Non-coding RNAs as regulators of gene expression and epigenetics

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

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

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The nuclear RNase III Drosha initiates microRNA processing

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Origins and Mechanisms of miRNAs and siRNAs

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Evolution and Functions of Long Noncoding RNAs

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Role for a bidentate ribonuclease in the initiation step of RNA interference

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Human DNA methylomes at base resolution show widespread epigenomic differences

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The widespread regulation of microRNA biogenesis, function and decay

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Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans

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

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

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Mammalian microRNAs predominantly act to decrease target mRNA levels

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Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

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

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

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Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

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RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

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Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans.

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Widespread transcription at neuronal activity-regulated enhancers

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The ENCODE (ENCyclopedia Of DNA Elements) Project

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The Polycomb group protein EZH2 directly controls DNA methylation

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A microRNA in a Multiple-Turnover RNAi Enzyme Complex

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

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Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

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Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis

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The Endothelial-Specific MicroRNA miR-126 Governs Vascular Integrity and Angiogenesis

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MicroRNA-133 controls cardiac hypertrophy

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A germline-specific class of small RNAs binds mammalian Piwi proteins

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miR-126 Regulates Angiogenic Signaling and Vascular Integrity

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Long Noncoding RNAs with Enhancer-like Function in Human Cells

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Predictive Effects of Circulating miR-221, miR-130a and miR-155 for Coronary Heart Disease: A Multi-Ethnic Study in China

Jia, Q.-W., Chen, Z.-H., Ding, X.-Q., Liu, J.-Y., Ge, P.-C., An, F.-H., Li, L.-H., Wang, L.-S., Ma, W.-Z., Yang, Z.-J., et al. (2017) · Cellular Physiology and Biochemistry · doi:10.1159/000478071 · Cited by 1,693 · see citing works

Antisense Transcription in the Mammalian Transcriptome

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Control of Stress-Dependent Cardiac Growth and Gene Expression by a MicroRNA

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The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus

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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 novel class of small RNAs bind to MILI protein in mouse testes

Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., et al. (2006) · Nature · doi:10.1038/nature04916 · Cited by 1,516 · see citing works

A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure

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Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

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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 · see citing works

Mechanisms of Polycomb gene silencing: knowns and unknowns

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MicroRNA-373 induces expression of genes with complementary promoter sequences

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MicroRNA-92a Controls Angiogenesis and Functional Recovery of Ischemic Tissues in Mice

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

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Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S. A., Long, J. C., Stern, D., Tammana, H., Helt, G. A., et al. (2005) · Science · doi:10.1126/science.1108625 · Cited by 1,175 · see citing works

A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila

Gunawardane, L. S., Saito, K., Nishida, K. M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H., & Siomi, M. C. (2007) · Science · doi:10.1126/science.1140494 · Cited by 1,173 · see citing works

The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2

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Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

Watanabe, T., Totoki, Y., Toyoda, A., Kaneda, M., Kuramochi‐Miyagawa, S., Obata, Y., Chiba, H., Kohara, Y., Kono, T., Nakano, T., et al. (2008) · Nature · doi:10.1038/nature06908 · Cited by 1,115 · see citing works

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

Tam, O. H., Aravin, A. A., Stein, P., Girard, A., Murchison, E. P., Cheloufi, S., Hodges, E. C., Anger, M., Sachidanandam, R., Schultz, R. M., et al. (2008) · Nature · doi:10.1038/nature06904 · Cited by 1,042 · see citing works

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

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Characterization of the piRNA Complex from Rat Testes

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The Small RNA Profile during Drosophila melanogaster Development

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

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DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testesPreprint

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Divergent transcription from active promoters

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MicroRNA-210 Modulates Endothelial Cell Response to Hypoxia and Inhibits the Receptor Tyrosine Kinase Ligand Ephrin-A3

Fasanaro, P., D'Alessandra, Y., Di Stefano, V., Melchionna, R., Romani, S., Pompilio, G., Capogrossi, M. C., & Martelli, F. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800731200 · Cited by 912 · see citing works

Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk

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miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs

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Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

Malone, C. D., Brennecke, J., Dus, M., Stark, A., McCombie, W. R., Sachidanandam, R., & Hannon, G. J. (2009) · Cell · doi:10.1016/j.cell.2009.03.040 · Cited by 864 · see citing works

Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase

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miR-133 and miR-30 Regulate Connective Tissue Growth Factor

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Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

Yu, W., Gius, D. R., Onyango, P. O., Muldoon‐Jacobs, K., Karp, J. E., Feinberg, A. P., & Cui, H. (2008) · Nature · doi:10.1038/nature06468 · Cited by 801 · see citing works

A Steroid Receptor Coactivator, SRA, Functions as an RNA and Is Present in an SRC-1 Complex

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Role of Dicer and Drosha for Endothelial MicroRNA Expression and Angiogenesis

Kuehbacher, A., Urbich, C., Zeiher, A. M., & Dimmeler, S. (2007) · Circulation Research · doi:10.1161/circresaha.107.153916 · Cited by 782 · see citing works

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Preker, P., Nielsen, J. S., Kammler, S., Lykke‐Andersen, S., Christensen, M. S., Mapendano, C. K., Schierup, M. H., & Jensen, T. H. (2008) · Science · doi:10.1126/science.1164096 · Cited by 777 · see citing works

MicroRNAs Play an Essential Role in the Development of Cardiac Hypertrophy

Sayed, D. H., Hong, C., Chen, I.-Y., Lypowy, J., & Abdellatif, M. (2007) · Circulation Research · doi:10.1161/01.res.0000257913.42552.23 · Cited by 777 · see citing works

Small dsRNAs induce transcriptional activation in human cells

Li, L., Okino, S. T., Zhao, H., Pookot, D., Place, R. F., Urakami, S., Enokida, H., & Dahiya, R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607015103 · Cited by 768 · see citing works

A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT

Willingham, A. T., Orth, A. P., Batalov, S., Peters, E. C., Wen, B., Aza‐Blanc, P., Hogenesch, J. B., & Schultz, P. G. (2005) · Science · doi:10.1126/science.1115901 · Cited by 732 · see citing works

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiationPreprint

Dinger, M. E., Amaral, P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B., Askarian-Amiri, M., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 729 · see citing works

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 · see citing works

Characterization of the piRNA Complex from Rat Testes

Iseni, F., Barge, A., Baudin, F., Blondel, D., Ruigrok, R. W. H., Schoehn, G., & Mavrakis, M. (2006) · Cited by 714 · see citing works

The <i>Evf-2</i> noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator

Feng, J., Bi, C., Clark, B. S., Mady, R., Shah, P., & Kohtz, J. D. (2006) · Genes &amp; Development · doi:10.1101/gad.1416106 · Cited by 712 · see citing works

MicroRNA-directed transcriptional gene silencing in mammalian cells

Kim, D. H., Sætrom, P., Snøve, O., & Rossi, J. J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808830105 · Cited by 705 · see citing works

Dicer Dependent MicroRNAs Regulate Gene Expression and Functions in Human Endothelial Cells

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

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On the road to reading the RNA-interference code

Siomi, H., & Siomi, M. C. (2009) · Nature · doi:10.1038/nature07754 · Cited by 674 · see citing works

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. C., Weng, C., & Klibanski, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702029200 · Cited by 654 · see citing works

MiRNA-Directed Regulation of VEGF and Other Angiogenic Factors under Hypoxia

Zhong, H., Lv, Q., Ye, W., Wong, C.-K. A., Cai, G., Gu, D., Ji, Y., Zhao, C., Wang, J., Yang, B. B., et al. (2006) · PLoS ONE · doi:10.1371/journal.pone.0000116 · Cited by 653 · see citing works

Characterization of a Germ-Line Deletion, Including the Entire INK4/ARF Locus, in a Melanoma-Neural System Tumor Family: Identification of ANRIL , an Antisense Noncoding RNA Whose Expression Coclusters with ARF

Pasmant, É., Laurendeau, I., Héron, D., Vidaud, M., Vidaud, D., & Bièche, I. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-2004 · Cited by 618 · see citing works

MicroRNAs Add a New Dimension to Cardiovascular Disease

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