Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.

Center for Molecular Medicine University Medical Center Utrecht Hubrecht Institute KNAW 3584 CT Utrecht The Netherlands;

Commissariat à l'Energie Atomique et aux Energies Alternatives iBiTec S Université Paris Sud CNRS FRE3377 F 91191 Gif sur Yvette cedex France;

Department of Computational Biology Max Planck Institute for Molecular Genetics 14195 Berlin Germany;

European Research Institute for the Biology of Ageing University of Groningen University Medical Center Groningen NL 9713 AV Groningen The Netherlands;

Groningen Bioinformatics Centre 9747AG Groningen The Netherlands;

Institut of Physiology Academy of Sciences of the Czech Republic Videnska 1083 CZ 14220 Prague 4 Czech Republic;

Max Delbrück Center for Molecular Medicine 13125 Berlin Germany;

Max Delbrück Center for Molecular Medicine 13125 Berlin Germany; Department of Computational Biology Max Planck Institute for Molecular Genetics 14195 Berlin Germany;

Max Delbrück Center for Molecular Medicine Partner site Berlin 13125 Berlin Germany

National Heart and Lung Institute Cardiovascular Genetics and Genomics London SW3 6NP United Kingdom; Duke NUS Graduate Medical School 169857 Singapore; National Heart Center Singapore 169609 Singapore;

See more in PubMed

Anders S, Huber W 2010. Differential expression analysis for sequence count data. Genome Biol 11: r106. PubMed PMC

Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, et al. 2010. The genome sequence of the spontaneously hypertensive rat: analysis and functional significance. Genome Res 20: 791–803 PubMed PMC

Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823–837 PubMed

Benjamini Y, Hochberg Y 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289–300

Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, et al. 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169–181 PubMed

Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, et al. 2008. Genetical genomics: spotlight on QTL hotspots. PLoS Genet 4: e1000232. PubMed PMC

Brem RB, Yvert G, Clinton R, Kruglyak L 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755 PubMed

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, et al. 2012. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390–394 PubMed PMC

Dempster A, Laird N, Rubin D 1977. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B Methodol 39: 1–38

Efron B 2004. Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J Am Stat Assoc 99: 96–104

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43–49 PubMed PMC

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. 2012. Ensembl 2012. Nucleic Acids Res 40: D84–D90 PubMed PMC

Fuda NJ, Ardehali MB, Lis JT 2009. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461: 186–192 PubMed PMC

Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, et al. 2010. A map of open chromatin in human pancreatic islets. Nat Genet 42: 255–259 PubMed PMC

Greer EL, Shi Y 2012. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13: 343–357 PubMed PMC

Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A 2011. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature 479: 365–371 PubMed PMC

Heinig M, Petretto E, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A, et al. 2010. A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 467: 460–464 PubMed PMC

Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, et al. 2005. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 37: 243–253 PubMed

Kadota M, Yang HH, Hu N, Wang C, Hu Y, Taylor PR, Buetow KH, Lee MP 2007. Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome. PLoS Genet 3: e81. PubMed PMC

Karlić R, Chung H-R, Lasserre J, Vlahovicek K, Vingron M 2010. Histone modification levels are predictive for gene expression. Proc Natl Acad Sci 107: 2926–2931 PubMed PMC

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, et al. 2010. Variation in transcription factor binding among humans. Science 328: 232–235 PubMed PMC

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, et al. 2013. Extensive variation in chromatin states across humans. Science 342: 750–752 PubMed PMC

Kouzarides T 2007. Chromatin modifications and their function. Cell 128: 693–705 PubMed

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22: 1813–1831 PubMed PMC

Leinonen R, Sugawara H, Shumway M 2011. The sequence read archive. Nucleic Acids Res 39: D19–D21 PubMed PMC

Li B, Carey M, Workman JL 2007. The role of chromatin during transcription. Cell 128: 707–719 PubMed

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079 PubMed PMC

Manke T, Heinig M, Vingron M 2010. Quantifying the effect of sequence variation on regulatory interactions. Hum Mutat 31: 477–483 PubMed

McDaniell R, Lee B-K, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, et al. 2010. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235–239 PubMed PMC

McDermott-Roe C, Ye J, Ahmed R, Sun X-M, Serafín A, Ware J, Bottolo L, Muckett P, Cañas X, Zhang J, et al. 2011. Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function. Nature 478: 114–118 PubMed PMC

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK 2013. Identification of genetic variants that affect histone modifications in human cells. Science 342: 747–749 PubMed PMC

Micsinai M, Parisi F, Strino F, Asp P, Dynlacht BD, Kluger Y 2012. Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res 40: e70. PubMed PMC

Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T-K, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553–560 PubMed PMC

Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG 2004. Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743–747 PubMed PMC

Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, et al. 2007. ArrayExpress–a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35: D747–D750 PubMed PMC

Petretto E, Sarwar R, Grieve I, Lu H, Kumaran MK, Muckett PJ, Mangion J, Schroen B, Benson M, Punjabi PP, et al. 2008. Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass. Nat Genet 40: 546–552 PubMed PMC

Pravenec M, Churchill PC, Churchill MC, Viklicky O, Kazdova L, Aitman TJ, Petretto E, Hubner N, Wallace CA, Zimdahl H, et al. 2008. Identification of renal Cd36 as a determinant of blood pressure and risk for hypertension. Nat Genet 40: 952–954 PubMed

Rieseberg LH, Archer MA, Wayne RK 1999. Transgressive segregation, adaptation and speciation. Heredity 83: 363–372 PubMed

Ringrose L, Paro R 2004. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38: 413–443 PubMed

Rockman MV, Kruglyak L 2006. Genetics of global gene expression. Nat Rev Genet 7: 862–872 PubMed

Saar K, Beck A, Bihoreau M-T, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, et al. 2008. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet 40: 560–566 PubMed PMC

Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al. 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297–302 PubMed

Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, et al. 2005. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37: 710–717 PubMed PMC

Schlesinger J, Schueler M, Grunert M, Fischer JJ, Zhang Q, Krueger T, Lange M, Tönjes M, Dunkel I, Sperling SR 2011. The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet 7: e1001313. PubMed PMC

Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, et al. 2010. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res 38: 5919–5928 PubMed PMC

Simonis M, Atanur SS, Linsen S, Guryev V, Ruzius F-P, Game L, Lansu N, de Bruijn E, van Heesch S, Jones SJM, et al. 2012. Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel. Genome Biol 13: r31. PubMed PMC

Soutourina J, Wydau S, Ambroise Y, Boschiero C, Werner M 2011. Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science 331: 1451–1454 PubMed

Storey JD 2003. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Stat 31: 2013–2035

Strimmer K 2008. A unified approach to false discovery rate estimation. BMC Bioinformatics 9: 303. PubMed PMC

Tanksley SD 1993. Mapping polygenes. Annu Rev Genet 27: 205–233 PubMed

Trapnell C, Pachter L, Salzberg SL 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105–1111 PubMed PMC

Venables WN, Ripley BD 2002. Modern applied statistics with S. Springer Science + Business Media, New York

Wingender E, Dietze P, Karas H, Knüppel R 1996. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24: 238–241 PubMed PMC

Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD 2005. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121: 859–872 PubMed

Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W 2009. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952–1958 PubMed PMC

Zee BM, Levin RS, Xu B, LeRoy G, Wingreen NS, Garcia BA 2010. In vivo residue-specific histone methylation dynamics. J Biol Chem 285: 3341–3350 PubMed PMC

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: r137. PubMed PMC

Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling

Systems Genetics Approaches in Rat Identify Novel Genes and Gene Networks Associated With Cardiac Conduction

Translational regulation shapes the molecular landscape of complex disease phenotypes

histoneHMM: Differential analysis of histone modifications with broad genomic footprints