Abstract
This chapter describes resources and technologies generated by the NIH Roadmap Epigenomics Program that may be useful to epigenomics researchers investigating a variety of diseases including cancer. Highlights include reference epigenome maps for a wide variety of human cells and tissues, the development of new technologies for epigenetic assays and imaging, the identification of novel epigenetic modifications, and an improved understanding of the role of epigenetic processes in a diversity of human diseases. We also discuss future needs in this area including exploration of epigenomic variation between individuals, single-cell epigenomics, environmental epigenomics, exploration of the use of surrogate tissues, and improved technologies for epigenome manipulation.
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References
Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33(Suppl):245–254
Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11:285–296
Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669–681
McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH (2013) Mosaic copy number variation in human neurons. Science 342:632–637
Jung D, Giallourakis C, Mostoslavsky R, Alt FW (2006) Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol 24:541–570
Feinberg AP (2010) Epigenomics reveals a functional genome anatomy and a new approach to common disease. Nat Biotechnol 28:1049–1052
Bell CG, Beck S (2010) The epigenomic interface between genome and environment in common complex diseases. Brief Funct Genomics 9:477–485
Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155:39–55
Meissner A (2010) Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 28:1079–1088
Beck S, Olek A, Walter J (1999) From genomics to epigenomics: a loftier view of life. Nat Biotechnol 17:1144
The American Association for Cancer Research Human Epigenome Task Force and the European Union, Network of Excellence, Scientific Advisory Board (2008) Moving AHEAD with an international human epigenome project. Nature 454:711–715
Jones PA, Martienssen R (2005) A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop. Cancer Res 65:11241–11246
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet al, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28:1045–1048
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153:1134–1148
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A (2013) Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153:1149–1163
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE (2013) Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152:642–654
Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342:1367–1372
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337:1190–1195
Chadwick LH (2012) The NIH Roadmap Epigenomics Program data resource. Epigenomics 4:317–324
Karnik R, Meissner A (2013) Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Cell Stem Cell 13:14–21
Aguilar-Valles A, Vaissiere T, Griggs EM, Mikaelsson MA, Takacs IF, Young EJ, Rumbaugh G, Miller CA (2013) Methamphetamine-associated memory is regulated by a writer and an eraser of permissive histone methylation. Biol Psychiatry 1:1–18, http://dx.doi.org/10.1016/j.biopsych.2013.09.014
Jirtle RL, Skinner MK (2007) Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253–262
Ganu RS, Harris RA, Collins K, Aagaard KM (2012) Early origins of adult disease: approaches for investigating the programmable epigenome in humans, nonhuman primates, and rodents. ILAR J 53:306–321
Zhang Z, Tan M, Xie Z, Dai L, Chen Y, Zhao Y (2011) Identification of lysine succinylation as a new post-translational modification. Nat Chem Biol 7:58–63
Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028
Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA (2012) Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep 1:83–90
Dhayalan A, Tamas R, Bock I, Tattermusch A, Dimitrova E, Kudithipudi S, Ragozin S, Jeltsch A (2011) The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. Hum Mol Genet 20:2195–2203
Lodhi N, Tulin AV (2011) PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq). Methods Mol Biol 780:191–208
Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J (2009) Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139:1290–1302
Baker SP, Phillips J, Anderson S, Qiu Q, Shabanowitz J, Smith MM, Yates JR III, Hunt DF, Grant PA (2010) Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae. Nat Cell Biol 12:294–298
Adli M, Bernstein BE (2011) Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6:1656–1668
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097–1105
Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7:133–136
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
Cipriany BR, Murphy PJ, Hagarman JA, Cerf A, Latulippe D, Levy SL, Benitez JJ, Tan CP, Topolancik J, Soloway PD, Craighead HG (2012) Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. Proc Natl Acad Sci U S A 109:8477–8482
Byrum SD, Raman A, Taverna SD, Tackett AJ (2012) ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep 2:198–205
Deal RB, Henikoff JG, Henikoff S (2010) Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328:1161–1164
Clowney EJ, LeGros MA, Mosley CP, Clowney FG, Markenskoff-Papadimitriou EC, Myllys M, Barnea G, Larabell CA, Lomvardas S (2012) Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151:724–737
Wang Y, Zhang YL, Hennig K, Gale JP, Hong Y, Cha A, Riley M, Wagner F, Haggarty SJ, Holson E, Hooker J (2013) Class I HDAC imaging using [(3)H]CI-994 autoradiography. Epigenetics 8:756–764
Schroeder FA, Chonde DB, Riley MM, Moseley CK, Granda ML, Wilson CM, Wagner FF, Zhang YL, Gale J, Holson EB, Haggarty SJ, Hooker JM (2013) FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors. Neurosci Lett 550:119–124
Yeh HH, Tian M, Hinz R, Young D, Shavrin A, Mukhapadhyay U, Flores LG, Balatoni J, Soghomonyan S, Jeong HJ, Pal A, Uthamanthil R, Jackson JN, Nishii R, Mizuma H, Onoe H, Kagawa S, Higashi T, Fukumitsu N, Alauddin M, Tong W, Herholz K, Gelovani JG (2013) Imaging epigenetic regulation by histone deacetylases in the brain using PET/MRI with 18F-FAHA. Neuroimage 64:630–639
Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92
Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153:307–319
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre V, Sigova AA, Hoke HA, Young RA (2013) Super-enhancers in the control of cell identity and disease. Cell 155:934–947
Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC, Weng YI, Deatherage DE, Chen Z, Pereira JS, Lopez R, Russo J, Wang Q, Lamartiniere CA, Nephew KP, Huang TH (2010) Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res 20:733–744
Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J (2012) Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol 13:R43
Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18:91–93
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64
Zhao YQ, Jordan IK, Lunyak VV (2013) Epigenetics components of aging in the central nervous system. Neurotherapeutics 10:647–663
Ben-Avraham D, Muzumdar RH, Atzmon G (2012) Epigenetic genome-wide association methylation in aging and longevity. Epigenomics 4:503–509
Hong CP, Park J, Roh TY (2011) Epigenetic regulation in cell reprogramming revealed by genome-wide analysis. Epigenomics 3:73–81
Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DW, Holmes C (2013) Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol 31:748–752
Zovkic IB, Guzman-Karlsson MC, Sweatt JD (2013) Epigenetic regulation of memory formation and maintenance. Learn Mem 20:61–74
Kantlehner M, Kirchner R, Hartmann P, Ellwart JW, Alunni-Fabbroni M, Schumacher A (2011) A high-throughput DNA methylation analysis of a single cell. Nucleic Acids Res 39:e44
Hayashi-Takanaka Y, Yamagata K, Wakayama T, Stasevich TJ, Kainuma T, Tsurimoto T, Tachibana M, Shinkai Y, Kurumizaka H, Nozaki N, Kimura H (2011) Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling. Nucleic Acids Res 39:6475–6488
Robison AJ, Nestler EJ (2011) Transcriptional and epigenetic mechanisms of addiction. Nat Rev Neurosci 12:623–637
Zhang TY, Labonte B, Wen XL, Turecki G, Meaney MJ (2013) Epigenetic mechanisms for the early environmental regulation of hippocampal glucocorticoid receptor gene expression in rodents and humans. Neuropsychopharmacology 38:111–123
Guerrero-Bosagna C, Savenkova M, Haque MM, Nilsson E, Skinner MK (2013) Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility. PLoS One 8:e59922
Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23:781–783
Acknowledgements
The views expressed in this chapter are solely those of the authors and may not necessarily reflect those of NIH. The authors would like to thank all of the researchers associated with the NIH Roadmap Epigenomics Program for their tireless efforts to help transform this scientific field. We thank NIH senior leadership for their vision in selecting Epigenomics as a Common Fund program, especially Nora Volkow (NIDA), Linda Birnbaum (NIEHS), and James Battey (NIDCD). We thank the Common Fund Office of Science Coordination for financial support and encouragement. We thank the NIH Epigenomics Work Group members for their efforts and support during the development of this program. We especially thank Olivier Blondel, Mark Caulder, Christine Colvis, Stephanie Courchesne, Elise Feingold, Michelle Freund, Astrid Haugen, Tanya Hoodbhoy, Patricia Labosky, Roger Little, Pat Mastin, Michael Pazin, Phil Smith, Randall Stewart, and Elizabeth Wilder for their efforts in helping implement this program.
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Satterlee, J.S. et al. (2015). Community Resources and Technologies Developed Through the NIH Roadmap Epigenomics Program. In: Verma, M. (eds) Cancer Epigenetics. Methods in Molecular Biology, vol 1238. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1804-1_2
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