A direct role for small non-coding RNAs in DNA damage response

d’Adda di Fagagna, 2008, Living on a break: cellular senescence as a DNA-damage response, Nat. Rev. Cancer, 8, 512, 10.1038/nrc2440 Fumagalli, 2012, Telomeric DNA damage is irreparable and causes persistent DNA damage response activation, Nat. Cell Biol., 14, 355, 10.1038/ncb2466 Clark, 2011, The reality of pervasive transcription, PLoS Biol., 9, e1000625, 10.1371/journal.pbio.1000625 Castel, 2013, RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond, Nat. Rev. Genet., 14, 100, 10.1038/nrg3355 Wang, 2008, Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature, 454, 126, 10.1038/nature06992 Huarte, 2010, A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response, Cell, 142, 409, 10.1016/j.cell.2010.06.040 Hung, 2011, Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters, Nat. Genet., 43, 621, 10.1038/ng.848 Hannon, 2002, RNA interference, Nature, 418, 244, 10.1038/418244a Kim, 2009, Biogenesis of small RNAs in animals, Nat. Rev. Mol. Cell Biol., 10, 126, 10.1038/nrm2632 Hu, 2010, ATM is down-regulated by N-Myc-regulated microRNA-421, Proc. Natl. Acad. Sci. U.S.A., 107, 1506, 10.1073/pnas.0907763107 Yan, 2010, Targeting DNA-PKcs and ATM with miR-101 sensitizes tumors to radiation, PLoS ONE, 5, e11397, 10.1371/journal.pone.0011397 Moskwa, 2011, miR-182-mediated downregulation of BRCA1 impacts DNA repair and sensitivity to PARP inhibitors, Mol. Cell, 41, 210, 10.1016/j.molcel.2010.12.005 Lal, 2009, miR-24-mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells, Nat. Struct. Mol. Biol., 16, 492, 10.1038/nsmb.1589 Wang, 2012, MiR-96 downregulates REV1 and RAD51 to promote cellular sensitivity to cisplatin and PARP inhibition, Cancer Res., 72, 4037, 10.1158/0008-5472.CAN-12-0103 Liu, 2011, ATM signals miRNA biogenesis through KSRP, Mol. Cell, 41, 367, 10.1016/j.molcel.2011.01.027 Kawai, 2012, BRCA1 regulates microRNA biogenesis via the DROSHA microprocessor complex, J. Cell Biol., 197, 201, 10.1083/jcb.201110008 Suzuki, 2009, Modulation of microRNA processing by p53, Nature, 460, 529, 10.1038/nature08199 Bensimon, 2010, ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage, Sci. Signal., 3, rs3, 10.1126/scisignal.2001034 Pryde, 2005, 53BP1 exchanges slowly at the sites of DNA damage and appears to require RNA for its association with chromatin, J. Cell Sci., 118, 2043, 10.1242/jcs.02336 Ganesan, 2002, BRCA1 supports XIST RNA concentration on the inactive X chromosome, Cell, 111, 393, 10.1016/S0092-8674(02)01052-8 Pfingsten, 2012, Mutually exclusive binding of telomerase RNA and DNA by Ku alters telomerase recruitment model, Cell, 148, 922, 10.1016/j.cell.2012.01.033 Kedde, 2006, Telomerase-independent regulation of ATR by human telomerase RNA, J. Biol. Chem., 281, 40503, 10.1074/jbc.M607676200 Bracht, 2013, Genomes on the edge: programmed genome instability in ciliates, Cell, 152, 406, 10.1016/j.cell.2013.01.005 Storici, 2007, RNA-templated DNA repair, Nature, 447, 338, 10.1038/nature05720 Shen, 2011, RNA-driven genetic changes in bacteria and in human cells, Mutat. Res., 717, 91, 10.1016/j.mrfmmm.2011.03.016 Francia, 2012, Site-specific DICER and DROSHA RNA products control the DNA-damage response, Nature, 488, 231, 10.1038/nature11179 Wei, 2012, A role for small RNAs in DNA double-strand break repair, Cell, 149, 101, 10.1016/j.cell.2012.03.002 Michalik, 2012, A small RNA response at DNA ends in Drosophila, Nucleic Acids Res., 40, 9596, 10.1093/nar/gks711 Shanbhag, 2010, ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks, Cell, 141, 970, 10.1016/j.cell.2010.04.038 Ichijima, 2011, MDC1 directs chromosome-wide silencing of the sex chromosomes in male germ cells, Genes Dev., 25, 959, 10.1101/gad.2030811 Gudjonsson, 2012, TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes, Cell, 150, 697, 10.1016/j.cell.2012.06.039 Chou, 2010, A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage, Proc. Natl. Acad. Sci. U.S.A., 107, 18475, 10.1073/pnas.1012946107 Pankotai, 2012, DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks, Nat. Struct. Mol. Biol., 19, 276, 10.1038/nsmb.2224 Iacovoni, 2010, High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome, EMBO J., 29, 1446, 10.1038/emboj.2010.38 Lukas, 2003, Distinct spatiotemporal dynamics of mammalian checkpoint regulators induced by DNA damage, Nat. Cell Biol., 5, 255, 10.1038/ncb945 Sinkkonen, 2010, Dicer is associated with ribosomal DNA chromatin in mammalian cells, PLoS ONE, 5, e12175, 10.1371/journal.pone.0012175 Lu, 2005, MicroRNA expression profiles classify human cancers, Nature, 435, 834, 10.1038/nature03702 Slade, 2011, DICER1 syndrome: clarifying the diagnosis, clinical features and management implications of a pleiotropic tumour predisposition syndrome, J. Med. Genet., 48, 273, 10.1136/jmg.2010.083790 Merritt, 2008, Dicer, Drosha, and outcomes in patients with ovarian cancer, N. Engl. J. Med., 359, 2641, 10.1056/NEJMoa0803785 Heravi-Moussavi, 2012, Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers, N. Engl. J. Med., 366, 234, 10.1056/NEJMoa1102903 Hill, 2009, DICER1 mutations in familial pleuropulmonary blastoma, Science, 325, 965, 10.1126/science.1174334 Melo, 2009, A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function, Nat. Genet., 41, 365, 10.1038/ng.317 Jafarnejad, 2013, Expression of the RNase III enzyme DROSHA is reduced during progression of human cutaneous melanoma, Mod. Pathol., 26, 902, 10.1038/modpathol.2012.225 Kumar, 2007, Impaired microRNA processing enhances cellular transformation and tumorigenesis, Nat. Genet., 39, 673, 10.1038/ng2003 Lin, 2010, microRNA signature and expression of Dicer and Drosha can predict prognosis and delineate risk groups in neuroblastoma, Cancer Res., 70, 7841, 10.1158/0008-5472.CAN-10-0970 Martello, 2010, A MicroRNA targeting dicer for metastasis control, Cell, 141, 1195, 10.1016/j.cell.2010.05.017 Su, 2010, TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAs, Nature, 467, 986, 10.1038/nature09459 Kumar, 2009, Dicer1 functions as a haploinsufficient tumor suppressor, Genes Dev., 23, 2700, 10.1101/gad.1848209 Esquela-Kerscher, 2006, Oncomirs – microRNAs with a role in cancer, Nat. Rev. Cancer, 6, 259, 10.1038/nrc1840 Halazonetis, 2008, An oncogene-induced DNA damage model for cancer development, Science, 319, 1352, 10.1126/science.1140735 Jackson, 2009, The DNA-damage response in human biology and disease, Nature, 461, 1071, 10.1038/nature08467 Jackson, 2013, Regulation of DNA damage responses by ubiquitin and SUMO, Mol. Cell, 49, 795, 10.1016/j.molcel.2013.01.017 Branzei, 2008, Regulation of DNA repair throughout the cell cycle, Nat. Rev. Mol. Cell Biol., 9, 297, 10.1038/nrm2351 Soutoglou, 2008, Activation of the cellular DNA damage response in the absence of DNA lesions, Science, 320, 1507, 10.1126/science.1159051 Mao, 2011, Biogenesis and function of nuclear bodies, Trends Genet., 27, 295, 10.1016/j.tig.2011.05.006 Shevtsov, 2011, Nucleation of nuclear bodies by RNA, Nat. Cell Biol., 13, 167, 10.1038/ncb2157 Clemson, 2009, An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles, Mol. Cell, 33, 717, 10.1016/j.molcel.2009.01.026 Kato, 2012, Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels, Cell, 149, 753, 10.1016/j.cell.2012.04.017 Brangwynne, 2009, Germline P granules are liquid droplets that localize by controlled dissolution/condensation, Science, 324, 1729, 10.1126/science.1172046