{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T18:27:49Z","timestamp":1770488869342,"version":"3.49.0"},"reference-count":89,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T00:00:00Z","timestamp":1600646400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T00:00:00Z","timestamp":1600646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Ecol Evol"],"DOI":"10.1038\/s41559-020-01310-1","type":"journal-article","created":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T16:05:04Z","timestamp":1600704304000},"page":"1713-1724","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["The methylation landscape and its role in domestication and gene regulation in the chicken"],"prefix":"10.1038","volume":"4","author":[{"given":"Andrey","family":"H\u00f6glund","sequence":"first","affiliation":[]},{"given":"Rie","family":"Henriksen","sequence":"additional","affiliation":[]},{"given":"Jesper","family":"Fogelholm","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1902-3002","authenticated-orcid":false,"given":"Allison M.","family":"Churcher","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1935-5875","authenticated-orcid":false,"given":"Carlos M.","family":"Guerrero-Bosagna","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5064-2093","authenticated-orcid":false,"given":"Alvaro","family":"Martinez-Barrio","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Johnsson","sequence":"additional","affiliation":[]},{"given":"Per","family":"Jensen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2329-2635","authenticated-orcid":false,"given":"Dominic","family":"Wright","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,9,21]]},"reference":[{"key":"1310_CR1","doi-asserted-by":"crossref","unstructured":"Jensen, P. & Wright, D. in Genetics and Behavior of Domestic Animals (eds Grandin, T. & Deesing, M. J.) 41\u201380 (Academic Press, 2014).","DOI":"10.1016\/B978-0-12-394586-0.00002-0"},{"key":"1310_CR2","first-page":"11","volume":"9","author":"D Wright","year":"2015","unstructured":"Wright, D. The genetic architecture of domestication in animals. Bioinform. Biol. Insights 9, 11\u201320 (2015).","journal-title":"Bioinform. Biol. Insights"},{"key":"1310_CR3","doi-asserted-by":"crossref","first-page":"12505","DOI":"10.1073\/pnas.91.26.12505","volume":"91","author":"A Fumihito","year":"1994","unstructured":"Fumihito, A., Miyake, T., Sumi, S. I., Ohno, S. & Kondo, N. One species of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc. Natl Acad. Sci. USA 91, 12505\u201312509 (1994).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1310_CR4","doi-asserted-by":"crossref","first-page":"6792","DOI":"10.1073\/pnas.93.13.6792","volume":"93","author":"A Fumihito","year":"1996","unstructured":"Fumihito, A. et al. Monophyletic origin and unique dispersal patterns of domestic fowls. Proc. Natl Acad. Sci. USA 93, 6792\u20136795 (1996).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1310_CR5","unstructured":"Frantz, L. A. & Larson, G. in Hybrid Communities: Biosocial Approaches to Domestication and Other Trans-species Relationships (eds St\u00e9panoff, C. & Vigne, J.-D.) Ch. 1 (Taylor & Francis, 2018)."},{"key":"1310_CR6","doi-asserted-by":"crossref","first-page":"6139","DOI":"10.1073\/pnas.1323964111","volume":"111","author":"G Larson","year":"2014","unstructured":"Larson, G. et al. Current perspectives and the future of domestication studies. Proc. Natl Acad. Sci. USA 111, 6139\u20136146 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1310_CR7","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev-ecolsys-110512-135813","volume":"45","author":"G Larson","year":"2014","unstructured":"Larson, G. & Fuller, D. Q. The evolution of animal domestication. Annu. Rev. Ecol. Evol. Syst. 45, 115\u2013136 (2014).","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"1310_CR8","doi-asserted-by":"publisher","unstructured":"Johnsson, M., Jonsson, K. B., Andersson, L., Jensen, P. & Wright, D. Quantitative trait locus and genetical genomics analysis identifies putatively causal genes for fecundity and brooding in the chicken. G3 (Bethesda) https:\/\/doi.org\/10.1534\/g3.115.024299 (2015).","DOI":"10.1534\/g3.115.024299"},{"key":"1310_CR9","doi-asserted-by":"publisher","unstructured":"Henriksen, R., Johnsson, M., Andersson, L., Jensen, P. & Wright, D. The domesticated brain: genetics of brain mass and brain structure in an avian species. Sci. Rep. 6, https:\/\/doi.org\/10.1038\/srep34031 (2016).","DOI":"10.1038\/srep34031"},{"key":"1310_CR10","doi-asserted-by":"crossref","first-page":"e1005250","DOI":"10.1371\/journal.pgen.1005250","volume":"11","author":"M Johnsson","year":"2015","unstructured":"Johnsson, M., Jonsson, K. B., Andersson, L., Jensen, P. & Wright, D. Genetic regulation of bone metabolism in the chicken: similarities and differences to mammalian systems. PLoS Genet. 11, e1005250 (2015).","journal-title":"PLoS Genet."},{"key":"1310_CR11","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-018-4441-3","volume":"19","author":"M Johnsson","year":"2018","unstructured":"Johnsson, M. et al. Genetical genomics of growth in a chicken model. BMC Genom. 19, 72 (2018).","journal-title":"BMC Genom."},{"key":"1310_CR12","doi-asserted-by":"crossref","first-page":"e1002914","DOI":"10.1371\/journal.pgen.1002914","volume":"8","author":"M Johnsson","year":"2012","unstructured":"Johnsson, M. et al. A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication. PLoS Genet. 8, e1002914 (2012).","journal-title":"PLoS Genet."},{"key":"1310_CR13","doi-asserted-by":"crossref","first-page":"341","DOI":"10.3390\/genes10050341","volume":"10","author":"J Fogelholm","year":"2019","unstructured":"Fogelholm, J. et al. Genetical genomics of tonic immobility in the chicken. Genes 10, 341 (2019).","journal-title":"Genes"},{"key":"1310_CR14","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1534\/genetics.118.300810","volume":"209","author":"M Johnsson","year":"2018","unstructured":"Johnsson, M. et al. Genetics and genomics of social behavior in a chicken model. Genetics 209, 209\u2013221 (2018).","journal-title":"Genetics"},{"key":"1310_CR15","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1534\/genetics.115.179010","volume":"202","author":"M Johnsson","year":"2016","unstructured":"Johnsson, M., Williams, M. J., Jensen, P. & Wright, D. Genetical genomics of behavior: a novel chicken genomic model for anxiety behavior. Genetics 202, 327\u2013340 (2016).","journal-title":"Genetics"},{"key":"1310_CR16","doi-asserted-by":"crossref","DOI":"10.1186\/s12711-018-0384-z","volume":"50","author":"J B\u00e9lteky","year":"2018","unstructured":"B\u00e9lteky, J. et al. Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans. Genet. Sel. Evol. 50, 13 (2018).","journal-title":"Genet. Sel. Evol."},{"key":"1310_CR17","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1080\/15592294.2019.1609868","volume":"14","author":"F P\u00e9rtille","year":"2019","unstructured":"P\u00e9rtille, F. et al. Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 14, 685\u2013707 (2019).","journal-title":"Epigenetics"},{"key":"1310_CR18","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-13-59","volume":"13","author":"D N\u00e4tt","year":"2012","unstructured":"N\u00e4tt, D. et al. Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. BMC Genom. 13, 59 (2012).","journal-title":"BMC Genom."},{"key":"1310_CR19","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/nar\/23.6.901","volume":"23","author":"K Gaston","year":"1995","unstructured":"Gaston, K. & Fried, M. CpG methylation has differential effects on the binding of YY1 and ETS proteins to the bi-directional promoter of the Surf-1 and Surf-2 genes. Nucleic Acids Res. 23, 901\u2013909 (1995).","journal-title":"Nucleic Acids Res."},{"key":"1310_CR20","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.146654.112","volume":"23","author":"IK Mann","year":"2013","unstructured":"Mann, I. K. et al. CG methylated microarrays identify a novel methylated sequence bound by the CEBPB| ATF4 heterodimer that is active in vivo. Genome Res. 23, 988\u2013997 (2013).","journal-title":"Genome Res."},{"key":"1310_CR21","doi-asserted-by":"crossref","first-page":"eaaj2239","DOI":"10.1126\/science.aaj2239","volume":"356","author":"Y Yin","year":"2017","unstructured":"Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).","journal-title":"Science"},{"key":"1310_CR22","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/ng.3522","volume":"48","author":"O Bogdanovi\u0107","year":"2016","unstructured":"Bogdanovi\u0107, O. et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat. Genet. 48, 417\u2013426 (2016).","journal-title":"Nat. Genet."},{"key":"1310_CR23","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.trecan.2016.08.004","volume":"2","author":"M Murtha","year":"2016","unstructured":"Murtha, M. & Esteller, M. Extraordinary cancer epigenomics: thinking outside the classical coding and promoter box. Trends Cancer 2, 572\u2013584 (2016).","journal-title":"Trends Cancer"},{"key":"1310_CR24","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0879-2","volume":"17","author":"H Heyn","year":"2016","unstructured":"Heyn, H. et al. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer. Genome Biol. 17, 11 (2016).","journal-title":"Genome Biol."},{"key":"1310_CR25","doi-asserted-by":"crossref","first-page":"60","DOI":"10.3389\/fgene.2015.00060","volume":"6","author":"DM Ruden","year":"2015","unstructured":"Ruden, D. M. et al. Epigenetics as an answer to Darwin\u2019s \u201cspecial difficulty,\u201d part 2: natural selection of metastable epialleles in honeybee castes. Front. Genet. 6, 60 (2015).","journal-title":"Front. Genet."},{"key":"1310_CR26","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1089\/dna.2010.1094","volume":"30","author":"C Anastasiadou","year":"2011","unstructured":"Anastasiadou, C., Malousi, A., Maglaveras, N. & Kouidou, S. Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers. DNA Cell Biol. 30, 267\u2013275 (2011).","journal-title":"DNA Cell Biol."},{"key":"1310_CR27","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1126\/science.1242510","volume":"342","author":"M Kasowski","year":"2013","unstructured":"Kasowski, M. et al. Extensive variation in chromatin states across humans. Science 342, 750\u2013752 (2013).","journal-title":"Science"},{"key":"1310_CR28","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1126\/science.1242463","volume":"342","author":"H Kilpinen","year":"2013","unstructured":"Kilpinen, H. et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342, 744\u2013747 (2013).","journal-title":"Science"},{"key":"1310_CR29","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1126\/science.1242429","volume":"342","author":"G McVicker","year":"2013","unstructured":"McVicker, G. et al. Identification of genetic variants that affect histone modifications in human cells. Science 342, 747\u2013749 (2013).","journal-title":"Science"},{"key":"1310_CR30","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.semcdb.2019.07.006","volume":"97","author":"C Guerrero-Bosagna","year":"2020","unstructured":"Guerrero-Bosagna, C. From epigenotype to new genotypes: relevance of epigenetic mechanisms in the emergence of genomic evolutionary novelty. Semin. Cell Dev. Biol. 97, 86\u201392 (2020).","journal-title":"Semin. Cell Dev. Biol."},{"key":"1310_CR31","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1126\/science.1246755","volume":"342","author":"TS Furey","year":"2013","unstructured":"Furey, T. S. & Sethupathy, P. Genetics driving epigenetics. Science 342, 705\u2013706 (2013).","journal-title":"Science"},{"key":"1310_CR32","volume":"12","author":"JT Bell","year":"2011","unstructured":"Bell, J. T. et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12, R10 (2011).","journal-title":"Genome Biol."},{"key":"1310_CR33","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1136\/annrheumdis-2017-212379","volume":"77","author":"J Imgenberg-Kreuz","year":"2018","unstructured":"Imgenberg-Kreuz, J. et al. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann. Rheum. Dis. 77, 736\u2013743 (2018).","journal-title":"Ann. Rheum. Dis."},{"key":"1310_CR34","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/ng.3721","volume":"49","author":"MJ Bonder","year":"2017","unstructured":"Bonder, M. J. et al. Disease variants alter transcription factor levels and methylation of their binding sites. Nat. Genet. 49, 131\u2013138 (2017).","journal-title":"Nat. Genet."},{"key":"1310_CR35","doi-asserted-by":"crossref","first-page":"e1000952","DOI":"10.1371\/journal.pgen.1000952","volume":"6","author":"JR Gibbs","year":"2010","unstructured":"Gibbs, J. R. et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 6, e1000952 (2010).","journal-title":"PLoS Genet."},{"key":"1310_CR36","doi-asserted-by":"crossref","first-page":"e05255","DOI":"10.7554\/eLife.05255","volume":"4","author":"MJ Dubin","year":"2015","unstructured":"Dubin, M. J. et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 4, e05255 (2015).","journal-title":"eLife"},{"key":"1310_CR37","volume":"2","author":"JE Aten","year":"2008","unstructured":"Aten, J. E., Fuller, T. F., Lusis, A. J. & Horvath, S. Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst. Biol. 2, 34 (2008).","journal-title":"BMC Syst. Biol."},{"key":"1310_CR38","doi-asserted-by":"crossref","unstructured":"Henriksen, R. et al. Intra-individual behavioural variability: a trait under genetic control. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/795864 (2019).","DOI":"10.1101\/795864"},{"key":"1310_CR39","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1152\/physiolgenomics.90245.2008","volume":"37","author":"CR Farber","year":"2009","unstructured":"Farber, C. R. et al. Genetic dissection of a major mouse obesity QTL (Carfhg2): integration of gene expression and causality modeling. Physiol. Genomics 37, 294\u2013302 (2009).","journal-title":"Physiol. Genomics"},{"key":"1310_CR40","doi-asserted-by":"crossref","first-page":"e1000642","DOI":"10.1371\/journal.pgen.1000642","volume":"5","author":"CL Plaisier","year":"2009","unstructured":"Plaisier, C. L. et al. A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet. 5, e1000642 (2009).","journal-title":"PLoS Genet."},{"key":"1310_CR41","doi-asserted-by":"crossref","first-page":"10474","DOI":"10.1038\/ncomms10474","volume":"7","author":"VN Laine","year":"2016","unstructured":"Laine, V. N. et al. Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat. Commun. 7, 10474 (2016).","journal-title":"Nat. Commun."},{"key":"1310_CR42","doi-asserted-by":"crossref","first-page":"e56411","DOI":"10.1371\/journal.pone.0056411","volume":"8","author":"Y Hu","year":"2013","unstructured":"Hu, Y. et al. Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers. PLoS ONE 8, e56411 (2013).","journal-title":"PLoS ONE"},{"key":"1310_CR43","doi-asserted-by":"crossref","first-page":"e1006141","DOI":"10.1371\/journal.pgen.1006141","volume":"12","author":"D Meng","year":"2016","unstructured":"Meng, D. et al. Limited contribution of DNA methylation variation to expression regulation in Arabidopsis thaliana. PLoS Genet. 12, e1006141 (2016).","journal-title":"PLoS Genet."},{"key":"1310_CR44","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1101\/gad.2.9.1136","volume":"2","author":"F Watt","year":"1988","unstructured":"Watt, F. & Molloy, P. L. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev. 2, 1136\u20131143 (1988).","journal-title":"Genes Dev."},{"key":"1310_CR45","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s13059-015-0581-9","volume":"16","author":"W Zhang","year":"2015","unstructured":"Zhang, W., Spector, T. D., Deloukas, P., Bell, J. T. & Engelhardt, B. E. Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. Genome Biol. 16, 14 (2015).","journal-title":"Genome Biol."},{"key":"1310_CR46","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1038\/ng1909","volume":"38","author":"F Eckhardt","year":"2006","unstructured":"Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378\u20131385 (2006).","journal-title":"Nat. Genet."},{"key":"1310_CR47","doi-asserted-by":"publisher","unstructured":"Perzel Mandell, K. A. et al. Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/823781 (2019).","DOI":"10.1101\/823781"},{"key":"1310_CR48","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.humpath.2018.03.013","volume":"77","author":"F Wang","year":"2018","unstructured":"Wang, F. et al. ACOT1 expression is associated with poor prognosis in gastric adenocarcinoma. Hum. Pathol. 77, 35\u201344 (2018).","journal-title":"Hum. Pathol."},{"key":"1310_CR49","volume":"19","author":"K Pang","year":"2019","unstructured":"Pang, K. et al. The ERH gene regulates migration and invasion in 5637 and T24 bladder cancer cells. BMC Cancer 19, 225 (2019).","journal-title":"BMC Cancer"},{"key":"1310_CR50","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0304-3835(03)00055-7","volume":"194","author":"S Yamaguchi","year":"2003","unstructured":"Yamaguchi, S., Asao, T., Nakamura, J.-I., Ide, M. & Kuwano, H. High frequency of DAP-kinase gene promoter methylation in colorectal cancer specimens and its identification in serum. Cancer Lett. 194, 99\u2013105 (2003).","journal-title":"Cancer Lett."},{"key":"1310_CR51","first-page":"3399","volume":"9","author":"N Kasai","year":"2017","unstructured":"Kasai, N. et al. Anti-tumor efficacy evaluation of a novel monoclonal antibody targeting neutral amino acid transporter ASCT2 using patient-derived xenograft mouse models of gastric cancer.Am. J. Transl. Res. 9, 3399\u20133410 (2017).","journal-title":"Am. J. Transl. Res."},{"key":"1310_CR52","doi-asserted-by":"publisher","unstructured":"Arrieta, O. et al. Gene Expression Signature to predict early development of brain metastasis in lung adenocarcinoma. J. Clin. Oncol. 33, https:\/\/doi.org\/10.1200\/jco.2015.33.15_suppl.e19064 (2015).","DOI":"10.1200\/jco.2015.33.15_suppl.e19064"},{"key":"1310_CR53","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/S0022-5347(18)34941-3","volume":"173","author":"M Sanchez-Carbayo","year":"2005","unstructured":"Sanchez-Carbayo, M. et al. 772: identification of genetic signatures associated with TP53 status in patients with bladder cancer. J. Urol. 173, 209\u2013210 (2005).","journal-title":"J. Urol."},{"key":"1310_CR54","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1007\/s10549-015-3401-8","volume":"151","author":"BY Hair","year":"2015","unstructured":"Hair, B. Y. et al. Body mass index associated with genome-wide methylation in breast tissue. Breast Cancer Res. Treat. 151, 453\u2013463 (2015).","journal-title":"Breast Cancer Res. Treat."},{"key":"1310_CR55","unstructured":"Case, C. Neural regenerating cells with alterations in DNA methylation. Google patent US10316288B2 (2019)."},{"key":"1310_CR56","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.gene.2012.03.046","volume":"500","author":"K-S Wang","year":"2012","unstructured":"Wang, K.-S. et al. A novel locus for body mass index on 5p15.2: a meta-analysis of two genome-wide association studies. Gene 500, 80\u201384 (2012).","journal-title":"Gene"},{"key":"1310_CR57","doi-asserted-by":"crossref","first-page":"418","DOI":"10.3109\/17482960802635397","volume":"10","author":"JM Morahan","year":"2009","unstructured":"Morahan, J. M., Yu, B., Trent, R. J. & Pamphlett, R. A genome-wide analysis of brain DNA methylation identifies new candidate genes for sporadic amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. 10, 418\u2013429 (2009).","journal-title":"Amyotroph. Lateral Scler."},{"key":"1310_CR58","first-page":"3399","volume":"5","author":"B Singh","year":"2016","unstructured":"Singh, B., Carpenter, G. & Coffey, R. J. EGF receptor ligands: recent advances. F1000Research 5, 3399\u20133410 (2016).","journal-title":"F1000Research"},{"key":"1310_CR59","doi-asserted-by":"crossref","first-page":"172","DOI":"10.2141\/jpsa.0170150","volume":"55","author":"H Xu","year":"2018","unstructured":"Xu, H. et al. Characterization of the Goose CAPN3 gene and its expression pattern in muscle tissues of sichuan white geese at different growth stages. J. Poult. Sci. 55, 172\u2013181 (2018).","journal-title":"J. Poult. Sci."},{"key":"1310_CR60","doi-asserted-by":"crossref","first-page":"2086","DOI":"10.18632\/oncotarget.23331","volume":"9","author":"Y-W Sha","year":"2018","unstructured":"Sha, Y.-W. et al. Sperm-egg fusion disorder in a Chinese male patient was associated with a rare ADAM20 variant. Oncotarget 9, 2086\u20132091 (2018).","journal-title":"Oncotarget"},{"key":"1310_CR61","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1111\/age.12943","volume":"51","author":"A Sigdel","year":"2020","unstructured":"Sigdel, A., Liu, L., Abdollahi-Arpanahi, R., Aguilar, I. & Pe\u00f1agaricano, F. Genetic dissection of reproductive performance of dairy cows under heat stress. Anim. Genet. 51, 511\u2013520 (2020).","journal-title":"Anim. Genet."},{"key":"1310_CR62","doi-asserted-by":"crossref","first-page":"2477","DOI":"10.1038\/sj.onc.1209272","volume":"25","author":"M Suzuki","year":"2006","unstructured":"Suzuki, M. et al. Site-specific DNA methylation by a complex of PU.1 and Dnmt3a\/b. Oncogene 25, 2477\u20132488 (2006).","journal-title":"Oncogene"},{"key":"1310_CR63","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1016\/j.celrep.2015.07.024","volume":"12","author":"MT Maurano","year":"2015","unstructured":"Maurano, M. T. et al. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 12, 1184\u20131195 (2015).","journal-title":"Cell Rep."},{"key":"1310_CR64","doi-asserted-by":"crossref","first-page":"e1001427","DOI":"10.1371\/journal.pbio.1001427","volume":"10","author":"HP Shulha","year":"2012","unstructured":"Shulha, H. P. et al. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol. 10, e1001427 (2012).","journal-title":"PLoS Biol."},{"key":"1310_CR65","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.ajhg.2010.02.005","volume":"86","author":"D Zhang","year":"2010","unstructured":"Zhang, D. et al. Genetic control of individual differences in gene-specific methylation in human brain. Am. J. Hum. Genet. 86, 411\u2013419 (2010).","journal-title":"Am. J. Hum. Genet."},{"key":"1310_CR66","doi-asserted-by":"crossref","first-page":"13557","DOI":"10.1007\/s13277-016-5199-3","volume":"37","author":"Y Du","year":"2016","unstructured":"Du, Y., Chen, Y., Wang, F. & Gu, L. miR-137 plays tumor suppressor roles in gastric cancer cell lines by targeting KLF12 and MYO1C. Tumor Biol. 37, 13557\u201313569 (2016).","journal-title":"Tumor Biol."},{"key":"1310_CR67","doi-asserted-by":"crossref","first-page":"e10028","DOI":"10.1371\/journal.pone.0010028","volume":"5","author":"J Liu","year":"2010","unstructured":"Liu, J., Morgan, M., Hutchison, K. & Calhoun, V. D. A study of the influence of sex on genome wide methylation. PLoS ONE 5, e10028 (2010).","journal-title":"PLoS ONE"},{"key":"1310_CR68","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.cmet.2011.04.002","volume":"13","author":"Y C\u00e1mara","year":"2011","unstructured":"C\u00e1mara, Y. et al. MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metab. 13, 527\u2013539 (2011).","journal-title":"Cell Metab."},{"key":"1310_CR69","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.ccr.2013.12.007","volume":"25","author":"L Wang","year":"2014","unstructured":"Wang, L. et al. CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell 25, 21\u201336 (2014).","journal-title":"Cancer Cell"},{"key":"1310_CR70","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.neuro.2019.11.002","volume":"76","author":"M Forcella","year":"2020","unstructured":"Forcella, M. et al. Neuronal specific and non-specific responses to cadmium possibly involved in neurodegeneration: a toxicogenomics study in a human neuronal cell model. Neurotoxicology 76, 162\u2013173 (2020).","journal-title":"Neurotoxicology"},{"key":"1310_CR71","doi-asserted-by":"crossref","first-page":"e12811","DOI":"10.1111\/adb.12811","volume":"25","author":"Z Cheng","year":"2020","unstructured":"Cheng, Z. et al. Genome-wide scan identifies opioid overdose risk locus close to MCOLN1. Addiction Biol. 25, e12811 (2020).","journal-title":"Addiction Biol."},{"key":"1310_CR72","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.1002\/ajmg.a.34255","volume":"155","author":"V Harrison","year":"2011","unstructured":"Harrison, V. et al. Compound heterozygous deletion of NRXN1 causing severe developmental delay with early onset epilepsy in two sisters. Am. J. Med. Genet. A 155, 2826\u20132831 (2011).","journal-title":"Am. J. Med. Genet. A"},{"key":"1310_CR73","volume":"7","author":"H Heinrich","year":"2017","unstructured":"Heinrich, H. et al. Attention, cognitive control and motivation in ADHD: linking event-related brain potentials and DNA methylation patterns in boys at early school age. Sci. Rep. 7, 3823 (2017).","journal-title":"Sci. Rep."},{"key":"1310_CR74","doi-asserted-by":"publisher","unstructured":"Frey, S. et al. Prenatal alcohol exposure is associated with adverse cognitive effects and distinct whole-genome DNA methylation patterns in primary school children. Front. Behav. Neurosci. 12, https:\/\/doi.org\/10.3389\/fnbeh.2018.00125 (2018).","DOI":"10.3389\/fnbeh.2018.00125"},{"key":"1310_CR75","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/j.ajhg.2007.12.009","volume":"82","author":"CR Marshall","year":"2008","unstructured":"Marshall, C. R. et al. Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet. 82, 477\u2013488 (2008).","journal-title":"Am. J. Hum. Genet."},{"key":"1310_CR76","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1242\/jcs.048975","volume":"122","author":"J Chang","year":"2009","unstructured":"Chang, J., Baloh, R. H. & Milbrandt, J. The NIMA-family kinase Nek3 regulates microtubule acetylation in neurons. J. Cell Sci. 122, 2274\u20132282 (2009).","journal-title":"J. Cell Sci."},{"key":"1310_CR77","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1152\/japplphysiol.00514.2004","volume":"98","author":"D Miller","year":"2005","unstructured":"Miller, D., Forrester, K., Leonard, C., Salo, P. & Bray, R. C. ACL deficiency impairs the vasoconstrictive efficacy of neuropeptide Y and phenylephrine in articular tissues: a laser speckle perfusion imaging study. J. Appl. Physiol. 98, 329\u2013333 (2005).","journal-title":"J. Appl. Physiol."},{"key":"1310_CR78","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1093\/gbe\/evz044","volume":"11","author":"HM Viitaniemi","year":"2019","unstructured":"Viitaniemi, H. M. et al. Seasonal variation in genome-wide DNA methylation patterns and the onset of seasonal timing of reproduction in great tits. Genome Biol. Evol. 11, 970\u2013983 (2019).","journal-title":"Genome Biol. Evol."},{"key":"1310_CR79","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1111\/mec.13519","volume":"25","author":"EC Verhulst","year":"2016","unstructured":"Verhulst, E. C. et al. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD 4 DNA methylation. Mol. Ecol. 25, 1801\u20131811 (2016).","journal-title":"Mol. Ecol."},{"key":"1310_CR80","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1007\/s10336-019-01684-5","volume":"160","author":"B Sepers","year":"2019","unstructured":"Sepers, B. et al. Avian ecological epigenetics: pitfalls and promises. J. Ornithol. 160, 1183\u20131203 (2019).","journal-title":"J. Ornithol."},{"key":"1310_CR81","first-page":"979751","volume":"2012","author":"AW Schrey","year":"2012","unstructured":"Schrey, A. W. et al. Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genetics Res. Int. 2012, 979751 (2012).","journal-title":"Genetics Res. Int."},{"key":"1310_CR82","first-page":"4016","volume":"220","author":"S Riyahi","year":"2017","unstructured":"Riyahi, S. et al. Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus. J. Exp. Biol. 220, 4016\u20134023 (2017).","journal-title":"J. Exp. Biol."},{"key":"1310_CR83","doi-asserted-by":"crossref","unstructured":"van Oers, K. & Naguib, M. in Animal Personalities: Behavior, Physiology, and Evolution (eds Maestripieri, D. & Carere, C.) 66\u201395 (Univ. Chicago Press, 2013).","DOI":"10.7208\/chicago\/9780226922065.003.0004"},{"key":"1310_CR84","doi-asserted-by":"crossref","first-page":"6148","DOI":"10.1111\/mec.13452","volume":"24","author":"AW Santure","year":"2015","unstructured":"Santure, A. W. et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Mol. Ecol. 24, 6148\u20136162 (2015).","journal-title":"Mol. Ecol."},{"key":"1310_CR85","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1111\/1755-0998.12778","volume":"18","author":"JM Kim","year":"2018","unstructured":"Kim, J. M. et al. A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol. Ecol. Resour. 18, 877\u2013891 (2018).","journal-title":"Mol. Ecol. Resour."},{"key":"1310_CR86","doi-asserted-by":"crossref","first-page":"e13100","DOI":"10.1371\/journal.pone.0013100","volume":"5","author":"C Guerrero-Bosagna","year":"2010","unstructured":"Guerrero-Bosagna, C., Settles, M., Lucker, B. & Skinner, M. K. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PLoS ONE 5, e13100 (2010).","journal-title":"PLoS ONE"},{"key":"1310_CR87","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1038\/ng1598","volume":"37","author":"M Weber","year":"2005","unstructured":"Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853\u2013862 (2005).","journal-title":"Nat. Genet."},{"key":"1310_CR88","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"1310_CR89","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","volume":"19","author":"KW Broman","year":"2003","unstructured":"Broman, K. W., Wu, H., Sen, S. & Churchill, G. A. R\/qtl: QTL maping in experimental crosses. Bioinformatics 19, 889\u2013890 (2003).","journal-title":"Bioinformatics"}],"container-title":["Nature Ecology &amp; Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41559-020-01310-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41559-020-01310-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41559-020-01310-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,6]],"date-time":"2022-12-06T04:17:58Z","timestamp":1670300278000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41559-020-01310-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,21]]},"references-count":89,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["1310"],"URL":"https:\/\/doi.org\/10.1038\/s41559-020-01310-1","relation":{},"ISSN":["2397-334X"],"issn-type":[{"value":"2397-334X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,21]]},"assertion":[{"value":"8 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}