Relationship between genome and epigenome - challenges and requirements for future research

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Almouzni, Geneviève ^a   Altucci, Lucia ^b   Amati, Bruno ^c,d   Ashley, Neil ^e   Baulcombe, David ^f   Beaujean, Nathalie ^g   Bock, Christoph ^h   Bongcam Rudloff, Erik ⁱ   Bousquet, Jean ^j   Braun, Sigurd ^k   Paillerets, Brigitte Bressac de ^l   Bussemakers, Marion ^m   Clarke, Laura ⁿ   Conesa, Ana ^o   Estivill, Xavier ^p,q   Fazeli, Alireza ^r,s   Grgurević, Neža ^t   Gut, Ivo ^u   Heijmans, Bastiaan T ^v   Hermouet, Sylvie ^w   Houwing Duistermaat, Jeanine ^v   Iacobucci, Ilaria ^x   Ilaš, Janez ^t   Kandimalla, Raju ^y   Krauss Etschmann, Susanne ^z   Lasko, Paul ^aa   Lehmann, Sören ^ab   Lindroth, Anders ^ac   Majdič, Gregor ^t   Marcotte, Eric ^ad   Martinelli, Giovanni ^x   Martinet, Nadine ^ae   Meyer, Eric ^a   Miceli, Cristina ^af   Mills, Ken ^ag   Moreno Villanueva, Maria ^ah   Morvan, Ghislaine ^ai   Nickel, Dörthe ^a   Niesler, Beate ^aj   Nowacki, Mariusz ^ak   Nowak, Jacek ^al   Ossowski, Stephan ^p,q   Pelizzola, Mattia ^c   Pochet, Roland ^am   Potočnik, Uroš ^t   Radwanska, Magdalena ^an   Raes, Jeroen ^ao,ap,aq   Rattray, Magnus ^ar   Robinson, Mark D ^as   Roelen, Bernard ^at   Sauer, Sascha ^au   Schinzer, Dieter ^av   Slagboom, Eline ^v   Spector, Tim ^aw   Stunnenberg, Hendrik G ^m   Tiligada, Ekaterini ^ax   Torres Padilla, Maria Elena ^ay   Tsonaka, Roula ^v   Soom, Ann V ^az   Vidaković, Melita ^ba   Widschwendter, Martin ^y   more..

^a CNRS   (France)

^b SECOND UNIVERSITY OF NAPLES   (Italy)

^c ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^d EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^g INRA Institut National de la Recherche Agronomique   (France)

^h CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences ^*  (Austria)

ⁱ SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^j UNIV MONTPELLIER   (France)

^k UNIVERSITY OF MUNICH   (Germany)

^l INSTITUT GUSTAVE ROUSSY   (France)

^m RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

ⁿ EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Italy)

^o CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^p CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^q UNIVERSITAT POMPEU FABRA   (Spain)

^r UNIVERSITY OF SHEFFIELD   (United Kingdom)

^s UNIVERSITY OF LJUBLJANA   (Slovenia)

^t UNIVERSITY OF MARIBOR   (Slovenia)

^u Centre Nacional d'Analisi Genomica   (Spain)

^v LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^w NANTES UNIVERSITY HOSPITAL   (France)

^x UNIVERSITY OF BOLOGNA   (Italy)

^y UNIVERSITY COLLEGE LONDON   (United Kingdom)

^z INSTITUTE OF EPIDEMIOLOGY   (Germany)

^aa MCGILL UNIVERSITY   (Canada)

^ab KAROLINSKA INSTITUTE   (Sweden)

^ac GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^ad CANADIAN INSTITUTES OF HEALTH RESEARCH   (Canada)

^ae UNIVERSITÉ DE NICE SOPHIA ANTIPOLIS   (France)

^af UNIVERSITY OF CAMERINO   (Italy)

^ag QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^ah UNIVERSITY OF KONSTANZ   (Germany)

^ai MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^aj UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^ak UNIVERSITY OF BERN   (Switzerland)

^al INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

^am UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^an Universite Libre de Bruxelles ^*  (Belgium)

^ao VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^ap UNIVERSITY OF LEUVEN   (Belgium)

^aq DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^ar UNIVERSITY OF MANCHESTER   (United Kingdom)

^as UNIVERSITY OF ZURICH   (Switzerland)

^at UTRECHT UNIVERSITY   (Netherlands)

^au MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^av OTTO VON GUERICKE UNIVERSITY   (Germany)

^aw KING'S COLLEGE LONDON   (United Kingdom)

^ax UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

^ay INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^az GHENT UNIVERSITY   (Belgium)

^ba Institute for Biological Research   (Serbia)

more..

Author keywords

Environment; Epigenome; Genome; Microbiome

Indexed keywords

AZACITIDINE;

AIR POLLUTION; ALLERGY; ARTICLE; CUTANEOUS T CELL LYMPHOMA; DISEASE PREDISPOSITION; DNA DAMAGE; DNA METHYLATION; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL FACTOR; EPIGENETICS; GENE EXPRESSION; GENE FUNCTION; LIFESPAN; LIFESTYLE; MYELODYSPLASTIC SYNDROME; NUTRITION; GENETIC EPIGENESIS; GENOME; GENOMICS; HUMAN; RESEARCH;

EPIGENESIS, GENETIC; EPIGENOMICS; GENOME; GENOMICS; HUMANS; RESEARCH;

EID: 84902300179     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-487     Document Type: Article

References (20)

1. 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. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322. 10.1038/nature08514 [doi].
2. Bird A. Perceptions of epigenetics. Nature 2007, 447:396-398. 10.1038/nature05913 [doi].
3. Mill J, Heijmans BT. From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet 2013, 14:585-594. 10.1038/nrg3405 [doi].
4. Kapeller J, Houghton LA, Monnikes H, Walstab J, Moller D, Bonisch H, Burwinkel B, Autschbach F, Funke B, Lasitschka F, Gassler N, Fischer C, Whorwell PJ, Atkinson W, Fell C, Buchner KJ, Schmidtmann M, Van DV I, Wisser AS, Berg T, Rappold G, Niesler B. First evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome. Hum Mol Genet 2008, 17:2967-2977. 10.1093/hmg/ddn195 [doi].
5. Anto JM, Pinart M, Akdis M, Auffray C, Bachert C, Basagana X, Carlsen KH, Guerra S, Von HL, Illi S, Kauffmann F, Keil T, Kiley JP, Koppelman GH, Lupinek C, Martinez FD, Nawijn MC, Postma DS, Siroux V, Smit HA, Sterk PJ, Sunyer J, Valenta R, Valverde S, Akdis CA, Annesi-Maesano I, Ballester F, Benet M, Cambon-Thomsen A, Chatzi L, et al. Understanding the complexity of IgE-related phenotypes from childhood to young adulthood: a Mechanisms of the Development of Allergy (MeDALL) seminar. J Allergy Clin Immunol 2012, 129:943-954. 10.1016/j.jaci.2012.01.047 [doi].
6. Krauss-Etschmann S, Bush A, Bellusci S, Brusselle GG, Dahlen SE, Dehmel S, Eickelberg O, Gibson G, Hylkema MN, Knaus P, Konigshoff M, Lloyd CM, Macciarini P, Mailleux A, Marsland BJ, Postma DS, Roberts G, Samakovlis C, Stocks J, Vandesompele J, Wjst M, Holloway J. Of flies, mice and men: a systematic approach to understanding the early life origins of chronic lung disease. Thorax 2013, 68:380-384. 10.1136/thoraxjnl-2012-201902 [doi].
7. Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Kuppers R, Lehrach H, Lengauer T, Lernmark A, Leslie D, et al. BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol 2012, 30:224-226. 10.1038/nbt.2153 [doi].
8. Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HH, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC, Benedetti R, Altucci L, Jansen JH, Walter J, Gut IG, Marks H, Stunnenberg HG. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 2013, 13:360-369. 10.1016/j.stem.2013.06.002 [doi].
9. Barker DJ, Winter PD, Osmond C, Margetts B, Simmonds SJ. Weight in infancy and death from ischaemic heart disease. Lancet 1989, 2:577-580.
10. Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A 2008, 105:17046-17049. 10.1073/pnas.0806560105 [doi].
11. Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, Von BM, McCoy KD, Macpherson AJ, Danska JS. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 2013, 339:1084-1088. 10.1126/science.1233521 [doi].
12. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, Savage DA, Mueller-Holzner E, Marth C, Kocjan G, Gayther SA, Jones A, Beck S, Wagner W, Laird PW, Jacobs IJ, Widschwendter M. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010, 20:440-446. 10.1101/gr.103606.109 [doi].
13. Soria G, Polo SE, Almouzni G. Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol Cell 2012, 46:722-734. 10.1016/j.molcel.2012.06.002 [doi].
14. Schenk T, Chen WC, Gollner S, Howell L, Jin L, Hebestreit K, Klein HU, Popescu AC, Burnett A, Mills K, Casero RA, Marton L, Woster P, Minden MD, Dugas M, Wang JC, Dick JE, Muller-Tidow C, Petrie K, Zelent A. Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia. Nat Med 2012, 18:605-611. 10.1038/nm.2661 [doi].
15. Dell'Aversana C, Lepore I, Altucci L. HDAC modulation and cell death in the clinic. Exp Cell Res 2012, 318:1229-1244. 10.1016/j.yexcr.2012.01.025 [doi].
16. McCabe MT, Ott HM, Ganji G, Korenchuk S, Thompson C, Van Aller GS, Liu Y, Graves AP, Della PA, Diaz E, LaFrance LV, Mellinger M, Duquenne C, Tian X, Kruger RG, McHugh CF, Brandt M, Miller WH, Dhanak D, Verma SK, Tummino PJ, Creasy CL. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 2012, 492:108-112. 10.1038/nature11606 [doi].
17. Gronbaek K, Hother C, Jones PA. Epigenetic changes in cancer. APMIS 2007, 115:1039-1059.
18. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, Jager N, Gnirke A, Stunnenberg HG, Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28:1106-1114. 10.1038/nbt.1681 [doi].
19. Stunnenberg HG, Hubner NC. Genomics meets proteomics: identifying the culprits in disease. Hum Genet 2013, 10. 1007/s00439-013-1376-2 [doi].
20. Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernandez JM, Rodriguez JM, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G. The EMBRACE web service collection. Nucleic Acids Res 2010, 38:W683-W688. 10.1093/nar/gkq297 [doi].