LNCcation: lncRNA localization and function

Biomolecular condensates: organizers of cellular biochemistry

Banani, S. F., Lee, H. O., Hyman, A., & Rosen, M. (2017) · Nature reviews. Molecular cell biology · doi:10.1038/nrm.2017.7 · Cited by 5,574 · see citing works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works

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 · see citing works

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 5,017 · see citing works

Non-coding RNAs in human disease

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

Circular RNAs are abundant, conserved, and associated with ALU repeats

Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., Marzluff, W. F., & Sharpless, N. E. (2013) · RNA · doi:10.1261/rna.035667.112 · Cited by 4,388 · see citing works

Liquid phase condensation in cell physiology and disease

Shin, Y., & Brangwynne, C. P. (2017) · Science · doi:10.1126/science.aaf4382 · Cited by 4,184 · see citing works

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

Zheng, G., Dahl, J. A., Niu, Y., Fedorcsak, P., Huang, C.-M., Li, C. J., Vågbø, C. B., Shi, Y., Wang, W.-L., Song, S.-H., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.10.015 · Cited by 3,550 · see citing works

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 · cited 2× · see citing works

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

Brangwynne, C. P., Eckmann, C. R., Courson, D. S., Rybarska, A., Hoege, C., Gharakhani, J., Jülicher, F., & Hyman, A. A. (2009) · Science · doi:10.1126/science.1172046 · Cited by 3,215 · see citing works

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. J., & Brown, P. O. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030733 · Cited by 2,457 · see citing works

Modular regulatory principles of large non-coding RNAs

Guttman, M., & Rinn, J. L. (2012) · Nature · doi:10.1038/nature10887 · Cited by 2,257 · see citing works

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 2,223 · see citing works

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011) · Cell · doi:10.1016/j.cell.2011.10.002 · Cited by 2,187 · see citing works

Principles and Properties of Stress Granules

Protter, D. S. W., & Parker, R. (2016) · Trends in Cell Biology · doi:10.1016/j.tcb.2016.05.004 · Cited by 1,738 · see citing works

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

Zhao, J. C., Sun, B. K., Erwin, J. A., Song, J., & Lee, J. T. (2008) · Science · doi:10.1126/science.1163045 · Cited by 1,580 · see citing works

A Long Noncoding RNA Activated by TGF-β Promotes the Invasion-Metastasis Cascade in Hepatocellular Carcinoma

Yuan, J., Yang, F., Wang, F., Ma, J., Guo, Y., Tao, Q.-F., Liu, F., Pan, W. X., Wang, T.-T., Zhou, C., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.03.010 · Cited by 1,515 · see citing works

Stress granules and processing bodies are dynamically linked sites of mRNP remodeling

Kedersha, N., Stoecklin, G., Ayodele, M. O., Yacono, P. W., Lykke‐Andersen, J., Fritzler, M. J., Scheuner, D. L., Kaufman, R. J., Golan, D. E., & Anderson, P. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200502088 · Cited by 1,494 · see citing works

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 · see citing works

Structure and function of long noncoding RNAs in epigenetic regulation

Mercer, T. R., & Mattick, J. S. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2480 · Cited by 1,436 · see citing works

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

Martell, J. D., Ting, A. Y., Rhee, H., Zou, P., Udeshi, N. D., Mootha, V. K., & Carr, S. A. (2012) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 1,330 · see citing works

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 1,261 · see citing works

A micropeptide encoded by a putative long noncoding RNA regulates muscle performance

Anderson, D. M., Anderson, K. M., Chang, C.-L., Makarewich, C. A., Nelson, B. R., McAnally, J. R., Kasaragod, P., Shelton, J. M., Liou, J., Bassel-Duby, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.009 · Cited by 1,216 · see citing works

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

Roundtree, I. A., Luo, G., Zhang, Z. S., Wang, X., Zhou, T., Cui, Y., Sha, J., Huang, X., Guerrero, L., Xie, P., et al. (2017) · eLife · doi:10.7554/elife.31311 · Cited by 1,213 · see citing works

The Landscape of long noncoding RNA classification

Laurent, G. S., Wahlestedt, C., & Kapranov, P. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.007 · Cited by 1,192 · see citing works

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

Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H. L., & Bartel, D. P. (2011) · Cell · doi:10.1016/j.cell.2011.11.055 · Cited by 1,162 · see citing works

Characterization of human plasma-derived exosomal RNAs by deep sequencing

Huang, X., Yuan, T., Tschannen, M., Sun, Z., Jacob, H. J., Du, M., Liang, M., Dittmar, R. L., Liu, Y. U., Liang, M., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-319 · Cited by 1,046 · see citing works

Linking Long Noncoding RNA Localization and Function

Chen, L. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.07.003 · Cited by 1,042 · see citing works

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 1,001 · see citing works

Stress Granule Assembly Is Mediated by Prion-like Aggregation of TIA-1

Farny, N. G., Kedersha, N., Ayodele, M. O., Shen, L., Stoecklin, G., Dember, L. M., & Anderson, P. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-08-0715 · Cited by 1,000 · see citing works

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 997 · see citing works

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 · see citing works

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

Fustin, J., Doi, M., Yamaguchi, Y., Hayashi, H., Nishimura, S., Yoshida, M., Isagawa, T., Morioka, M. S., Kakeya, H., Manabe, I., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.026 · Cited by 980 · see citing works

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P., & Krause, H. M. (2007) · Cell · doi:10.1016/j.cell.2007.08.003 · Cited by 967 · see citing works

LincRNA-p21 Suppresses Target mRNA Translation

Yoon, J., 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 · see citing works

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 · see citing works

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 903 · see citing works

RNA granules: post-transcriptional and epigenetic modulators of gene expression

Anderson, P., & Kedersha, N. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2694 · Cited by 866 · see citing works

Nuclear SpecklesPreprint

Spector, D. L., & Lamond, A. I. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000646 · Cited by 842 · see citing works

XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure.

Clemson, C., McNeil, J. A., Willard, H. F., et al. (1996) · The Journal of Cell Biology · doi:10.1083/jcb.132.3.259 · Cited by 806 · see citing works

P-Body Purification Reveals the Condensation of Repressed mRNA Regulons

Hubstenberger, A., Courel, M., Bénard, M., Souquère, S., Ernoult‐Lange, M., Chouaib, R., Zhou, Y., Morlot, J.-B., Munier, A., Fradet, M., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.003 · Cited by 793 · see citing works

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

Khong, A., Matheny, T., Jain, S., Mitchell, S. F., Wheeler, J., & Parker, R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.015 · Cited by 760 · see citing works

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

Guttman, M., Russell, P., Ingolia, N. T., Weissman, J. S., & Lander, E. S. (2013) · Cell · doi:10.1016/j.cell.2013.06.009 · Cited by 745 · see citing works

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

Hangauer, M. J., Vaughn, I. W., & McManus, M. T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003569 · Cited by 738 · see citing works

N6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis

Chen, R., Chen, X., Xia, L., Zhang, J., Pan, Z., Ma, X.-D., Han, K., Chen, J., Judde, J.-G., Déas, O., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12651-2 · Cited by 736 · see citing works

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

Nelson, B. R., Makarewich, C. A., Anderson, D. M., Winders, B. R., Troupes, C. D., Wu, F.-F., Reese, A. L., McAnally, J. R., Chen, X.-W., Kavalali, E., et al. (2016) · Science · doi:10.1126/science.aad4076 · Cited by 730 · see citing works

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 729 · see citing works

Processing bodies require RNA for assembly and contain nontranslating mRNAs

Teixeira, D., Sheth, U., Valencia-Sanchez, M. A., Brengues, M., & Parker, R. (2005) · RNA · doi:10.1261/rna.7258505 · Cited by 728 · see citing works

Genome-wide transcription and the implications for genomic organization

Kapranov, P., Willingham, A. T., & Gingeras, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2083 · Cited by 720 · see citing works

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

Huang, J., Chen, M., Chen, D., Gao, X.-C., Zhu, S., Huang, H., Hu, M., Zhu, H., & Yan, G. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.015 · Cited by 711 · see citing works

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili, M. N., Dunagin, M. C., McClanahan, P. D., Biaesch, A. G., Padovan-Merhar, O. M., Regev, A., Rinn, J. L., & Raj, A. (2015) · Genome biology · doi:10.1186/s13059-015-0586-4 · Cited by 684 · see citing works

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

Imamura, K., Imamachi, N., Akizuki, G., Kumakura, M., Kawaguchi, A., Nagata, K., Kato, A., Kawaguchi, Y., Sato, H., Yoneda, M., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.01.009 · Cited by 680 · see citing works

Targeting noncoding RNAs in disease

Adams, B. D., Parsons, C., Walker, L., Zhang, W. C., & Slack, F. J. (2017) · Journal of Clinical Investigation · doi:10.1172/jci84424 · Cited by 672 · see citing works

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

Shah, S., Lubeck, E., Zhou, W., & Cai, L. (2016) · Neuron · doi:10.1016/j.neuron.2016.10.001 · Cited by 671 · see citing works

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

Chen, L., & Carmichael, G. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.027 · Cited by 662 · see citing works

Pervasive functional translation of noncanonical human open reading frames

Chen, J., Brunner, A., Cogan, J. Z., Nuñez, J. K., Fields, A. P., Adamson, B., Itzhak, D. N., Li, J. Y., Mann, M., Leonetti, M. D., et al. (2020) · Science · doi:10.1126/science.aay0262 · Cited by 654 · see citing works

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 653 · see citing works

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 649 · see citing works

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

Fazal, F. M., Han, S., Parker, K. R., Kaewsapsak, P., Xu, J., Boettiger, A. N., Chang, H. Y., & Ting, A. Y. (2019) · Cell · doi:10.1016/j.cell.2019.05.027 · Cited by 648 · see citing works

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 631 · see citing works

The Translational Landscape of the Human Heart

van Heesch, S., Witte, F., Schneider-Lunitz, V., Schulz, J. F., Adami, E., Faber, A. B., Kirchner, M., Maatz, H., Blachut, S., Sandmann, C.-L., et al. (2019) · Cell · doi:10.1016/j.cell.2019.05.010 · Cited by 619 · see citing works

In the right place at the right time: visualizing and understanding mRNA localization

Buxbaum, A. R., Haimovich, G., & Singer, R. H. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3918 · Cited by 610 · see citing works

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 · see citing works

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 · see citing works

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

Matsumoto, A., Pasut, A., Matsumoto, M., Yamashita, R., Fung, J., Monteleone, E., Saghatelian, A., Nakayama, K., Clohessy, J., & Pandolfi, P. (2016) · Nature · doi:10.1038/nature21034 · Cited by 594 · see citing works

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

Kleaveland, B., Shi, C. Y., Stefano, J., & Bartel, D. P. (2018) · Cell · doi:10.1016/j.cell.2018.05.022 · Cited by 594 · see citing works

Genome-wide analysis of long noncoding RNA stabilityPreprint

Clark, M. B., Johnston, R. L., Inostroza-Ponta, M., Fox, A. H., Fortini, E., Moscato, P., Dinger, M. E., & Mattick, J. S. (2012) · Genome Research · doi:10.1101/gr.131037.111 · Cited by 593 · see citing works

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 583 · see citing works

The LINK-A lncRNA activates normoxic HIF1α signalling in triple-negative breast cancer

Lin, A., Li, C., Xing, Z., Hu, Q., Liang, K., Han, L., Wang, C., Hawke, D. H., Wang, S., Zhang, Y., et al. (2016) · Nature Cell Biology · doi:10.1038/ncb3295 · Cited by 561 · see citing works

Long non-coding RNAs as a source of new peptides

Ruiz‐Orera, J., Messeguer, X., Subirana, J. A., & Albà, M. M. (2014) · eLife · doi:10.7554/elife.03523 · Cited by 537 · see citing works

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

Ulitsky, I. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.85 · Cited by 533 · see citing works

Stress Granules and Processing Bodies in Translational ControlPreprint

Ivanov, P. V., Kedersha, N., & Anderson, P. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032813 · Cited by 501 · see citing works

Mating Type Switching in Yeast Controlled by Asymmetric Localization of ASH1 mRNA

Long, R. M., Singer, R. H., Meng, X., et al. (1997) · Science · doi:10.1126/science.277.5324.383 · Cited by 499 · see citing works

Translation dynamics of single mRNAs in live cells and neurons

Wu, B., Eliscovich, C., Yoon, Y. J., & Singer, R. H. (2016) · Science · doi:10.1126/science.aaf1084 · Cited by 497 · see citing works

Disruption of GW bodies impairs mammalian RNA interference

Jakymiw, A., Lian, S., Eystathioy, T., Li, S., Satoh, M., Hamel, J. C., Fritzler, M. J., & Chan, E. K. L. (2005) · Nature Cell Biology · doi:10.1038/ncb1334 · Cited by 496 · see citing works

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 · see citing works

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

Treeck, B. V., Protter, D. S. W., Matheny, T., Khong, A., Link, C. D., & Parker, R. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800038115 · Cited by 482 · see citing works

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

Hirose, T., Virnicchi, G., Tanigawa, A., Naganuma, T., Li, R., Kimurâ, H., Yokoi, T., Nakagawa, S., Bénard, M., Fox, A. H., et al. (2013) · Molecular Biology of the Cell · doi:10.1091/mbc.e13-09-0558 · Cited by 475 · see citing works

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 · see citing works

Getting RNA and Protein in Phase

Weber, S. C., & Brangwynne, C. P. (2012) · Cell · doi:10.1016/j.cell.2012.05.022 · Cited by 463 · see citing works

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAsPreprint

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C., Chakrabortty, S. K., Djebali, S., Curado, J., Snyder, M. P., Gingeras, T., & Guigó, R. (2012) · Genome Research · doi:10.1101/gr.134445.111 · Cited by 463 · see citing works

Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides

Lennox, K. A., & Behlke, M. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1206 · Cited by 454 · see citing works

Cancer Exosomes Perform Cell-Independent MicroRNA Biogenesis and Promote Tumorigenesis

Melo, S. A., Sugimoto, H., O'Connell, J. T., Kato, N., Villanueva, A., Vidal, A., Qiu, L., Vitkin, E., Perelman, L., Melo, C., et al. (2014) · Cancer Cell · doi:10.1016/j.ccell.2014.09.005 · Cited by 453 · see citing works

A 360° view of circular RNAs: From biogenesis to functions

Wilusz, J. E. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1478 · Cited by 438 · see citing works

Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes

Smith, C. M., & STEITZ, J. A. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.12.6897 · Cited by 437 · see citing works

Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules

Leung, A., Calabrese, J. M., & Sharp, P. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0608845103 · Cited by 428 · see citing works

Long noncoding RNAs are rarely translated in two human cell linesPreprint

Bánfai, B., Jia, H., Khatun, J., Wood, E., Risk, B., Gundling, W. E., Kundaje, A., Gunawardena, H. P., Yu, Y., Xie, L., et al. (2012) · Genome Research · doi:10.1101/gr.134767.111 · Cited by 393 · see citing works

Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer

Li, Q., Shao, Y., Zhang, X., Zheng, T., Miao, M., Qin, L., Wang, B., Ye, G., Xiao, B., & Guo, J. (2014) · Tumor Biology · doi:10.1007/s13277-014-2807-y · Cited by 392 · see citing works

m6A-induced lncRNA RP11 triggers the dissemination of colorectal cancer cells via upregulation of Zeb1

Wu, Y., Yang, X., Chen, Z., Tian, L., Jiang, G., Chen, F., Li, J., An, P., Lu, L., Luo, N., et al. (2019) · Molecular Cancer · doi:10.1186/s12943-019-1014-2 · Cited by 390 · see citing works

Mechanistic insights into mammalian stress granule dynamics

Panas, M. D., Ivanov, P. V., & Anderson, P. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201609081 · Cited by 374 · see citing works

The MBNL3 splicing factor promotes hepatocellular carcinoma by increasing PXN expression through the alternative splicing of lncRNA-PXN-AS1

Yuan, J.-H., Liu, X.-N., Wang, T.-T., Pan, W., Tao, Q.-F., Zhou, W.-P., Wang, F., & Sun, S.-H. (2017) · Nature Cell Biology · doi:10.1038/ncb3538 · Cited by 367 · see citing works

PNPASE Regulates RNA Import into Mitochondria

Wang, G., Chen, H.-W., Oktay, Y., Zhang, J., Allen, E. L., Smith, G. M., Fan, K. C., Hong, J. S., French, S. W., McCaffery, J. M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.06.035 · Cited by 366 · cited 1× · see citing works

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

van Heesch, S., van Iterson, M., Jacobi, J., Boymans, S., Essers, P., de Bruijn, E., Hao, W., MacInnes, A. W., Cuppen, E. P. J. G., & Simonis, M. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r6 · Cited by 362 · see citing works

KRAS-dependent sorting of miRNA to exosomes

Cha, D. J., Franklin, J. L., Dou, Y., Liu, Q., Higginbotham, J. N., Beckler, M. D., Weaver, A. M., Vickers, K. C., Prasad, N., Levy, S., et al. (2015) · eLife · doi:10.7554/elife.07197 · Cited by 360 · see citing works

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 358 · see citing works

Translocation of a localized maternal mRNA to the vegetal pole of Xenopus oocytes

Melton, D. A. (1987) · Nature · doi:10.1038/328080a0 · Cited by 343 · see citing works

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 · see citing works

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 · see citing works

Long non‐coding RNAs with low expression levels in cells are enriched in secreted exosomes

Deligezer, U., Özgür, E., Çetinkaya, M. B., Işın, M., & Dalay, N. (2014) · Cell Biology International · doi:10.1002/cbin.10301 · Cited by 327 · see citing works

A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAsPreprint

Huang, C., Liang, D., Tatomer, D. C., & Wilusz, J. E. (2018) · Genes & Development · doi:10.1101/gad.314856.118 · Cited by 327 · see citing works

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

Kutter, C., Watt, S., Stefflova, K., Wilson, M. D., Gonçalves, Â., Ponting, C. P., Odom, D. T., & Marques, A. C. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002841 · Cited by 324 · see citing works

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer

Du, Z., Sun, T., Hacisuleyman, E., Fei, T., Wang, X., Brown, M. A., Rinn, J. L., Lee, M. G.-S., Chen, Y., Kantoff, P. W., et al. (2016) · Nature Communications · doi:10.1038/ncomms10982 · Cited by 317 · see citing works

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 · see citing works

Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs

Brown, J. A., Valenstein, M. L., Yario, T. A., Tycowski, K. T., & STEITZ, J. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217338109 · Cited by 311 · see citing works

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Johnson, R., & Guigó, R. (2014) · RNA · doi:10.1261/rna.044560.114 · Cited by 308 · see citing works

Visualization of Dynamics of Single Endogenous mRNA Labeled in Live Mouse

Park, H. Y., Lim, H., Yoon, Y. J., Follenzi, A., Nwokafor, C., Lopez-Jones, M., Meng, X., & Singer, R. H. (2014) · Science · doi:10.1126/science.1239200 · Cited by 308 · see citing works

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 305 · see citing works

Extracellular Vesicle-Mediated Transfer of a Novel Long Noncoding RNA TUC339: A Mechanism of Intercellular Signaling in Human Hepatocellular Cancer

Kogure, T., Yan, I. K., Lin, W.-L., & Patel, T. (2013) · Genes & Cancer · doi:10.1177/1947601913499020 · Cited by 303 · see citing works

Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions

Mili, S., Moissoglu, K., & Macara, I. G. (2008) · Nature · doi:10.1038/nature06888 · Cited by 302 · see citing works

Stress-specific differences in assembly and composition of stress granules and related foci

Aulas, A., Fay, M. M., Lyons, S. M., et al. (2017) · Journal of Cell Science · doi:10.1242/jcs.199240 · Cited by 297 · see citing works

In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport

Grünwald, D., & Singer, R. H. (2010) · Nature · doi:10.1038/nature09438 · Cited by 295 · see citing works

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 · see citing works

miR-1289 and “Zipcode”-like Sequence Enrich mRNAs in Microvesicles

Bolukbasi, M. F., Mizrak, A., Ozdener, G. B., Madlener, S., Ströbel, T., Erkan, E. P., Fan, J., Breakefield, X. O., & Saydam, O. (2012) · Molecular Therapy — Nucleic Acids · doi:10.1038/mtna.2011.2 · Cited by 290 · see citing works

Droplet organelles?

Courchaine, E. M., Lü, A., & Neugebauer, K. M. (2016) · The EMBO Journal · doi:10.15252/embj.201593517 · Cited by 289 · see citing works

Modulation of RNA Condensation by the DEAD-Box Protein eIF4A

Tauber, D., Tauber, G. A., Khong, A., Treeck, B. V., Pelletier, J., & Parker, R. (2020) · Cell · doi:10.1016/j.cell.2019.12.031 · Cited by 283 · see citing works

Cell cycle regulation by long non-coding RNAs

Kitagawa, M., Kitagawa, K., Kotake, Y., Niida, H., & Ohhata, T. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1423-0 · Cited by 280 · see citing works

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

Chew, G.-L., Pauli, A., Rinn, J. L., Regev, A., Schier, A. F., & Valen, E. (2013) · Development · doi:10.1242/dev.098343 · Cited by 275 · see citing works

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

Stein, C. S., Jadiya, P., Zhang, X., McLendon, J. M., Abouassaly, G. M., Witmer, N. H., Anderson, E. J., Elrod, J. W., & Boudreau, R. L. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.002 · Cited by 271 · see citing works

Expression of the Long Non-Coding RNA HOTAIR Correlates with Disease Progression in Bladder Cancer and Is Contained in Bladder Cancer Patient Urinary Exosomes

Berrondo, C., Flax, J. D., Kucherov, V., Siebert, A. L., Osinski, T. L., Rosenberg, A. F., Fucile, C., Richheimer, S., & Beckham, C. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0147236 · Cited by 267 · see citing works

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 264 · see citing works

Systematic Characterization of Stress-Induced RNA Granulation

Namkoong, S., Ho, A., Woo, Y. M., Kwak, H., & Lee, J. H. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.02.025 · Cited by 248 · see citing works

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

Padrón, A., Iwasaki, S., & Ingolia, N. T. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.030 · Cited by 245 · see citing works

Splicing promotes rapid and efficient mRNA export in mammalian cells

Valencia, P., Dias, A. P., & Reed, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800250105 · Cited by 241 · see citing works

Identification of cis - and trans -acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

Miyagawa, R., Tano, K., Mizuno, R., Nakamura, Y., Ijiri, K., Rakwal, R., Shibato, J., Masuo, Y., Mayeda, A., Hirose, T., et al. (2012) · RNA · doi:10.1261/rna.028639.111 · Cited by 237 · see citing works

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 235 · see citing works

P-Bodies: Cytosolic Droplets for Coordinated mRNA Storage.

Standart, N., & Weil, D. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.005 · Cited by 231 · see citing works

Circulating Long RNAs in Serum Extracellular Vesicles: Their Characterization and Potential Application as Biomarkers for Diagnosis of Colorectal Cancer

Dong, L., Lin, W., Qi, P., Xu, M., Wu, X., Ni, S., Huang, D., Weng, W., Tan, C., Sheng, W., et al. (2016) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-16-0006 · Cited by 224 · see citing works

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 224 · see citing works

HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNA RMRPPreprint

Noh, J., Kim, K. M., Abdelmohsen, K., Yoon, J.-H., Panda, A., Munk, R., Kim, J., Curtis, J., Moad, C. A., Wohler, C., et al. (2016) · Genes & Development · doi:10.1101/gad.276022.115 · Cited by 213 · see citing works

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

Jiang, L., Shao, C., Wu, Q., Chen, G., Zhou, J., Yang, B., Li, H., Gou, L., Zhang, Y., Wang, Y., et al. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3455 · Cited by 212 · see citing works

Long non‐coding RNA modifies chromatin

Saxena, A., & Carninci, P. (2011) · BioEssays · doi:10.1002/bies.201100084 · Cited by 211 · see citing works

A long non-coding RNA, GAS5, plays a critical role in the regulation of miR-21 during osteoarthritis

Song, J., Ahn, C., Chun, C. H., et al. (2014) · Journal of Orthopaedic Research® · doi:10.1002/jor.22718 · Cited by 211 · see citing works

ALS/FTD-Associated C9ORF72 Repeat RNA Promotes Phase Transitions In Vitro and in Cells

Fay, M. M., Anderson, P., & Ivanov, P. V. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.093 · Cited by 197 · see citing works

RNA Processing and ExportPreprint

Hocine, S., Singer, R. H., & Grünwald, D. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000752 · Cited by 196 · see citing works

Characterization of the RNA content of chromatinPreprint

Mondal, T., Rasmussen, M., Pandey, G. K., Isaksson, A., & Kanduri, C. (2010) · Genome Research · doi:10.1101/gr.103473.109 · Cited by 195 · see citing works

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

Kaewsapsak, P., Shechner, D. M., Mallard, W., Rinn, J. L., & Ting, A. Y. (2017) · eLife · doi:10.7554/elife.29224 · Cited by 193 · see citing works

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Mukherjee, N., Calviello, L., Hirsekorn, A., de Pretis, S., Pelizzola, M., & Ohler, U. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3325 · Cited by 181 · see citing works

Activity-dependent spatially localized miRNA maturation in neuronal dendrites

Sambandan, S., Akbalık, G., Kochen, L., Rinne, J. S., Kahlstatt, J., Glock, C., Tushev, G., Alvarez‐Castelao, B., Heckel, A., & Schuman, E. M. (2017) · Science · doi:10.1126/science.aaf8995 · Cited by 179 · see citing works

Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes

Ahadi, A., Brennan, S. E., Kennedy, P. J., Hutvágner, G., & Tran, N. (2016) · Scientific Reports · doi:10.1038/srep24922 · Cited by 175 · see citing works

The RNA Degradation Pathway Regulates the Function of GAS5 a Non-Coding RNA in Mammalian Cells

Tani, H., Torimura, M., & Akimitsu, N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055684 · Cited by 174 · see citing works

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

Zhang, B., Gunawardane, L. S., Niazi, F., Jahanbani, F., Chen, X., & Valadkhan, S. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.01673-13 · Cited by 169 · see citing works

Functional and Selective RNA Interference in Developing Axons and Growth Cones

Hengst, U., Cox, L. J., Macosko, E. Z., & Jaffrey, S. R. (2006) · Journal of Neuroscience · doi:10.1523/jneurosci.5229-05.2006 · Cited by 163 · see citing works

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

Smith, J. E., Alvarez‐Dominguez, J. R., Kline, N., Huynh, N. J., Geisler, S. J., Hu, W., Coller, J. M., & Baker, K. E. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.05.023 · Cited by 163 · see citing works

Polyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1

Beaulieu, Y. B., Kleinman, C. L., Landry-Voyer, A.-M., Majewski, J., & Bachand, F. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003078 · Cited by 161 · see citing works

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 · see citing works

Spatial Organization of the Cell Cytoplasm by Position-Dependent Phase Separation

Lee, C. F., Brangwynne, C. P., Gharakhani, J., Hyman, A. A., & Jülicher, F. (2013) · Physical Review Letters · doi:10.1103/physrevlett.111.088101 · Cited by 156 · see citing works

Non-coding RNAs: key regulators of mammalian transcription

Kugel, J. F., & Goodrich, J. A. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.12.003 · Cited by 156 · see citing works

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 154 · see citing works

Universal Alternative Splicing of Noncoding Exons

Deveson, I. W., Brunck, M. E. G., Blackburn, J., Tseng, E., Hon, T., Clark, T. A., Clark, M. B., Crawford, J., Dinger, M. E., Nielsen, L. K., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.005 · Cited by 151 · see citing works

Mammalian Polynucleotide Phosphorylase Is an Intermembrane Space RNase That Maintains Mitochondrial Homeostasis

Chen, H.-W., Rainey, R. N., Balatoni, C. E., Dawson, D. W., Troke, J. J., Wasiak, S., Hong, J. S., McBride, H. M., Koehler, C., Teitell, M., et al. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01002-06 · Cited by 149 · see citing works

Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles

Li, R., Harvey, A. R., Hodgetts, S. I., & Fox, A. H. (2017) · RNA · doi:10.1261/rna.059477.116 · Cited by 149 · see citing works

Long Non-coding RNA Growth Arrest-specific Transcript 5 (GAS5) Inhibits Liver Fibrogenesis through a Mechanism of Competing Endogenous RNA

Yu, F., Zheng, J., Mao, Y., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.683813 · Cited by 144 · see citing works

“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription

Melé, M., & Rinn, J. L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.011 · Cited by 143 · see citing works

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

Amaral, P., Leonardi, T., Han, N., Viré, E. A., Gascoigne, D. K., Arias‐Carrasco, R., Büscher, M., Pandolfini, L., Zhang, A., Pluchino, S., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1405-5 · Cited by 137 · see citing works

A long noncoding RNA distributed in both nucleus and cytoplasm operates in the PYCARD-regulated apoptosis by coordinating the epigenetic and translational regulation

Miao, H., Wang, L., Zhan, H., Dai, J., Chang, Y., Wu, F., Liu, T., Liu, Z., Gao, C., Li, L., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008144 · Cited by 136 · see citing works

The role of GW/P-bodies in RNA processing and silencing

Jakymiw, A., Pauley, K. M., Li, S., Ikeda, K., Lian, S., Eystathioy, T., Satoh, M., Fritzler, M. J., & Chan, E. K. L. (2007) · Journal of Cell Science · doi:10.1242/jcs.03429 · Cited by 131 · see citing works

Exosome-mediated delivery of MALAT1 induces cell proliferation in breast cancer

Zhang, P., Zhou, H., Lu, K., Lu, Y., Wang, Y., & Feng, T. (2018) · OncoTargets and Therapy · doi:10.2147/ott.s155134 · Cited by 129 · see citing works

Long noncoding RNAs in B-cell development and activation

Brazão, T. F., Johnson, J. S., Müller, J., Heger, A., Ponting, C. P., & Tybulewicz, V. L. J. (2016) · Blood · doi:10.1182/blood-2015-11-680843 · Cited by 126 · see citing works

SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation

Vendramin, R., Verheyden, Y., Ishikawa, H., Goedert, L., Nicolas, É., Saraf, K., Armaos, A., Ponti, R. D., Izumikawa, K., Mestdagh, P., et al. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0143-4 · Cited by 124 · see citing works

Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality

Pitchiaya, S., Mourão, M., Jalihal, A. P., Xiao, L., Jiang, X., Chinnaiyan, A. M., Schnell, S. D., & Walter, N. G. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.001 · Cited by 123 · see citing works

High‐throughput identification of RNA nuclear enrichment sequences

Shukla, C. J., McCorkindale, A. L., Gerhardinger, C., Korthauer, K. D., Cabili, M. N., Shechner, D. M., Irizarry, R. A., Maass, P. G., & Rinn, J. L. (2018) · The EMBO Journal · doi:10.15252/embj.201798452 · Cited by 122 · see citing works

Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions

Mardakheh, F. K., Paul, A., Kuemper, S., Sadok, A., Paterson, H., McCarthy, A., Yuan, Y., & Marshall, C. J. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.10.005 · Cited by 120 · see citing works

Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processingPreprint

Goldfarb, K. C., & Cech, T. R. (2017) · Genes & Development · doi:10.1101/gad.286963.116 · Cited by 119 · see citing works

Human thermogenic adipocyte regulation by the long noncoding RNA LINC00473

Tran, K., Brown, E. L., DeSouza, T., Jespersen, N. Z., Nandrup-Bus, C., Yang, Q., Yang, Z., Desai, A., Min, S. Y., Rojas-Rodriguez, R., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0205-x · Cited by 119 · see citing works

High-resolution three-dimensional mapping of mRNA export through the nuclear pore

Ma, J., Liu, Z., Michelotti, N., et al. (2013) · Nature Communications · doi:10.1038/ncomms3414 · Cited by 117 · see citing works

Predictive models of subcellular localization of long RNAs

Zuckerman, B. M., & Ulitsky, I. (2019) · RNA · doi:10.1261/rna.068288.118 · Cited by 115 · see citing works

Detection of a long non-coding RNA (CCAT1) in living cells and human adenocarcinoma of colon tissues using FIT–PNA molecular beacons

Kam, Y., Rubinstein, A., Naik, S., et al. (2013) · Cancer Letters · doi:10.1016/j.canlet.2013.02.014 · Cited by 111 · see citing works

Non-coding RNAs in muscle differentiation and musculoskeletal disease

Ballarino, M., Morlando, M., Fatica, A., & Bozzoni, I. (2016) · Journal of Clinical Investigation · doi:10.1172/jci84419 · Cited by 110 · see citing works

Mechanisms of Long Noncoding RNA Nuclear Retention

Guo, C., Xu, G., & Chen, L. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.07.001 · Cited by 110 · see citing works

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells

Bouvrette, L. P. B., Cody, N. A. L., Bergalet, J., Lefebvre, F. A., Diot, C., Wang, X., Blanchette, M., & Lécuyer, É. (2017) · RNA · doi:10.1261/rna.063172.117 · Cited by 107 · see citing works

Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

Bresson, S. M., Hunter, O. V., Hunter, A. C., & Conrad, N. K. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005610 · Cited by 106 · see citing works

Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Kourtidis, A., Ngok, S. P., Pulimeno, P., Feathers, R. W., Shull, L. C., Baker, T. R., Carr, J. M., Yan, I. K., Borgés, S., Perez, E. A., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3227 · Cited by 105 · see citing works

Telomeric repeat-containing RNA (TERRA) constitutes a nucleoprotein component of extracellular inflammatory exosomes

Wang, Z., Deng, Z., Dahmane, N., Tsai, K., Wang, P., Williams, D., Kossenkov, A. V., Showe, L. C., Zhang, R., Huang, Q., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505962112 · Cited by 105 · see citing works

The human mitochondrial transcriptome and the RNA‐binding proteins that regulate its expression

Rackham, O., Mercer, T. R., & Filipovska, A. (2012) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1128 · Cited by 104 · see citing works

Transcriptome-Wide Comparison of Stress Granules and P-Bodies Reveals that Translation Plays a Major Role in RNA Partitioning

Matheny, T., Rao, B. S., & Parker, R. (2019) · Molecular and Cellular Biology · doi:10.1128/mcb.00313-19 · Cited by 104 · see citing works

Multidomain Peptidyl Prolyl cis/trans Isomerases

Schiene‐Fischer, C. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.11.012 · Cited by 103 · see citing works

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

Palazzo, A. F., & Lee, E. S. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00440 · Cited by 102 · see citing works

Spatial distribution of messenger RNA in the cytoskeletal framework of ascidian eggs

Jeffery, W. R. (1984) · Developmental Biology · doi:10.1016/0012-1606(84)90335-x · Cited by 101 · see citing works

Extracellular matrix stiffness and cell contractility control RNA localization to promote cell migration

Wang, T., Hamilla, S. M., Cam, M. C., Aranda‐Espinoza, H., & Mili, S. (2017) · Nature Communications · doi:10.1038/s41467-017-00884-y · Cited by 99 · see citing works

SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation

Zucchelli, S., Cotella, D., Takahashi, H., Carrieri, C., Cimatti, L., Fasolo, F., Jones, M. H., Sblattero, D., Sanges, R., Santoro, C., et al. (2015) · RNA Biology · doi:10.1080/15476286.2015.1060395 · Cited by 98 · see citing works

LncRNA EPR controls epithelial proliferation by coordinating Cdkn1a transcription and mRNA decay response to TGF-β

Rossi, M. S., Bucci, G., Rizzotto, D., Bordo, D., Marzi, M. J., Puppo, M., Flinois, A., Spadaro, D., Citi, S., Emionite, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09754-1 · Cited by 98 · see citing works

GAS5 long non-coding RNA in malignant pleural mesothelioma

Renganathan, A., Kresoja‐Rakic, J., Echeverry, N., et al. (2014) · Molecular Cancer · doi:10.1186/1476-4598-13-119 · Cited by 97 · see citing works

A synergistic network of interactions promotes the formation of in vitro processing bodies and protects mRNA against decapping

Schütz, S., Nöldeke, E. R., & Sprangers, R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx353 · Cited by 95 · see citing works

Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

Wang, Y., Chen, L., Chen, B., Li, X., Kang, J., Fan, K., Hu, Y., Xu, J., Yi, L., Yang, J.-Q., et al. (2013) · Cell Death and Disease · doi:10.1038/cddis.2013.292 · Cited by 92 · see citing works

Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells

Landerer, E., Villegas, J., Burzio, V. A., Oliveira, L., Villota, C., López, C., Restovic, F., Martínez, R., Castillo, O., & Burzio, L. (2011) · Cellular Oncology · doi:10.1007/s13402-011-0018-8 · Cited by 91 · see citing works

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

Benhalevy, D., Anastasakis, D. G., & Hafner, M. (2018) · Nature Methods · doi:10.1038/s41592-018-0220-y · Cited by 91 · see citing works

Knockdown of GAS5 Inhibits Atherosclerosis Progression via Reducing EZH2-Mediated ABCA1 Transcription in ApoE−/− Mice

Meng, X., Yao, H.-H., Wang, L., Yu, M., Shi, S., Yuan, Z.-X., & Liu, J. (2019) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2019.10.034 · Cited by 89 · see citing works

Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size

Perry, R. B., Rishal, I., Doron‐Mandel, E., Kalinski, A. L., Medzihradszky, K. F., Terenzio, M., Alber, S., Koley, S., Lin, A., Rozenbaum, M., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.07.005 · Cited by 84 · see citing works

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

Rhee, H.-W., Zou, P., Udeshi, N. D., Martell, J. D., Mootha, V. K., Carr, S. A., & Ting, A. Y. (2013) · Science · doi:10.1126/science.1230593 · Cited by 83 · see citing works

Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line

Chen, M., Xu, R., Ji, H. L., Greening, D. W., Rai, A., Izumikawa, K., Ishikawa, H., Takahashi, N., & Simpson, R. J. (2016) · Scientific Reports · doi:10.1038/srep38397 · Cited by 82 · see citing works

Axonal precursor miRNAs hitchhike on endosomes and locally regulate the development of neural circuits

Corradi, E., Costa, I. D., Gavoci, A., Iyer, A., Roccuzzo, M., Otto, T. A., Oliani, E., Bridi, S., Strohbuecker, S., Rodriguez, G. S., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102513 · Cited by 80 · see citing works

Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAsPreprint

Carlevaro-Fita, J., Polidori, T., Das, M., Navarro, C., Zoller, T. I., & Johnson, R. (2018) · Genome Research · doi:10.1101/gr.229922.117 · Cited by 77 · see citing works

Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor

Schmidt, K., Weidmann, C. A., Hilimire, T. A., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2019.12.011 · Cited by 77 · see citing works

Single mRNA Tracking in Live Cells

Park, H. Y., Buxbaum, A. R., & Singer, R. H. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)72003-6 · Cited by 75 · see citing works

An LTR Retrotransposon-Derived Long Noncoding RNA lncMER52A Promotes Hepatocellular Carcinoma Progression by Binding p120-Catenin

Wu, Y., Zhao, Y., Huan, L., Zhao, J., Zhou, Y., Xu, L., Hu, Z., Liu, Y., Chen, Z., Wang, L., et al. (2020) · Cancer Research · doi:10.1158/0008-5472.can-19-2115 · Cited by 72 · see citing works

nc886 is induced by TGF-β and suppresses the microRNA pathway in ovarian cancer

Ahn, J., Lee, H., Lee, J., Lee, Y.-S., Park, J., Kim, S., Hwang, J.-A., Kunkeaw, N., Jung, S. Y., Kim, T. J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03556-7 · Cited by 71 · see citing works

Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential

Yuan, M., Yang, B., Rothschild, G., Mann, J. J., Sanford, L. D., Tang, X., Huang, C., Wang, C., & Zhang, W. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01519-z · Cited by 246 · see citing works

Liver fibrosis: from basic science towards clinical progress, focusing on the central role of hepatic stellate cells

Akkız, H., Gieseler, R. K., & Canbay, A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25147873 · Cited by 191 · see citing works

The ENCODE Project Decoded

Stailey, M. (2012) · Microreviews in Cell and Molecular Biology

The Study of OCDMA Encode/Decode Using Multilayer Films

Ze, G. (2001) · Beijing Youdian Xueyuan xuebao

Extrapolating ENCODE data to the whole human genome

Costantini, M., Filippo, M. D., & Bernardi, G. (2008) · Gene · doi:10.1016/j.gene.2008.02.013 · Cited by 2 · see citing works

Using the ENCODE Resource for Functional Annotation of Genetic VariantsPreprint

Pazin, M. J. (2015) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top084988 · Cited by 30 · see citing works

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Luo, Y., Hitz, B. C., Gabdank, I., Hilton, J. A., Kagda, M. S., Lam, B. R., Myers, Z., Sud, P., Jou, J., Lin, K. Z., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1062 · Cited by 949 · see citing works