References
- Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006; 442:203-7; PMID:16751777
- Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian piwi proteins. Nature 2006; 442:199-202; PMID:16751776
- Grivna ST, Beyret E, Wang Z, Lin H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 2006; 20:1709-14; PMID:16766680; http://dx.doi.org/10.1101/gad.1434406
- Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 2006; 20:1732-43; PMID:16766679; http://dx.doi.org/10.1101/gad.1425706
- Bamezai S, Rawat VP, Buske C. Concise review: the piwi-piRNA axis: pivotal beyond transposon silencing. Stem Cells 2012; 30:2603-11; PMID:22996918; http://dx.doi.org/10.1002/stem.1237
- Kim VN. Small RNAs just got bigger: piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 2006; 20:1993-7; PMID:16882976; http://dx.doi.org/10.1101/gad.1456106
- Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 2011; 12:246-58; PMID:21427766; http://dx.doi.org/10.1038/nrm3089
- Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP. Early origins and evolution of microRNAs and piwi-interacting RNAs in animals. Nature 2008; 455:1193-7; PMID:18830242; http://dx.doi.org/10.1038/nature07415
- Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, Hannon GJ. Specialized piRNA pathways act in germline and somatic tissues of the drosophila ovary. Cell 2009; 137:522-35; PMID:19395010; http://dx.doi.org/10.1016/j.cell.2009.03.040
- Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A. Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Res 2012; 40:10950-63; PMID:22965116; http://dx.doi.org/10.1093/nar/gks839
- Zheng K, Wang PJ. Blockade of pachytene piRNA biogenesis reveals a novel requirement for maintaining post-meiotic germline genome integrity. PLoS Genet 2012; 8:e1003038; PMID:23166510; http://dx.doi.org/10.1371/journal.pgen.1003038
- Aravin AA, Hannon GJ, Brennecke J. The piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 2007; 318:761-4; PMID:17975059; http://dx.doi.org/10.1126/science.1146484
- Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in drosophila. Cell 2007; 128:1089-103; PMID:17346786; http://dx.doi.org/10.1016/j.cell.2007.01.043
- Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 2008; 31:785-99; PMID:18922463; http://dx.doi.org/10.1016/j.molcel.2008.09.003
- Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y, Ijiri TW, et al. DNA methylation of retrotransposon genes is regulated by piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 2008; 22:908-17; PMID:18381894; http://dx.doi.org/10.1101/gad.1640708
- Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 2007; 316:744-7; PMID:17446352; http://dx.doi.org/10.1126/science.1142612
- Gan H, Lin X, Zhang Z, Zhang W, Liao S, Wang L, Han C. piRNA profiling during specific stages of mouse spermatogenesis. RNA 2011; 17:1191-203; PMID:21602304; http://dx.doi.org/10.1261/rna.2648411
- Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 2008; 322:1387-92; PMID:19039138; http://dx.doi.org/10.1126/science.1165171
- Lee EJ, Banerjee S, Zhou H, Jammalamadaka A, Arcila M, Manjunath BS, Kosik KS. Identification of piRNAs in the central nervous system. RNA 2011; 17:1090-9; PMID:21515829; http://dx.doi.org/10.1261/rna.2565011
- Cichocki F, Lenvik T, Sharma N, Yun G, Anderson SK, Miller JS. Cutting edge: KIR antisense transcripts are processed into a 28-Base PIWI-like RNA in human NK cells. J Immunol 2010; 185:2009-12; PMID:20631304; http://dx.doi.org/10.4049/jimmunol.1000855
- Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 2012; 149:693-707; PMID:22541438; http://dx.doi.org/10.1016/j.cell.2012.02.057
- Ross RJ, Weiner MM, Lin H. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 2014; 505:353-9; PMID:24429634; http://dx.doi.org/10.1038/nature12987
- Peng JC, Lin H. Beyond transposons: the epigenetic and somatic functions of the piwi-piRNA mechanism. Curr Opin Cell Biol 2013; PMID:23465540; http://dx.doi.org/10.1016/j.ceb.2013.01.010
- Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M. Maternal mRNA deadenylation and decay by the piRNA pathway in the early drosophila embryo. Nature 2010; 467:1128-32; PMID:20953170; http://dx.doi.org/10.1038/nature09465
- Li MA, Alls JD, Avancini RM, Koo K, Godt D. The large maf factor traffic jam controls gonad morphogenesis in drosophila. Nat Cell Biol 2003; 5:994-1000; PMID:14578908; http://dx.doi.org/10.1038/ncb1058
- Qi H, Watanabe T, Ku HY, Liu N, Zhong M, Lin H. The yb body, a major site for piwi-associated RNA biogenesis and a gateway for piwi expression and transport to the nucleus in somatic cells. J Biol Chem 2011; 286:3789-97; PMID:21106531; http://dx.doi.org/10.1074/jbc.M110.193888
- Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC. A regulatory circuit for piwi by the large maf gene traffic jam in drosophila. Nature 2009; 461:1296-9; PMID:19812547; http://dx.doi.org/10.1038/nature08501
- Esposito T, Magliocca S, Formicola D, Gianfrancesco F. piR_015520 belongs to piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One 2011; 6:e22727; PMID:21818375; http://dx.doi.org/10.1371/journal.pone.0022727
- Zhang Y, Romanish MT, Mager DL. Distributions of transposable elements reveal hazardous zones in mammalian introns. PLoS Comput Biol 2011; 7:e1002046; PMID:21573203; http://dx.doi.org/10.1371/journal.pcbi.1002046
- Sela N, Kim E, Ast G. The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol 2010; 11:R59; PMID:20525173; http://dx.doi.org/10.1186/gb-2010-11-6-r59
- Lee JH, Jung C, Javadian-Elyaderani P, Schweyer S, Schutte D, Shoukier M, Karimi-Busheri F, Weinfeld M, Rasouli-Nia A, Hengstler JG, et al. Pathways of proliferation and antiapoptosis driven in breast cancer stem cells by stem cell protein piwil2. Cancer Res 2010; 70:4569-79; PMID:20460541; http://dx.doi.org/10.1158/0008-5472.CAN-09-2670
- Lee JH, Schutte D, Wulf G, Fuzesi L, Radzun HJ, Schweyer S, Engel W, Nayernia K. Stem-cell protein piwil2 is widely expressed in tumors and inhibits apoptosis through activation of stat3/bcl-X-L pathway. Hum Mol Genet 2006; 15:201-11; PMID:16377660; http://dx.doi.org/10.1093/hmg/ddi430
- Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A. iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-seq. BMC bioinformatics 2013; 14:362; PMID:24330401; http://dx.doi.org/10.1186/1471-2105-14-362
- Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, et al. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse rasgrf1 locus. Science 2011; 332:848-52; PMID:21566194; http://dx.doi.org/10.1126/science.1203919
- Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. A major epigenetic programming mechanism guided by piRNAs. Dev Cell 2013; 24:502-16; PMID:23434410; http://dx.doi.org/10.1016/j.devcel.2013.01.023
- Yin H, Blanchard KL. DNA methylation represses the expression of the human erythropoietin gene by two different mechanisms. Blood 2000; 95:111-9; PMID:10607693
- Peng B, Hurt EM, Hodge DR, Thomas SB, Farrar WL. DNA hypermethylation and partial gene silencing of human thymine- DNA glycosylase in multiple myeloma cell lines. Epigenetics 2006; 1:138-45; PMID:17965616; http://dx.doi.org/10.4161/epi.1.3.2938
- Vincent A, Ducourouble MP, Van Seuningen I. Epigenetic regulation of the human mucin gene MUC4 in epithelial cancer cell lines involves both DNA methylation and histone modifications mediated by DNA methyltransferases and histone deacetylases. FASEB J 2008; 22:3035-45; PMID:18492726; http://dx.doi.org/10.1096/fj.07-103390
- Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-85; PMID:17072317; http://dx.doi.org/10.1038/ng1909
- Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 2012; 8:e1002781; PMID:22737091; http://dx.doi.org/10.1371/journal.pgen.1002781
- Hackett JA, Surani MA. DNA methylation dynamics during the mammalian life cycle. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110328; PMID:23166392; http://dx.doi.org/10.1098/rstb.2011.0328
- Sai Lakshmi S, Agrawal S. piRNABank: a web resource on classified and clustered piwi-interacting RNAs. Nucleic Acids Res 2008; 36:D173-7; PMID:17881367; http://dx.doi.org/10.1093/nar/gkm696
- Sanders SJ, Ercan-Sencicek AG, Hus V, Luo R, Murtha MT, Moreno-De-Luca D, Chu SH, Moreau MP, Gupta AR, Thomson SA, et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 williams syndrome region, are strongly associated with autism. Neuron 2011; 70:863-85; PMID:21658581; http://dx.doi.org/10.1016/j.neuron.2011.05.002
- Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98:288-95; PMID:21839163; http://dx.doi.org/10.1016/j.ygeno.2011.07.007
- Dennis G, Jr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol 2003; 4:P3; PMID:12734009; http://dx.doi.org/10.1186/gb-2003-4-5-p3
- Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44-57; PMID:19131956; http://dx.doi.org/10.1038/nprot.2008.211