Human factors and pathways essential for mediating epigenetic gene silencing

References

• Holliday R. Epigenetics: a historical overview. Epigenetics 2006; 1:76 - 80; http://dx.doi.org/10.4161/epi.1.2.2762; PMID: 17998809
   PubMed Web of Science ®Google Scholar
• Meissner A. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 2010; 28:1079 - 88; http://dx.doi.org/10.1038/nbt.1684; PMID: 20944600
   PubMed Web of Science ®Google Scholar
• Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet 2013; 14:204 - 20; http://dx.doi.org/10.1038/nrg3354; PMID: 23400093
   PubMed Web of Science ®Google Scholar
• Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. An operational definition of epigenetics. Genes Dev 2009; 23:781 - 3; http://dx.doi.org/10.1101/gad.1787609; PMID: 19339683
   PubMed Web of Science ®Google Scholar
• Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011; 21:381 - 95; http://dx.doi.org/10.1038/cr.2011.22; PMID: 21321607
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006; 31:89 - 97; http://dx.doi.org/10.1016/j.tibs.2005.12.008; PMID: 16403636
   PubMed Web of Science ®Google Scholar
• Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 2013; 502:472 - 9; http://dx.doi.org/10.1038/nature12750; PMID: 24153300
   PubMed Web of Science ®Google Scholar
• Rothbart SB, Strahl BD. Interpreting the language of histone and DNA modifications. Biochim Biophys Acta 2014; 1839:627 - 43; http://dx.doi.org/10.1016/j.bbagrm.2014.03.001; PMID: 24631868
   PubMed Web of Science ®Google Scholar
• Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science 2010; 330:612 - 6; http://dx.doi.org/10.1126/science.1191078; PMID: 21030644
   PubMed Web of Science ®Google Scholar
• Probst AV, Dunleavy E, Almouzni G. Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 2009; 10:192 - 206; http://dx.doi.org/10.1038/nrm2640; PMID: 19234478
   PubMed Web of Science ®Google Scholar
• Bickmore WA, van Steensel B. Genome architecture: domain organization of interphase chromosomes. Cell 2013; 152:1270 - 84; http://dx.doi.org/10.1016/j.cell.2013.02.001; PMID: 23498936
   PubMed Web of Science ®Google Scholar
• Collas P, Lund EG, Oldenburg AR. Closing the (nuclear) envelope on the genome: how nuclear lamins interact with promoters and modulate gene expression. Bioessays 2014; 36:75 - 83; http://dx.doi.org/10.1002/bies.201300138; PMID: 24272858
   PubMed Web of Science ®Google Scholar
• Berger SL. The complex language of chromatin regulation during transcription. Nature 2007; 447:407 - 12; http://dx.doi.org/10.1038/nature05915; PMID: 17522673
   PubMed Web of Science ®Google Scholar
• Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 2009; 10:295 - 304; http://dx.doi.org/10.1038/nrg2540; PMID: 19308066
   PubMed Web of Science ®Google Scholar
• Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010; 28:817 - 25; http://dx.doi.org/10.1038/nbt.1662; PMID: 20657582
   PubMed Web of Science ®Google Scholar
• Gardner KE, Allis CD, Strahl BD. Operating on chromatin, a colorful language where context matters. J Mol Biol 2011; 409:36 - 46; http://dx.doi.org/10.1016/j.jmb.2011.01.040; PMID: 21272588
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128:683 - 92; http://dx.doi.org/10.1016/j.cell.2007.01.029; PMID: 17320506
   PubMed Web of Science ®Google Scholar
• Taby R, Issa JP. Cancer epigenetics. CA Cancer J Clin 2010; 60:376 - 92; http://dx.doi.org/10.3322/caac.20085; PMID: 20959400
   PubMed Web of Science ®Google Scholar
• Boumber Y, Issa JP. Epigenetics in cancer: what’s the future?. Oncology (Williston Park) 2011; 25:220 - 6, 228; PMID: 21548464
   PubMed Web of Science ®Google Scholar
• Marks PA. The clinical development of histone deacetylase inhibitors as targeted anticancer drugs. Expert Opin Investig Drugs 2010; 19:1049 - 66; http://dx.doi.org/10.1517/13543784.2010.510514; PMID: 20687783
   PubMed Web of Science ®Google Scholar
• Santos FP, Kantarjian H, Garcia-Manero G, Issa JP, Ravandi F. Decitabine in the treatment of myelodysplastic syndromes. Expert Rev Anticancer Ther 2010; 10:9 - 22; http://dx.doi.org/10.1016/j.stem.2009.03.005; PMID: 19341620
   PubMed Web of Science ®Google Scholar
• Feng B, Ng JH, Heng JC, Ng HH. Molecules that promote or enhance reprogramming of somatic cells to induced pluripotent stem cells. Cell Stem Cell 2009; 4:301 - 12; http://dx.doi.org/10.1016/j.stem.2009.03.005; PMID: 19341620
   PubMed Web of Science ®Google Scholar
• Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD, Skalka AM, Katz RA. Identification of a functional network of human epigenetic silencing factors. J Biol Chem 2010; 285:422 - 33; http://dx.doi.org/10.1074/jbc.M109.064667; PMID: 19880521
   PubMed Web of Science ®Google Scholar
• Tsui M, Xie T, Orth JD, Carpenter AE, Rudnicki S, Kim S, Shamu CE, Mitchison TJ. An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor. PLoS One 2009; 4:e7339; http://dx.doi.org/10.1371/journal.pone.0007339; PMID: 19802393
   PubMedGoogle Scholar
• Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013; 41:D808 - 15; http://dx.doi.org/10.1093/nar/gks1094; PMID: 23203871
   PubMed Web of Science ®Google Scholar
• Meulmeester E, Melchior F. Cell biology: SUMO. Nature 2008; 452:709 - 11; http://dx.doi.org/10.1038/452709a; PMID: 18401402
   PubMed Web of Science ®Google Scholar
• Wilkinson KA, Henley JM. Mechanisms, regulation and consequences of protein SUMOylation. Biochem J 2010; 428:133 - 45; http://dx.doi.org/10.1042/BJ20100158; PMID: 20462400
   PubMed Web of Science ®Google Scholar
• Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 2004; 15:595 - 605; http://dx.doi.org/10.1016/j.molcel.2004.06.043; PMID: 15327775
   PubMed Web of Science ®Google Scholar
• Raynal NJ, Si J, Taby RF, Gharibyan V, Ahmed S, Jelinek J, Estécio MR, Issa JP. DNA methylation does not stably lock gene expression but instead serves as a molecular mark for gene silencing memory. Cancer Res 2012; 72:1170 - 81; http://dx.doi.org/10.1158/0008-5472.CAN-11-3248; PMID: 22219169
   PubMed Web of Science ®Google Scholar
• Si J, Boumber YA, Shu J, Qin T, Ahmed S, He R, Jelinek J, Issa JP. Chromatin remodeling is required for gene reactivation after decitabine-mediated DNA hypomethylation. Cancer Res 2010; 70:6968 - 77; http://dx.doi.org/10.1158/0008-5472.CAN-09-4474; PMID: 20713525
   PubMed Web of Science ®Google Scholar
• Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ 3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 2002; 16:919 - 32; http://dx.doi.org/10.1101/gad.973302; PMID: 11959841
   PubMed Web of Science ®Google Scholar
• Segré CV, Chiocca S. Regulating the regulators: the post-translational code of class I HDAC1 and HDAC2. J Biomed Biotechnol 2011; 2011:690848; http://dx.doi.org/10.1155/2011/690848; PMID: 21197454
   PubMed Web of Science ®Google Scholar
• Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, Bentley DL. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol 2007; 14:240 - 2; http://dx.doi.org/10.1038/nsmb1200; PMID: 17310255
   PubMed Web of Science ®Google Scholar
• Girdwood D, Bumpass D, Vaughan OA, Thain A, Anderson LA, Snowden AW, Garcia-Wilson E, Perkins ND, Hay RT. P300 transcriptional repression is mediated by SUMO modification. Mol Cell 2003; 11:1043 - 54; http://dx.doi.org/10.1016/S1097-2765(03)00141-2; PMID: 12718889
   PubMed Web of Science ®Google Scholar
• Ashburner BP, Westerheide SD, Baldwin AS Jr.. The p65 (RelA) subunit of NF-kappaB interacts with the histone deacetylase (HDAC) corepressors HDAC1 and HDAC2 to negatively regulate gene expression. Mol Cell Biol 2001; 21:7065 - 77; http://dx.doi.org/10.1128/MCB.21.20.7065-7077.2001; PMID: 11564889
   PubMed Web of Science ®Google Scholar
• Zhang Y, Iratni R, Erdjument-Bromage H, Tempst P, Reinberg D. Histone deacetylases and SAP18, a novel polypeptide, are components of a human Sin3 complex. Cell 1997; 89:357 - 64; http://dx.doi.org/10.1016/S0092-8674(00)80216-0; PMID: 9150135
   PubMed Web of Science ®Google Scholar
• Matyash A, Singh N, Hanes SD, Urlaub H, Jäckle H. SAP18 promotes Krüppel-dependent transcriptional repression by enhancer-specific histone deacetylation. J Biol Chem 2009; 284:3012 - 20; http://dx.doi.org/10.1074/jbc.M806163200; PMID: 19049982
   PubMed Web of Science ®Google Scholar
• Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, et al. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 2012; 149:1474 - 87; http://dx.doi.org/10.1016/j.cell.2012.04.035; PMID: 22726435
   PubMed Web of Science ®Google Scholar
• David G, Neptune MA, DePinho RA. SUMO-1 modification of histone deacetylase 1 (HDAC1) modulates its biological activities. J Biol Chem 2002; 277:23658 - 63; http://dx.doi.org/10.1074/jbc.M203690200; PMID: 11960997
   PubMed Web of Science ®Google Scholar
• Ribet D, Hamon M, Gouin E, Nahori MA, Impens F, Neyret-Kahn H, Gevaert K, Vandekerckhove J, Dejean A, Cossart P. Listeria monocytogenes impairs SUMOylation for efficient infection. Nature 2010; 464:1192 - 5; http://dx.doi.org/10.1038/nature08963; PMID: 20414307
   PubMed Web of Science ®Google Scholar
• Fujita N, Watanabe S, Ichimura T, Tsuruzoe S, Shinkai Y, Tachibana M, Chiba T, Nakao M. Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J Biol Chem 2003; 278:24132 - 8; http://dx.doi.org/10.1074/jbc.M302283200; PMID: 12711603
   PubMed Web of Science ®Google Scholar
• Uchimura Y, Ichimura T, Uwada J, Tachibana T, Sugahara S, Nakao M, Saitoh H. Involvement of SUMO modification in MBD1- and MCAF1-mediated heterochromatin formation. J Biol Chem 2006; 281:23180 - 90; http://dx.doi.org/10.1074/jbc.M602280200; PMID: 16757475
   PubMed Web of Science ®Google Scholar
• Ichimura T, Watanabe S, Sakamoto Y, Aoto T, Fujita N, Nakao M. Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins. J Biol Chem 2005; 280:13928 - 35; http://dx.doi.org/10.1074/jbc.M413654200; PMID: 15691849
   PubMed Web of Science ®Google Scholar
• Nathan D, Ingvarsdottir K, Sterner DE, Bylebyl GR, Dokmanovic M, Dorsey JA, Whelan KA, Krsmanovic M, Lane WS, Meluh PB, et al. Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev 2006; 20:966 - 76; http://dx.doi.org/10.1101/gad.1404206; PMID: 16598039
   PubMed Web of Science ®Google Scholar
• Shiio Y, Eisenman RN. Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci U S A 2003; 100:13225 - 30; http://dx.doi.org/10.1073/pnas.1735528100; PMID: 14578449
   PubMed Web of Science ®Google Scholar
• Nagpal K, Watanabe KS, Tsao BP, Tsokos GC. Ikaros represses protein phosphatase 2A (PP2A) expression through an intronic binding site. J Biol Chem 2014; In press http://dx.doi.org/10.1074/jbc.M114.558197; PMID: 24692537
   PubMed Web of Science ®Google Scholar
• Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, et al, Children’s Oncology Group. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 2009; 360:470 - 80; http://dx.doi.org/10.1056/NEJMoa0808253; PMID: 19129520
   PubMed Web of Science ®Google Scholar
• Peterson EA, Petty EM. Conquering the complex world of human septins: implications for health and disease. Clin Genet 2010; 77:511 - 24; http://dx.doi.org/10.1111/j.1399-0004.2010.01392.x; PMID: 20236126
   PubMed Web of Science ®Google Scholar
• Cerveira N, Bizarro S, Teixeira MR. MLL-SEPTIN gene fusions in hematological malignancies. Biol Chem 2011; 392:713 - 24; http://dx.doi.org/10.1515/BC.2011.072; PMID: 21714766
   PubMed Web of Science ®Google Scholar
• Cervoni N, Detich N, Seo SB, Chakravarti D, Szyf M. The oncoprotein Set/TAF-1beta, an inhibitor of histone acetyltransferase, inhibits active demethylation of DNA, integrating DNA methylation and transcriptional silencing. J Biol Chem 2002; 277:25026 - 31; http://dx.doi.org/10.1074/jbc.M202256200; PMID: 11978794
   PubMed Web of Science ®Google Scholar
• Quentmeier H, Schneider B, Röhrs S, Romani J, Zaborski M, Macleod RA, Drexler HG. SET-NUP214 fusion in acute myeloid leukemia- and T-cell acute lymphoblastic leukemia-derived cell lines. J Hematol Oncol 2009; 2:3; http://dx.doi.org/10.1186/1756-8722-2-3; PMID: 19166587
   PubMed Web of Science ®Google Scholar
• Isermann P, Lammerding J. Nuclear mechanics and mechanotransduction in health and disease. Curr Biol 2013; 23:R1113 - 21; http://dx.doi.org/10.1016/j.cub.2013.11.009; PMID: 24355792
   PubMed Web of Science ®Google Scholar
• Winograd-Katz SE, Fässler R, Geiger B, Legate KR. The integrin adhesome: from genes and proteins to human disease. Nat Rev Mol Cell Biol 2014; 15:273 - 88; http://dx.doi.org/10.1038/nrm3769; PMID: 24651544
   PubMed Web of Science ®Google Scholar
• Mehta AK, Majumdar SS, Alam P, Gulati N, Brahmachari V. Epigenetic regulation of cytomegalovirus major immediate-early promoter activity in transgenic mice. Gene 2009; 428:20 - 4; http://dx.doi.org/10.1016/j.gene.2008.09.033; PMID: 18976699
   PubMed Web of Science ®Google Scholar
• Poleshko A, Shalginskikh N, Katz RA. Identification of epigenetic silencing factors by siRNA screening. In Epigenomics: From Chromatin Biology to Therapeutics, edited by K. Appasani (Cambridge University Press, New York, 2012), Chap. 3.
   Google Scholar
• Poleshko A, Mansfield KM, Burlingame CC, Andrake MD, Shah NR, Katz RA. The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. Cell Rep 2013; 5:292 - 301; http://dx.doi.org/10.1016/j.celrep.2013.09.024; PMID: 24209742
   PubMed Web of Science ®Google Scholar
• Reddy KL, Zullo JM, Bertolino E, Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 2008; 452:243 - 7; http://dx.doi.org/10.1038/nature06727; PMID: 18272965
   PubMed Web of Science ®Google Scholar
• Shevelyov YY, Nurminsky DI. The nuclear lamina as a gene-silencing hub. Curr Issues Mol Biol 2012; 14:27 - 38; PMID: 21795760
   PubMed Web of Science ®Google Scholar
• Poleshko A, Katz RA. Specifying peripheral heterochromatin during nuclear lamina reassembly. Nucleus 2014; 5:32 - 9; http://dx.doi.org/10.4161/nucl.28167; PMID: 24637393
   PubMed Web of Science ®Google Scholar
• Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C, Adams PD, Skalka AM, Katz RA. Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response. J Virol 2008; 82:2313 - 23; http://dx.doi.org/10.1128/JVI.01882-07; PMID: 18094192
   PubMed Web of Science ®Google Scholar
• Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44 - 57; http://dx.doi.org/10.1038/nprot.2008.211; PMID: 19131956
   PubMed Web of Science ®Google Scholar
• Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 2008; 45:81 - 94; http://dx.doi.org/10.2144/000112900; PMID: 18611170
   PubMed Web of Science ®Google Scholar
• Zhang Z, Meng T, He J, Li M, Tong LJ, Xiong B, Lin L, Shen J, Miao ZH, Ding J. MT7, a novel compound from a combinatorial library, arrests mitosis via inhibiting the polymerization of microtubules. Invest New Drugs 2010; 28:715 - 28; http://dx.doi.org/10.1007/s10637-009-9303-z; PMID: 19705064
   PubMed Web of Science ®Google Scholar