telomeres is essential for histone trymethylation marks at telomeric heterochromatin

Montero, J. J., de Silanes, I. L., Megı́as, D., Fraga, M. F., Castells-García, Á., & Blasco, M. A. (2018) · Nature Communications · doi:10.1038/s41467-018-03916-3 · Cited by 152

A BRCA1‐interacting lncRNA regulates homologous recombination

Sharma, V., Khurana, S., Kubben, N., Abdelmohsen, K., Oberdoerffer, P., Gorospe, M., & Misteli, T. (2015) · EMBO Reports · doi:10.15252/embr.201540437 · Cited by 151

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

Rosa, S., Duncan, S., & Dean, C. (2016) · Nature Communications · doi:10.1038/ncomms13031 · Cited by 151

Trials and Tribulations of MicroRNA Therapeutics

Seyhan, A. A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031469 · Cited by 381

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Bartosovic, M., & Castelo-Branco, G. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01535-4 · Cited by 146

The Information Theory of Aging

Lu, Y. R., Tian, X., & Sinclair, D. A. (2023) · Nature Aging · doi:10.1038/s43587-023-00527-6 · Cited by 141

Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders

Aliperti, V., Skonieczna, J., & Cerase, A. (2021) · Non-Coding RNA · doi:10.3390/ncrna7020036 · Cited by 137

State-of-the-Art OMICS Strategies against Toxic Effects of Heavy Metals in Plants: A Review

Rahman, S. U., Nawaz, M. F., Gul, S., Yasin, G., Hussain, B., Li, Y., & Cheng, H. (2022) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2022.113952 · Cited by 106

Direct relationship between the level of p53 stabilization induced by rRNA synthesis-inhibiting drugs and the cell ribosome biogenesis rate

Scala, F., Brighenti, E., Govoni, M., Imbrogno, E., Fornari, F., Treré, D., Montanaro, L., & Derenzini, M. (2015) · Oncogene · doi:10.1038/onc.2015.147 · Cited by 59

Regulation of ribosome biogenesis within the nucleolus

Leary, D. J., & Huang, S. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03143-x · Cited by 132

Nucleolar stress and sugar response in plants

Maekawa, S., & Yanagisawa, S. (2018) · Plant Signaling & Behavior · doi:10.1080/15592324.2018.1442975 · Cited by 13

A review from biological mapping to computation-based subcellular localization

Li, J., Zou, Q., & Yuan, L. (2023) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2023.04.015 · Cited by 21

Critical role for nucleostemin in protein synthesis and muscle cell differentiation

Romanova, L. G., Hirai, H., Asakura, A., et al. (2008) · The FASEB Journal · doi:10.1096/fasebj.22.1_supplement.1060.1