基因组学与应用生物学

参考文献

Amaral P.P.,and Mattick J.S.,2008,Noncoding RNA in development,Mamm Genome,19(7-8):454-492

Amaral P.P.,Dinger M.E.,Mercer T.R.,and Mattick J.S.,2008,The eukaryotic genome as an RNA machine,Science,319(5871):1787-1789

Aravin A.A.,Sachidanandam R.,Girard A.,Fejestoth K.,and Hannon G.J.,2007,Developmentally regulated piRNA clusters implicate MILI in transposon control,Science,316(5825):744-747

Bayne E.H.,and Allshire R.C.,2005,RNA-directed transcriptional gene silencing in mammals,Trends.Genet,21(7):370-373

Bernstein E.,and Allis C.D.,2005,RNA meets chromatin,Genes Dev.,19(14):1635-1655

Bestor T.H.,2000,The DNA methyltransferases of mammals,Hum.Mol.Genet.,9(16):2395-2402

Benetti R.,Gonzalo S.,Jaco I.,Mu觡oz P.,Gonzalez S.,Schoeftner S.,Murchison E.,Andl T.,Chen T.,and Klatt P.,2008,A mammalian microRNA cluster controls DNA methylation and telomere recombination via RBL2-dependent regulation of DNA methyltransferases,Nat.Struct Mol.Biol.,15(3):268-279

Capuano F.,Mülleder M.,Kok R.,Blom H.J.,and Ralser M.,2014,Cytosine DNA methylation is found in drosophila melanogaster but absent in saccharomyces cerevisiae,schizosaccharomyces pombe,and other yeast species,Anal.Chem.,86(8):3697-3702

Carmell M.A.,Girard A.,Hj V.D.K.,Bourc'His D.,Bestor T.H.,de Rooij D.G.,and Hannon G.J.,2007,MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline,Dev.Cell,12(4):503-514

Chang Y.,Sun L.,Kokura K.,Horton J.R.,Fukuda M.,Espejo A.,Izumi V.,Koomen J.M.,Bedford M.T.,and Zhang X.,2011,MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a,Nat.Commun.,2(1):533

Chen H.,Kazemier H.G.,de Groote M.L.,Ruiters M.H.,Xu G.L.,and Rots M.G.,2014,Induced DNA demethylation by targeting ten-eleven translocation 2 to the human ICAM promoter,Nucleic Acids Res.,42(3):1563-1574

Chen T.,Tsujimoto N.,and Li E.,2004,The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin,Mol.Cell Biol.,24(20):9048-9058

Cierpicki T.,Risner L.E.,Grembecka J.,Lukasik S.M.,Popovic R.,Omonkowska M.,Shultis D.D.,Zeleznik-Le N.J.,and Bushweller J.H.,2010,Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9leukemia,Nat.Struct Mol.Biol.,17(1):62-68

Collins R.,and Cheng X.,2010,A case study in cross-talk:the histone lysine methyltransferases G9a and GLP,Nucleic Acids Res.,38(11):3503-3511

Cosgrove M.S.,and Patel A.,2010,Mixed lineage leukemia:a structure-function perspective of the MLL1 protein,Febs J.,277(8):1832-1842

Costa F.F.,2008,Non-coding RNAs,epigenetics and complexity,Gene,410(1):9-17

de Groote M.L.,Verschure P.J.,and Rots M.G.,2012,Epigenetic editing:targeted rewriting of epigenetic marks to modulate expression of selected target genes,Nucleic Acids Res.,40(21):10596-10613

Dhayalan A.,Rajavelu A.,Rathert P.,Tamas R.,Jurkowska R.Z.,Ragozin S.,and Jeltsch A.,2010,The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation,J.Biol.Chem.,285(34):26114-26120

Dodge J.E.,Ramsahoye B.H.,Wo Z.G.,Okano M.,and Li E.,2002,De novo methylation of MMLY provirus in embryonic stem cells:CpG versus non-CpG methylation,Gene,289(1-2):41-48

Ehrlich M.,Gamasosa M.A.,Huang L.H.,Midgett R.M.,Kuo K.C.,Mccune R.A.,and Gehrke C.,1982,Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells,Nucleic Acids Res.,10(8):2709-2721

Evans H.H.,and Evans T.E.,1970,Methylation of the deoxyribonucleic acid of physarum polycephalum at various periods during the mitotic cycle,J.Bio.Chem.,245(23):6436-6441

Fabbri M.,Garzon R.,Cimmino A.,Liu Z.,Zanesi N.,Callegari E.,Liu S.,Alder H.,Costinean S.,and Fernandez-Cymering C.,2007,MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and3B,Proc.Natl.Acad Sci.USA,104(40):15805-15810

Fu Y.,Luo G.Z.,Chen K.,Deng X.,Yu M.,Han D.,Hao Z.,Liu J.,Lu X.,Dore L.C.,Weng X.,Ji Q.,Mets L.,and He C.,2015,N6-methyldeoxyadenosine marks active transcription start sites in chlamydomonas,Cell,161(4):879-892

Ghildiyal M.,and Zamore P.,2009,Small silencing RNAs:an expanding universe,Nat.Rev.Genet,10(2):94-108

Goll M.G.,Kirpekar F.,Maggert K.A.,Yoder J.A.,Hsieh C.L.,and Zhang X.,2006,Methylation of t RNAAsp by the DNA methyltransferase homolog Dnmt2,Science,311(5759):395-398

Greer E.L.,Blanco M.A.,Gu L.,Sendinc E.,Liu J.,Aristizábal-Corrales D.,Hsu C.H.,Aravind L.,He C.,and Shi Y.,2015,DNA methylation on N6 adenine in C.elegans,Cell,161(4):868-878

Grewal S.I.,and Rice J.C.,2004,Regulation of heterochromatin by histone methylation and small RNAs,Curr.Opin.Cell Biol.,16(3):230-238

Haines T.R.,Rodenhiser D.I.,and Ainsworth P.J.,2001,Allele-specific non-cpg methylation of the NF1 gene during early mouse development,Dev.Biol.,240(2):585-598

Han J.,Kim D.,and Morris K.V.,2007,Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells,Proc.Natl.Acad Sci.USA,104(30):12422-12427

Hawkins P.G.,and Morris K.V.,2008,RNA and transcriptional modulation of gene expression,Cell Cycle,7(5):602-607

Heyn H.,and Esteller M.,2015,An adenine code for DNA:a second life for N6-methyladenine,Cell,161(4):710-713

Holliday R.,and Pugh J.E.,1975,DNA modification mechanisms and gene activity during development,Science,187(4173):226-232

J覿hner D.,Stuhlmann H.,Stewart C.L.,Harbers K.,L觟hler J.,Simon I.,and Jaenisch R.,1982,De novo methylation and expression of retroviral genomes during mouse embryogenesis,Nature,298(5875):623-628

Kawasaki H.,and Taira K.,2004,Induction of DNA methylation and gene silencing by short interfering RNAs in human cells,Nature,431(7005):211-217

Kawasaki H.,Taira K.,and Morris K.V.,2005,Si RNA induced transcriptional gene silencing in mammalian cells,Cell Cycle,4(3):442-448

Kokura K.,Sun L.,Bedford M.T.,and Fang J.,2010,MethylH3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion,Embo.J.,29(21):3673-3687

Kulis M.,Merkel A.,Heath S.,Queirós A.C.,Schuyler R.P.,Castellano G.,Beekman R.,Raineri E.,and Esteve A.,2015,Whole-genome fingerprint of the DNA methylome during human B-cell differentiation,Nature Genetics,47(7):746-756

Kuramochi-Miyagawa S.,Watanabe T.,Gotoh K.,Totoki Y.,Toyoda A.,Ikawa M.,Asada N.,Kojima K.,Yamaguchi Y.,and Ijiri T.W.,2008,DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MI-WI2 in murine fetal testes,Genes Dev.,22(7):908-917

Lister R.,Mukamel E.A.,Nery J.R.,Urich M.,Puddifoot C.A.,Johnson N.D.,Lucero J.,Huang Y.,Dwork A.J.,and Schultz M.D.,2013,Global epigenomic reconfiguration during mammalian brain development,Science,341(6146):629

Lister R.,Pelizzola M.,Dowen R.H.,Hawkins R.D.,Hon G.,Tontifilippini J.,Nery J.R.,Lee L.,and Ye Z.,2009,Human DNA methylomes at base resolution show widespread epigenomic differences,Nature,462(7271):315-322

Maeder M.L.,Angstman J.F.,Richardson M.E.,Linder S.J.,Cascio V.M.,Tsai S.Q.,Ho Q.H.,Sander J.D.,Reyon D.,Bernstein B.E.,Costello J.F.,Wilkinson M.F.,and Joung J.K.,2013,Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins,Nat.Biotechnol.,31(12):1137-1142

Mattick J.S.,and Makunin I.V.,2006,Non-coding RNA,Hum.Mol.Genet.,15(1):17-29

Meissner A.,Mikkelsen T.S.,Gu H.,Wernig M.,Hanna J.,Sivachenko A.,Zhang X.,Bernstein B.E.,Nusbaum C.,and Jaffe D.B.,2008,Genome-scale DNA methylation maps of pluripotent and differentiated cells,Nature,454(7205):766-770

Milne T.A.,Briggs S.D.,Brock H.W.,Martin M.E.,Gibbs D.,Allis C.D.,and Hess J.L.,2002,MLL targets SET domain methyltransferase activity to Hox gene promoters,Mol.Cell,10(5):1107-1117

Morris K.V.,Chan S.W.,Jacobsen S.E.,and Looney D.J.,2004,Small interfering RNA-induced transcriptional gene silencing in human cells,Science,305(5688):1289-1292

Nakayama J.,Rice J.C.,Strahl B.D.,Allis C.D.,and Grewal S.I.,2001,Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly,Science,292(5514):110-113

Okano M.,Bell D.W.,Haber D.A.,and Li E.,1999,DNAmethyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development,Cell,99(3):247-257

Ooi S.K.,Qiu C.,Bernstein E.,Li K.,Jia D.,Yang Z.,Erdjument-Bromage H.,Tempst P.,Lin S-P.,and Allis C.D.,2007,Dnmt3l connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA,Nature,448(7154):714-717

Ponting C.P.,Oliver P.L.,and Reik W.,2009,Evolution and functions of long noncoding RNAs,Cell,136(4):629-641

Reik W.,2007,Stability and flexibility of epigenetic gene regulation in mammalian development,Nature,447(7143):425-432

Riggs A.D.,1975,X inactivation,differentiation,and DNAmethylation,Cytogenet Genome Res.,14(1):9-25

Rivenbark A.G.,Stolzenburg S.,Beltran A.S.,Yuan X.,Rots M.G.,Strahl B.D.,and Blancafort P.,2012,Epigenetic reprogramming of cancer cells via targeted DNA methylation,Epigenetics,7(4):350-360

Rosenfeld J.A.,Wang Z.,Schones D.E.,Zhao K.,Desalle R.,and Zhang M.Q.,2009,Determination of enriched histone modifications in non-genic portions of the human genome,BMCGenomics,10(1):143

Shinkai Y.,and Tachibana M.,2011,H3K9 methyltransferase G9a and the related molecule GLP,Genes Dev.,25(8):781-788

Siddique A.N.,Nunna S.,Rajavelu A.,Zhang Y.,Jurkowska R.Z.,Reinhardt R.,Rots M.G.,Ragozin S.,Jurkowski T.P.,and Jeltsch A.,2013,Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity,J.Mol.Biol.,425(3):479-491

Sinkkonen L.,Hugenschmidt T.,Berninger P.,Gaidatzis D.,Mohn F.,Artus-Revel C.G.,Zavolan M.,Svoboda P.,and Filipowicz W.,2008,MicroRNAs control de novo DNAmethylation through regulation of transcriptional repressors in mouse embryonic stem cells,Nat.Struct.Mol.Biol.,15(3):259-267

Smith S.S.,Kaplan B.E.,Sowers L.C.,and Newman E.M.,1992,Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation,Proc.Natl.Acad.Sci.,89(10):4744-4748

Song J.,Rechkoblit O.,Bestor T.H.,and Patel D.J.,2011,Structure of Dnmt1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation,Science,331(6020):1036-1040

Stadler M.B.,Murr R.,Burger L.,Ivanek R.,Lienert F.,Sch觟ler A.,van Nimwegen E.,Wirbelauer C.,Oakeley E.J.,Gaidatzis D.,Tiwari V.K.,and Schübeler D.,2011,DNA-binding factors shape the mouse methylome at distal regulatory regions,Nature,480(7378):490-550

Stein R.,Razin A.,and Cedar H.,1982,In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells,Proc.Natl.Aca.,79(11):3418-3422

Straussman R.,Nejman D.,Roberts D.,Steinfeld I.,Blum B.,Benvenisty N.,Simon I.,Yakhini Z.,and Cedar H.,2009,Developmental programming of CpG island methylation profiles in the human genome,Nat.Struct.Mol.Biol.,16(5):564-571

Terranova R.,Agherbi H.,Boned A.,Meresse S.,and Djabali M.,2006,Histone and DNA methylation defects at Hox genes in mice expressing a SET domain-truncated form of MLL,Proc.Natl.Acad Sci.,103(17):6629-6634

Vardimon L.,Kressmann A.,Cedar H.,Maechler M.,and Doerfier W.,1982,Expression of a cloned adenovirus gene is inhibited by in vitro methylation,Proc.Natl.Acad.,79(4):1073-1077

Weber M.,and Schübeler D.,2007,Genomic patterns of DNAmethylation:targets and function of an epigenetic mark,Curr.Opin.Cell Biol.,19(3):273-280

Wu T.P.,Wang T.,Seetin M.G.,Lai Y.,Zhu S.,Lin K.,Liu Y.F.,Byrum S.D.,Mackintosh S.G.,Zhong M.,Tackett A.,Wang G.,Hon L.S.,Fang G.,Swenberg J.A.,and Xiao A.Z.,2016,DNA methylation on N6-adenine in mammalian embryonic stem cells,Nature,532(7599):329-333

Yu H.,2009,Epigenetics:advances of non-coding RNAs regulation in mammalian cells,Yichung(Hereditas),31(11):1077-1086(于红,2009,表观遗传学:生物细胞非编码RNA调控的研究进展,遗传,31(11):1077-1086)

Zaratiegui M.,Irvine D.V.,and Martienssen R.A.,2007,Noncoding RNAs and gene silencing,Cell,128(4):763-776

Zemach A.,Mcdaniel I.E.,Silva P.,and Zilberman D.,2010,Genome-wide evolutionary analysis of eukaryotic DNAmethylation,Science,328(5980):916-919

Zhang G.,Huang H.,Liu D.,Cheng Y.,Liu X.,Zhang W.,Yin R.,Zhang D.,Zhang P.,Liu J.,Li C.,Liu B.,Luo Y.,Zhu Y.,Zhang N.,He S.,He C.,Wang H.,and Chen D.,2015,N6-methyladenine DNA modification in drosophila,Cell,161(4):893-906