Genetic and Epigenetic Gene Regulation

Publications

Selected publications

Heinig M*, Adriaens ME*, Schafer S*, van Deutekom HWM, Lodder EM, Ware JS, Schneider V, Felkin LE, Creemers EE, Meder B, Katus HA, Rühle F, Stoll M, Cambien F, Villard E, Charron P, Varro A, Bishopric NH, George AL Jr, Dos Remedios C, Moreno-Moral A, Pesce F, Bauerfeind A, Rüschendorf F, Rintisch C, Petretto E, Barton PJ, Cook SA, Pinto YM, Bezzina CR, Hubner N. Genome Biol. 2017; 18:170

Budach S, Heinig M*, Marsico A*. Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. Genetics. 2016; pii: genetics.116.187153.

Heinig M, Colome-Tatche M, Rintisch C, Schäfer S, Pravenec M, Hubner N, Vingron M, Johannes F. histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics. 2015; 16:60

Rintisch C*, Heinig M*, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colome-Tatche M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, and Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res. 2014; 24(6):942-53

Heinig M*, Petretto E*, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A, Hummel O, Lee YA, Paskas S, Rintisch C, Saar K, Cooper J, Buchan R, Gray EE, Cyster JG; Cardiogenics Consortium, Erdmann J, Hengstenberg C, Maouche S, Ouwehand WH, Rice CM, Samani NJ, Schunkert H, Goodall AH, Schulz H, Roider HG, Vingron M, Blankenberg S, Münzel T, Zeller T, Szymczak S, Ziegler A, Tiret L, Smyth DJ, Pravenec M, Aitman TJ, Cambien F, Clayton D, Todd JA, Hubner N, Cook SA. A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature. 2010; 467(7314):460-4

Manke T*, Heinig M*, and Vingron M. Quantifying the effect of sequence variation on regulatory interactions. Hum Mutat. 2010; 31(4):477-83

* authors contributed equally to the work

Full list of publications

Yan X, Wang Z, Schmidt V, Gauert A, Willnow TE, Heinig M, Poy MN. Cadm2 regulates body weight and energy homeostasis in mice. Mol Metab. 2017; pii: S2212-8778(17)30772

Heinig M*, Adriaens ME*, Schafer S*, van Deutekom HWM, Lodder EM, Ware JS, Schneider V, Felkin LE, Creemers EE, Meder B, Katus HA, Rühle F, Stoll M, Cambien F, Villard E, Charron P, Varro A, Bishopric NH, George AL Jr, Dos Remedios C, Moreno-Moral A, Pesce F, Bauerfeind A, Rüschendorf F, Rintisch C, Petretto E, Barton PJ, Cook SA, Pinto YM, Bezzina CR, Hubner N. Genome Biol. 2017; 18:170

Rathjen T, Yan X, Kononenko NL, Ku MC, Song K, Ferrarese L, Tarallo V, Puchkov D, Kochlamazashvili G, Brachs S, Varela L, Szigeti-Buck K, Yi CX, Schriever SC, Tattikota SG, Carlo AS, Moroni M, Siemens J, Heuser A, van der Weyden L, Birkenfeld AL, Niendorf T, Poulet JFA, Horvath TL, Tschöp MH, Heinig M, Trajkovski M, Haucke V, Poy MN. Regulation of body weight and energy homeostasis by neuronal cell adhesion molecule 1. Nat Neurosci. 2017;20(8):1096-1103

Davari K, Lichti J, Gallus C, Greulich F, Uhlenhaut NH, Heinig M, Friedel CC, Glasmacher E. Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses. Cell Rep. 2017;19(3):643-654

McDermott-Roe C, Leleu M, Rowe GC, Palygin O, Bukowy JD, Kuo J, Rech M, Hermans-Beijnsberger S, Schaefer S, Adami E, Creemers EE, Heinig M, Schroen B, Arany Z, Petretto E, Geurts AM. Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PLoS One. 2017;12(2):e0170458

Maatz H, van Heesch S, Kreuchwig F, Faber A, Adami E, Hubner N, Heinig M. Epigenetics and Control of RNAs. Methods Mol Biol. 2017;1488:217-237.

van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio LA, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW. 52 Genetic Loci Influencing Myocardial Mass. J Am Coll Cardiol. 2016; 68(13):1435-1448

Budach S, Heinig M*, Marsico A*. Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. Genetics. 2016; pii: genetics.116.187153.

Ojeda FM, Müller C, Börnigen D, Trégouët DA, Schillert A, Heinig M, Zeller T, Schnabel RB. Comparison of Cox Model Methods in A Low-dimensional Setting with Few Events. Genomics Proteomics Bioinformatics. 2016; pii: S1672-0229(16)30039-0

de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C. A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses. Genome Med. 2016; 8(1):28.

Marenholz I, Esparza-Gordillo J, Rüschendorf F, Bauerfeind A, Strachan DP, Spycher BD, Baurecht H, Margaritte-Jeannin P, Sääf A, Kerkhof M, Ege M, Baltic S, Matheson MC, Li J, Michel S, Ang WQ, McArdle W, Arnold A, Homuth G, Demenais F, Bouzigon E, Söderhäll C, Pershagen G, de Jongste JC, Postma DS, Braun-Fahrländer C, Horak E, Ogorodova LM, Puzyrev VP, Bragina EY, Hudson TJ, Morin C, Duffy DL, Marks GB, Robertson CF, Montgomery GW, Musk B, Thompson PJ, Martin NG, James A, Sleiman P, Toskala E, Rodriguez E, Fölster-Holst R, Franke A, Lieb W, Gieger C, Heinzmann A, Rietschel E, Keil T, Cichon S, Nöthen MM, Pennell CE, Sly PD, Schmidt CO, Matanovic A, Schneider V, Heinig M, Hübner N, Holt PG, Lau S, Kabesch M, Weidinger S, Hakonarson H, Ferreira MA, Laprise C, Freidin MB, Genuneit J, Koppelman GH, Melén E, Dizier MH, Henderson AJ, Lee YA. Meta-analysis identifies seven susceptibility loci involved in the atopic march. Nat Commun. 2015; 6:8804.

Lindblom RP, Berg A, Ström M, Aeinehband S, Dominguez CA, Al Nimer F, Abdelmagid N, Heinig M, Zelano J, Harnesk K, Hübner N, Nilsson B, Ekdahl KN, Diez M, Cullheim S, Piehl F. Complement receptor 2 is up regulated in the spinal cord following nerve root injury and modulates the spinal cord response. J Neuroinflammation. 2015; 12:192.

Binger KJ, Gebhardt M, Heinig M, Rintisch C, Schroeder A, Neuhofer W, Hilgers K, Manzel A, Schwartz C, Kleinewietfeld M, Voelkl J, Schatz V, Linker RA, Lang F, Voehringer D, Wright MD, Hubner N, Dechend R, Jantsch J, Titze J, Müller DN. High salt reduces the activation of IL-4- and IL-13-stimulated macrophages. J Clin Invest. 2015;125(11):4223-38.

Schafer S, Miao K, Benson CC, Heinig M, Cook SA, Hubner N. Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI). Curr Protoc Hum Genet. 2015;87:11.16.1-11.16.14.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration. Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol. 2015;33(9):933-40.

Schafer S, Adami E, Heinig M, Rodrigues KE, Kreuchwig F, Silhavy J, van Heesch S, Simaite D, Rajewsky N, Cuppen E, Pravenec M, Vingron M, Cook SA, Hubner N. Translational regulation shapes the molecular landscape of complex disease phenotypes. Nat Commun. 2015;6:7200

Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E; the Genetic and Environmental Risk for Alzheimer's Disease (GERAD1) Consortium, Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M. Quantitative Interaction Proteomics of Neurodegenerative Disease Proteins. Cell Rep. 2015; pii: S2211-1247(15)00431-3. doi: 10.1016/j.celrep.2015.04.030.

Jantsch J, Schatz V, Friedrich D, Schröder A, Kopp C, Siegert I, Maronna A, Wendelborn D, Linz P, Binger KJ, Gebhardt M, Heinig M, Neubert P, Fischer F, Teufel S, David JP, Neufert C, Cavallaro A, Rakova N, Küper C, Beck FX, Neuhofer W, Muller DN, Schuler G, Uder M, Bogdan C, Luft FC, Titze J. Cutaneous na(+) storage strengthens the antimicrobial barrier function of the skin and boosts macrophage-driven host defense. Cell Metab. 2015; 21(3):493-501

Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JA, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJ, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJ, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med. 2015; 7(270):270ra6

Heinig M, Colome-Tatche M, Rintisch C, Schäfer S, Pravenec M, Hubner N, Vingron M, Johannes F. histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics 2015; 16:60

Maatz H, Jens M, Liss M, Schafer S, Heinig M, Kirchner M, Adami E, Rintisch C, Dauksaite V, Radke MH, Selbach M, Barton PJ, Cook SA, Rajewsky N, Gotthardt M, Landthaler M, Hubner N. RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. J Clin Invest. 2014; 124(8):3419-30

Rintisch C*, Heinig M*, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colome-Tatche M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, and Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res. 2014; 24(6):942-53

Lindblom RP, Ström M, Heinig M, Al Nimer F, Aeinehband S, Berg A, Dominguez CA, Vijayaraghavan S, Zhang XM, Harnesk K, Zelano J, Hübner N, Cullheim S, Darreh-Shori T, Diez M, Piehl F. Unbiased expression mapping identifies a link between the complement and cholinergic systems in the rat central nervous system. J Immunol. 2014; 192(3):1138-53

Arndt AK, Schafer S, Drenckhahn JD, Sabeh MK, Plovie ER, Caliebe A, Klopocki E, Musso G, Werdich AA, Kalwa H, Heinig M, Padera RF, Wassilew K, Bluhm J, Harnack C, Martitz J, Barton PJ, Greutmann M, Berger F, Hubner N, Siebert R, Kramer HH, Cook SA, MacRae CA, Klaassen S. Fine mapping of the 1p36 deletion syndrome identifies mutation of PRDM16 as a cause of cardiomyopathy. Am J Hum Genet. 2013; 93(1):67-77

Rat Genome Sequencing and Mapping Consortium. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat Genet. 2013; 45(7):767-75

Morrissey C, Grieve IC, Heinig M, Atanur S, Petretto E, Pravenec M, Hubner N, Aitman TJ. Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat. Physiol Genomics. 2011; 43(21):1207-18

Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, El Masri N, Roider HG, Manke T and Vingron M. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc. 2011; 6(12):1860-9

Heinig M*, Petretto E*, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A, Hummel O, Lee YA, Paskas S, Rintisch C, Saar K, Cooper J, Buchan R, Gray EE, Cyster JG; Cardiogenics Consortium, Erdmann J, Hengstenberg C, Maouche S, Ouwehand WH, Rice CM, Samani NJ, Schunkert H, Goodall AH, Schulz H, Roider HG, Vingron M, Blankenberg S, Münzel T, Zeller T, Szymczak S, Ziegler A, Tiret L, Smyth DJ, Pravenec M, Aitman TJ, Cambien F, Clayton D, Todd JA, Hubner N, Cook SA. A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature. 2010; 467(7314):460-4

Manke T*, Heinig M*, and Vingron M. Quantifying the effect of sequence variation on regulatory interactions. Hum Mutat. 2010; 31(4):477-83

Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, Sarwar R, Pravenec M, Hubner N, Aitman TJ, Cook SA, Richardson S.: New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol. 2010; 6(4):e1000737

The STAR Consortium. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008; 40(5):560-6

Monti J, Fischer J, Paskas S, Heinig M, Schulz H, Gösele C, Heuser A, Fischer R, Schmidt C, Schirdewan A, Gross V, Hummel O, Maatz H, Patone G, Saar K, Vingron M, Weldon SM, Lindpaintner K, Hammock BD, Rohde K, Dietz R, Cook SA, Schunck W, Luft FC, Hubner N: Soluble epoxide hydrolase is a susceptibility factor for heart failure in a rat model of human disease. Nat Genet. 2008; 40(5):529-37

Toedling J, Schmeier S, Heinig M, Georgi B and Roepcke S: MACAT - MicroArray Chromosome Analysis Tool. Bioinformatics. 2005; 21(9):2112-3

Heinig M, Frishman D: STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res. 2004; 32(Web Server issue):W500-2

* authors contributed equally to the work