The emerging role of lncRNAs in cancer

Signatures of mutational processes in human cancer

Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990

Natural RNA circles function as efficient microRNA sponges

Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013) · Nature · doi:10.1038/nature11993 · Cited by 7,985

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

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M.-C., Hung, T., Argani, P., Rinn, J. L., et al. (2010) · Nature · doi:10.1038/nature08975 · Cited by 5,218

Landscape of transcription in human cells

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187

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

Derrien, T., Johnson, R., Bussotti, G., 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 5,061

Non-coding RNAs in human disease

Esteller, M. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3074 · Cited by 4,825

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., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P. J., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,244

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098

The landscape of somatic copy-number alteration across human cancers

Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., & Rinn, J. L. (2011) · Genes & Development · doi:10.1101/gad.17446611 · Cited by 3,502

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., & Chang, H. Y. (2010) · Science · doi:10.1126/science.1192002 · Cited by 3,290

Cancer epigenetics: from mechanism to therapy

Dawson, M. A., & Kouzarides, T. (2012) · Cell · doi:10.1016/j.cell.2012.06.013 · Cited by 3,203

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825

The landscape of long noncoding RNAs in the human transcriptome

Iyer, M. K., Niknafs, Y. S., Malik, R., Singhal, U., Sahu, A., Hosono, Y., Barrette, T. R., Prensner, J. R., Evans, J. R., Zhao, S., et al. (2015) · Nature Genetics · doi:10.1038/ng.3192 · Cited by 2,738

lincRNAs: Genomics, Evolution, and Mechanisms

Ulitsky, I., & Bartel, D. P. (2013) · Cell · doi:10.1016/j.cell.2013.06.020 · Cited by 2,608

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

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W. J., & Pandolfi, P. P. (2010) · Nature · doi:10.1038/nature09144 · Cited by 2,323

Modular regulatory principles of large non-coding RNAs

Guttman, M., & Rinn, J. L. (2012) · Nature · doi:10.1038/nature10887 · Cited by 2,265

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

Tripathi, V., Ellis, J. D., Shen, Z., Song, D. Y., Pan, Q., Watt, A. T., Freier, S. M., Bennett, C. F., Sharma, A., Bubulya, P. A., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.08.011 · Cited by 2,219

MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer

Ji, P., Diederichs, S., Wang, W., Böing, S., Metzger, R., Schneider, P. M., Tidow, N., Brandt, B., Buerger, H., Bulk, E., et al. (2003) · Oncogene · doi:10.1038/sj.onc.1206928 · Cited by 2,189

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,858

RNA-guided genetic silencing systems in bacteria and archaea

Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851

The hallmarks of cancer: A long non-coding RNA point of view

Gutschner, T., & Diederichs, S. (2012) · RNA Biology · doi:10.4161/rna.20481 · Cited by 1,802

Ultraconserved Elements in the Human Genome

Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004) · Science · doi:10.1126/science.1098119 · Cited by 1,732

MicroRNAs and other non-coding RNAs as targets for anticancer drug development

Ling, H., Fabbri, M., & Calin, G. A. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4140 · Cited by 1,465

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

RNA Targeting Therapeutics: Molecular Mechanisms of Antisense Oligonucleotides as a Therapeutic Platform

Bennett, C. F., & Swayze, E. E. (2010) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.010909.105654 · Cited by 1,374

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 1,269

Noncoding RNA Gas5 Is a Growth Arrest– and Starvation-Associated Repressor of the Glucocorticoid Receptor

Kino, T., Hurt, D. E., Ichijo, T., Nader, N., & Chrousos, G. P. (2010) · Science Signaling · doi:10.1126/scisignal.2000568 · Cited by 1,231

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H., & Bartel, D. P. (2011) · Cell · doi:10.1016/j.cell.2011.11.055 · 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., Wang, P., et al. (2011) · Nature Genetics · doi:10.1038/ng.848 · Cited by 1,163

RNA therapeutics: beyond RNA interference and antisense oligonucleotides

Kole, R., Krainer, A. R., & Altman, S. (2012) · Nature Reviews Drug Discovery · doi:10.1038/nrd3625 · Cited by 1,152

An improved zinc-finger nuclease architecture for highly specific genome editing

Miller, J. C., Holmes, M. C., Wang, J., Guschin, D. Y., Lee, Y.-L., Rupniewski, I., Beausejour, C. M., Waite, A. J., Wang, N. S., Kim, K. A., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1319 · Cited by 1,051

DD3: a new prostate-specific gene, highly overexpressed in prostate cancer.

Bussemakers, M. J. G., van Bokhoven, A., Verhaegh, G. W. C. T., Smit, F. P., Karthaus, H. F. M., Schalken, J. A., Debruyne, F. M. J., Ru, N., & Isaacs, W. B. (1999) · PubMed · Cited by 1,051

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 1,029

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15INK4B tumor suppressor gene

Kotake, Y., Nakagawa, T., Kitagawa, K., Suzuki, S., Liu, N., Kitagawa, M., & Xiong, Y. (2011) · Oncogene · doi:10.1038/onc.2010.568 · Cited by 1,001

LncRNA: A link between RNA and cancer

Yang, G., Lu, X., & Yuan, L. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.08.012 · Cited by 991

The evolution of lncRNA repertoires and expression patterns in tetrapods

Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J. C., Grützner, F., & Kaessmann, H. (2014) · Nature · doi:10.1038/nature12943 · Cited by 984

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

Engreitz, J. M., Pandya-Jones, A., McDonel, P., Shishkin, A., Sirokman, K., Surka, C., Kadri, S., Xing, J., Goren, A., Lander, E. S., et al. (2013) · Science · doi:10.1126/science.1237973 · Cited by 983

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

Grote, P., Wittler, L., Hendrix, D., 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 975

LincRNA-p21 Suppresses Target mRNA Translation

Yoon, J.-H., Abdelmohsen, K., Srikantan, S., Yang, X., Martindale, J. L., De, S., Huarte, M., Zhan, M., Becker, K. G., & Gorospe, M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.027 · Cited by 962

Non-coding recurrent mutations in chronic lymphocytic leukaemia

Puente, X. S., Beà, S., Valdés-Mas, R., Villamor, N., Gutiérrez-Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., et al. (2015) · Nature · doi:10.1038/nature14666 · Cited by 829

The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

Keniry, A., Oxley, D., Monnier, P., Kyba, M., Dandolo, L., Smits, G., & Reik, W. (2012) · Nature Cell Biology · doi:10.1038/ncb2521 · Cited by 814

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

Yu, W., Gius, D., Onyango, P., Muldoon-Jacobs, K., Karp, J., Feinberg, A. P., & Cui, H. (2008) · Nature · doi:10.1038/nature06468 · Cited by 801

GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer

Mourtada-Maarabouni, M., Pickard, M. R., Hedge, V. L., Farzaneh, F., & Williams, G. T. (2009) · Oncogene · doi:10.1038/onc.2008.373 · Cited by 775

Characterization of HULC, a Novel Gene With Striking Up-Regulation in Hepatocellular Carcinoma, as Noncoding RNA

Panzitt, K., Tschernatsch, M. M. O., Guelly, C., Moustafa, T., Stradner, M., Strohmaier, H. M., Buck, C. R., Denk, H., Schroeder, R., Trauner, M., et al. (2007) · Gastroenterology · doi:10.1053/j.gastro.2006.08.026 · Cited by 771

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

Xiang, J.-F., Yin, Q.-F., Chen, T., Zhang, Y., Zhang, X.-O., Wu, Z., Zhang, S., Wang, H.-B., Ge, J., Lu, X., et al. (2014) · Cell Research · doi:10.1038/cr.2014.35 · Cited by 726

PVT1 dependence in cancer with MYC copy-number increase

Tseng, Y.-Y., Moriarity, B. S., Gong, W., Akiyama, R., Tiwari, A., Kawakami, H., Ronning, P., Reuland, B., Guenther, K., Beadnell, T. C., et al. (2014) · Nature · doi:10.1038/nature13311 · Cited by 722

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 720

Ultraconserved Regions Encoding ncRNAs Are Altered in Human Leukemias and Carcinomas

Calin, G. A., Liu, C.-G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E. J., Wojcik, S. E., et al. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.07.027 · Cited by 719

MALAT1 — a paradigm for long noncoding RNA function in cancer

Gutschner, T., Hämmerle, M., & Diederichs, S. (2013) · Journal of Molecular Medicine · doi:10.1007/s00109-013-1028-y · Cited by 719

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 716

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription

Zhang, F., Cong, L., Lodato, S., Kosuri, S., Church, G. M., & Arlotta, P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1775 · Cited by 712

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

West, J. A., Davis, C. P., Sunwoo, H., Simon, M. D., Sadreyev, R. I., Wang, P. I., Tolstorukov, M. Y., & Kingston, R. E. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.012 · Cited by 709

DD3PCA3-based Molecular Urine Analysis for the Diagnosis of Prostate Cancer

Hessels, D., Klein Gunnewiek, J. M. T., van Oort, I., Karthaus, H. F. M., van Leenders, G. J. L., van Balken, B., Kiemeney, L. A., Witjes, J. A., & Schalken, J. A. (2003) · European Urology · doi:10.1016/s0302-2838(03)00201-x · Cited by 704

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., Spence, M., et al. (2013) · eLife · doi:10.7554/elife.01749 · Cited by 678

A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial–mesenchymal transition

Beltran, M., Puig, I., Peña, C., García, J. M., Álvarez, A. B., Peña, R., Bonilla, F., & de Herreros, A. G. (2008) · Genes & Development · doi:10.1101/gad.455708 · 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 676

The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex

Prensner, J. R., Iyer, M. K., Sahu, A., Asangani, I. A., Cao, Q., Patel, L., Vergara, I. A., Davicioni, E., Erho, N., Ghadessi, M., et al. (2013) · Nature Genetics · doi:10.1038/ng.2771 · Cited by 669

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

Yang, L., Lin, C., Jin, C., Yang, J. C., Tanasa, B., Li, W., Merkurjev, D., Ohgi, K. A., Meng, D., Zhang, J., et al. (2013) · Nature · doi:10.1038/nature12451 · Cited by 657

Activation of p53 by MEG3 Non-coding RNA

Zhou, Y., Zhong, Y., Wang, Y., Zhang, X., Batista, D. L., Gejman, R., Ansell, P. J., Zhao, J., Weng, C., & Klibanski, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702029200 · Cited by 653

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 652

The H19 Non-Coding RNA Is Essential for Human Tumor Growth

Matouk, I. J., DeGroot, N., Mezan, S., Ayesh, S., Abu-lail, R., Hochberg, A., & Galun, E. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000845 · Cited by 650

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

Chakravarty, D., Sboner, A., Nair, S. S., Giannopoulou, E., Li, R., Hennig, S., Mosquera, J. M., Pauwels, J., Park, K., Kossai, M., et al. (2014) · Nature Communications · doi:10.1038/ncomms6383 · Cited by 621

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 cancer

Ling, H., Spizzo, R., Atlasi, Y., Nicoloso, M., Shimizu, M., Redis, R. S., Nishida, N., Gafà, R., Song, J., Guo, Z., et al. (2013) · Genome Research · doi:10.1101/gr.152942.112 · Cited by 602

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

Zhang, B., Arun, G., Mao, Y. S., Lazar, Z., Hung, G., Bhattacharjee, G., Xiao, X., Booth, C. J., Wu, J., Zhang, C., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.06.003 · Cited by 598

Non-coding recurrent mutations in chronic lymphocytic leukaemia

Puente, X. S., Beà, S., Valdés-Mas, R., Villamor, N., Gutiérrez-Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., et al. (2016) · Nature · doi:10.1038/nature18910 · Cited by 546

Exosomes as intercellular signalosomes and pharmacological effectors

Record, M., Subra, C., Silvente-Poirot, S., & Poirot, M. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2011.02.011 · Cited by 537

Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice

Yildirim, E., Kirby, J. E., Brown, D. E., Mercier, F. E., Sadreyev, R. I., Scadden, D. T., & Lee, J. T. (2013) · Cell · doi:10.1016/j.cell.2013.01.034 · Cited by 522

Towards a therapy for Angelman syndrome by targeting a long non-coding RNA

Meng, L., Ward, A. J., Chun, S., Bennett, C. F., Beaudet, A. L., & Rigo, F. (2015) · Nature · doi:10.1038/nature13975 · Cited by 518

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

Engreitz, J. M., Sirokman, K., McDonel, P., Shishkin, A. A., Surka, C., Russell, P., Grossman, S. R., Chow, A. Y., Guttman, M., & Lander, E. S. (2014) · Cell · doi:10.1016/j.cell.2014.08.018 · Cited by 500

Large non-coding RNAs: missing links in cancer?

Huarte, M., & Rinn, J. L. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq353 · Cited by 484

Repression of the Long Noncoding RNA-LET by Histone Deacetylase 3 Contributes to Hypoxia-Mediated Metastasis

Yang, F., Huo, X.-S., Yuan, S.-X., Zhang, L., Zhou, W.-P., Wang, F., & Sun, S.-H. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.010 · Cited by 477

lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals

Xing, Z., Lin, A., Li, C., Liang, K., Wang, S., Liu, Y., Park, P. K., Qin, L., Wei, Y., Hawke, D. H., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.013 · Cited by 447

The genomic binding sites of a noncoding RNA

Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B. A., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., & Kingston, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113536108 · Cited by 446

Promiscuous RNA binding by Polycomb repressive complex 2

Davidovich, C., Zheng, L., Goodrich, K. J., & Cech, T. R. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2679 · Cited by 440

Principles for the post-GWAS functional characterization of cancer risk loci

Freedman, M. L., Monteiro, A. N. A., Gayther, S. A., Coetzee, G. A., Risch, A., Plass, C., Casey, G., De Biasi, M., Carlson, C., Duggan, D., et al. (2011) · Nature Genetics · doi:10.1038/ng.840 · Cited by 438

P53-regulated long non-coding RNA TUG1 affects cell proliferation in human non-small cell lung cancer, partly through epigenetically regulating HOXB7 expression

Zhang, E.-B., Yin, D.-D., Sun, M., Kong, R., Liu, X.-H., You, L.-H., Han, L., Xia, R., Wang, K.-M., Yang, J.-S., et al. (2014) · Cell Death & Disease · doi:10.1038/cddis.2014.201 · Cited by 427

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 412

Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development

Eißmann, M., Gutschner, T., Hämmerle, M., Günther, S., Caudron-Herger, M., Groß, M., Schirmacher, P., Rippe, K., Braun, T., Zörnig, M., et al. (2012) · RNA Biology · doi:10.4161/rna.21089 · Cited by 395

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression

Cunnington, M. S., Santibanez Koref, M., Mayosi, B. M., Burn, J., & Keavney, B. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000899 · Cited by 379

A Functional Genomic Approach Identifies FAL1 as an Oncogenic Long Noncoding RNA that Associates with BMI1 and Represses p21 Expression in Cancer

Hu, X., Feng, Y., Zhang, D., Zhao, S. D., Hu, Z., Greshock, J., Zhang, Y., Yang, L., Zhong, X., Wang, L.-P., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.009 · Cited by 379

Long noncoding RNA ANRIL indicates a poor prognosis of gastric cancer and promotes tumor growth by epigenetically silencing of miR-99a/miR-449a

Zhang, E.-B., Kong, R., Yin, D.-D., You, L.-H., Sun, M., Han, L., Xu, T.-P., Xia, R., Yang, J.-S., De, W., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.1902 · Cited by 351

The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation

Pandey, G. K., Mitra, S., Subhash, S., Hertwig, F., Kanduri, M., Mishra, K., Fransson, S., Ganeshram, A., Mondal, T., Bandaru, S., et al. (2014) · Cancer Cell · doi:10.1016/j.ccell.2014.09.014 · Cited by 343

Translating dosage compensation to trisomy 21

Jiang, J., Jing, Y., Cost, G. J., Chiang, J.-C., Kolpa, H. J., Cotton, A. M., Carone, D. M., Carone, B. R., Shivak, D. A., Guschin, D. Y., et al. (2013) · Nature · doi:10.1038/nature12394 · Cited by 335

PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer

Srikantan, V., Zou, Z., Petrovics, G., Xu, L., Augustus, M., Davis, L., Livezey, J. R., Connell, T., Sesterhenn, I. A., Yoshino, K., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.22.12216 · Cited by 333

Junk DNA and the long non-coding RNA twist in cancer genetics

Ling, H., Vincent, K., Pichler, M., Fodde, R., Berindan-Neagoe, I., Slack, F. J., & Calin, G. A. (2015) · Oncogene · doi:10.1038/onc.2014.456 · Cited by 328

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

Li, L., Liu, B., Wapinski, O. L., Tsai, M.-C., Qu, K., Zhang, J., Carlson, J. C., Lin, M., Fang, F., Gupta, R. A., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.09.003 · Cited by 317

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

Nakagawa, S., Naganuma, T., Shioi, G., & Hirose, T. (2011) · Journal of Cell Biology · doi:10.1083/jcb.201011110 · Cited by 308

A long noncoding RNA connects c-Myc to tumor metabolism

Hung, C.-L., Wang, L.-Y., Yu, Y.-L., Chen, H.-W., Srivastava, S., Petrovics, G., & Kung, H.-J. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1415669112 · Cited by 302

Androgen‐responsive long noncoding RNA CTBP1‐AS promotes prostate cancer

Takayama, K., Horie‐Inoue, K., Katayama, S., Suzuki, T., Tsutsumi, S., Ikeda, K., Urano, T., Fujimura, T., Takagi, K., Takahashi, S., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.99 · Cited by 278

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

Perez-Llamas, C., & Lopez-Bigas, N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019541 · Cited by 265

PintlincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar, O., Marchese, F. P., Athie, A., Sánchez, Y., González, J., Segura, V., Huang, L., Moreno, I., Navarro, A., Monzó, M., et al. (2013) · Genome Biology · doi:10.1186/gb-2013-14-9-r104 · Cited by 265

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.-C., et al. (2014) · Development · doi:10.1242/dev.110544 · Cited by 259

The Long Non-Coding RNA PCAT-1 Promotes Prostate Cancer Cell Proliferation through cMyc

Prensner, J. R., Chen, W., Han, S., Iyer, M. K., Cao, Q., Kothari, V., Evans, J. R., Knudsen, K. E., Paulsen, M. T., Ljungman, M., et al. (2014) · Neoplasia · doi:10.1016/j.neo.2014.09.001 · Cited by 256

PCAT-1 , a Long Noncoding RNA, Regulates BRCA2 and Controls Homologous Recombination in Cancer

Prensner, J. R., Chen, W., Iyer, M. K., Cao, Q., Ma, T., Han, S., Sahu, A., Malik, R., Wilder-Romans, K., Navone, N., et al. (2014) · Cancer Research · doi:10.1158/0008-5472.can-13-3159 · Cited by 251

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

Ho, T.-T., Zhou, N., Huang, J., Koirala, P., Xu, M., Fung, R., Wu, F., & Mo, Y.-Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1198 · Cited by 244

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

Jia, L., Landan, G., Pomerantz, M., Jaschek, R., Herman, P., Reich, D., Yan, C., Khalid, O., Kantoff, P., Oh, W., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000597 · Cited by 237

Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human

Schorderet, P., & Duboule, D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002071 · Cited by 236

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 192

Long Non-Coding RNAs: Challenges for Diagnosis and Therapies

Sánchez, Y., & Huarte, M. (2013) · Nucleic Acid Therapeutics · doi:10.1089/nat.2012.0414 · 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. H., 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

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

Léveillé, N., Melo, C. A., Rooijers, K., Díaz-Lagares, A., Melo, S. A., Korkmaz, G., Lopes, R., Moqadam, F. A., Maia, A. R., Wijchers, P. J., et al. (2015) · Nature Communications · doi:10.1038/ncomms7520 · Cited by 183

Long non-coding RNAs and chromatin modifiers: Their place in the epigenetic code

Marchese, F. P., & Huarte, M. (2014) · Epigenetics · doi:10.4161/epi.27472 · Cited by 178

Long non-coding RNA HOTAIR in carcinogenesis and metastasis

Zhang, J., Zhang, P., Wang, L., Piao, H.-L., & Ma, L. (2014) · Acta Biochimica et Biophysica Sinica · doi:10.1093/abbs/gmt117 · Cited by 171

Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9

Han, J., Zhang, J., Chen, L., Shen, B., Zhou, J., Hu, B., Du, Y., Tate, P. H., Huang, X., & Zhang, W. (2014) · RNA Biology · doi:10.4161/rna.29624 · Cited by 168

Physiological roles of long noncoding RNAs: insight from knockout mice

Li, L., & Chang, H. Y. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.06.003 · Cited by 167

Methods for comprehensive experimental identification of RNA-protein interactions

McHugh, C. A., Russell, P., & Guttman, M. (2014) · Genome Biology · doi:10.1186/gb4152 · Cited by 166

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 158

The role of long non-coding RNAs in genome formatting and expression

Angrand, P., Vennin, C., Bourhis, X. L., & Adriaenssens, É. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00165 · Cited by 157

Polymorphisms in the H19 Gene and the Risk of Bladder Cancer

Verhaegh, G. W. C. T., Verkleij, L., Vermeulen, S. H. H. M., den Heijer, M., Witjes, J. A., & Kiemeney, L. A. L. M. (2008) · European Urology · doi:10.1016/j.eururo.2008.01.060 · Cited by 141

Tag SNPs in long non-coding RNA H19 contribute to susceptibility to gastric cancer in the Chinese Han population

Yang, C., Tang, R., Ma, X., Wang, Y., Luo, D., Xu, Z., Zhu, Y., & Yang, L. (2015) · Oncotarget · doi:10.18632/oncotarget.3840 · Cited by 131

Characterization of BCAR4, a novel oncogene causing endocrine resistance in human breast cancer cells

Godinho, M., Meijer, D., Setyono-Han, B., Dorssers, L. C. J., & van Agthoven, T. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22503 · Cited by 119

Deletion of PTENP1 Pseudogene in Human Melanoma

Poliseno, L., Haimovic, A., Christos, P. J., de Miera, E. C. V. Y. S., Shapiro, R. L., Pavlick, A. C., Berman, R. S., Darvishian, F., & Osman, I. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.232 · Cited by 102

The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer

Prensner, J. R., Sahu, A., Iyer, M. K., Malik, R., Chandler, B. C., Asangani, I. A., Poliakov, A., Vergara, I. A., Alshalalfa, M., Jenkins, R. B., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.1846 · Cited by 100

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs

Zheng, G. X. Y., Do, B. T., Webster, D. E., Khavari, P. A., & Chang, H. Y. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2842 · Cited by 98

MYC regulates the non-coding transcriptome

Hart, J. R., Roberts, T. C., Weinberg, M. S., Morris, K. V., & Vogt, P. K. (2014) · Oncotarget · doi:10.18632/oncotarget.3033 · Cited by 85

Androgen responsive intronic non-coding RNAs

Louro, R., Nakaya, H. I., Amaral, P., Festa, F., Sogayar, M. C., da Silva, A. M., Verjovski‐Almeida, S., & Reis, E. M. R. (2007) · BMC Biology · doi:10.1186/1741-7007-5-4 · Cited by 82

The long non-coding RNA ERIC is regulated by E2F and modulates the cellular response to DNA damage

Feldstein, O., Nizri, T., Doniger, T., Jacob, J., Rechavi, G., & Ginsberg, D. (2013) · Molecular Cancer · doi:10.1186/1476-4598-12-131 · Cited by 73

Androgen Receptor Overexpression in Prostate Cancer Linked to Purα Loss from a Novel Repressor Complex

Wang, L. G., Johnson, E. M., Kinoshita, Y., Babb, J. S., Buckley, M. T., Liebes, L., Melamed, J., Liu, X., Kurek, R., Ossowski, L., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-6017 · Cited by 70

Lessons from Functional Analysis of Genome-Wide Association Studies

Sur, I., Tuupanen, S., Whitington, T., Aaltonen, L. A., & Taipale, J. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-0789 · Cited by 68

Long noncoding RNAs as a novel component of the Myc transcriptional network

Winkle, M., van den Berg, A., Tayari, M. M., Sietzema, J. G., Terpstra, M. M., Kortman, G., de Jong, D., Visser, L., Diepstra, A., Kok, K., et al. (2015) · The FASEB Journal · doi:10.1096/fj.14-263889 · Cited by 55

Long non-coding RNAs: definitions, functions, challenges and recommendations

Mattick, J. S., Amaral, P. P., Carninci, P., Carpenter, S., Chang, H. Y., Chen, L.-L., Chen, R., Dean, C., Dinger, M. E., Fitzgerald, K. A., et al. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00566-8 · Cited by 2,356

Integrated genomic characterization of pancreatic ductal adenocarcinoma

Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., Robertson, A. G., Cherniack, A. D., Gupta, M., Getz, G., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.007 · Cited by 2,019

LNCipedia 5: towards a reference set of human long non-coding RNAs

Volders, P.-J., Anckaert, J., Verheggen, K., Nuytens, J., Martens, L., Mestdagh, P., & Vandesompele, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1031 · Cited by 547

Potential of long non‐coding RNAs in cancer patients: From biomarkers to therapeutic targets

Chandra Gupta, S., & Nandan Tripathi, Y. (2017) · International Journal of Cancer · doi:10.1002/ijc.30546 · Cited by 527

Long Noncoding RNA in Cancer: Wiring Signaling Circuitry

Lin, C., & Yang, L. (2018) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.11.008 · Cited by 488