{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:30:53Z","timestamp":1791221453702,"version":"4.1.0"},"reference-count":85,"publisher":"Elsevier BV","issue":"7","license":[{"start":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T00:00:00Z","timestamp":1648771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T00:00:00Z","timestamp":1648771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,12,29]],"date-time":"2021-12-29T00:00:00Z","timestamp":1640736000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["201906170058"],"award-info":[{"award-number":["201906170058"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003792","name":"Hj\u00e4rnfonden","doi-asserted-by":"publisher","award":["FO2017-0075"],"award-info":[{"award-number":["FO2017-0075"]}],"id":[{"id":"10.13039\/501100003792","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003792","name":"Hj\u00e4rnfonden","doi-asserted-by":"publisher","award":["FO2018-0162"],"award-info":[{"award-number":["FO2018-0162"]}],"id":[{"id":"10.13039\/501100003792","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["RM1-HG007735"],"award-info":[{"award-number":["RM1-HG007735"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["VR-2017-02074"],"award-info":[{"award-number":["VR-2017-02074"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008659","name":"European Committee for Treatment and Research in Multiple Sclerosis","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["P50 NS062684"],"award-info":[{"award-number":["P50 NS062684"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["K99AG059918"],"award-info":[{"award-number":["K99AG059918"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U01AG072573"],"award-info":[{"award-number":["U01AG072573"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2019-01360"],"award-info":[{"award-number":["2019-01360"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2018-05973"],"award-info":[{"award-number":["2018-05973"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["681893"],"award-info":[{"award-number":["681893"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003748","name":"Svenska Sallskapet for Medicinsk Forskning","doi-asserted-by":"publisher","award":["JUB2019"],"award-info":[{"award-number":["JUB2019"]}],"id":[{"id":"10.13039\/501100003748","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009252","name":"Science for Life Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009252","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002794","name":"Cancerfonden","doi-asserted-by":"publisher","award":["CAN2016\/555"],"award-info":[{"award-number":["CAN2016\/555"]}],"id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007013","name":"F. Hoffmann-La Roche","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007013","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004047","name":"Karolinska Institutet","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004047","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg Foundation","doi-asserted-by":"publisher","award":["2019-0107"],"award-info":[{"award-number":["2019-0107"]}],"id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg Foundation","doi-asserted-by":"publisher","award":["2019-0089"],"award-info":[{"award-number":["2019-0089"]}],"id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Neuron"],"published-print":{"date-parts":[[2022,4]]},"DOI":"10.1016\/j.neuron.2021.12.034","type":"journal-article","created":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T02:55:57Z","timestamp":1643597757000},"page":"1193-1210.e13","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":104,"title":["Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility"],"prefix":"10.1016","volume":"110","author":[{"given":"Mandy","family":"Meijer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eneritz","family":"Agirre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mukund","family":"Kabbe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cassandra A.","family":"van Tuijn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abeer","family":"Heskol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Mendanha Falc\u00e3o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Bartosovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie","family":"Kirby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Calini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7465-7652","authenticated-orcid":false,"given":"M. Ryan","family":"Corces","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Montine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingqi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Howard Y.","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dheeraj","family":"Malhotra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gon\u00e7alo","family":"Castelo-Branco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.neuron.2021.12.034_bib1","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/s41586-021-03892-7","article-title":"A lymphocyte-microglia-astrocyte axis in chronic active multiple sclerosis","volume":"597","author":"Absinta","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib2","doi-asserted-by":"crossref","first-page":"3333","DOI":"10.1093\/bioinformatics\/btr570","article-title":"Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data","volume":"27","author":"Althammer","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib3","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.cell.2006.02.041","article-title":"A bivalent chromatin structure marks key developmental genes in embryonic stem cells","volume":"125","author":"Bernstein","year":"2006","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib4","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1093\/bioinformatics\/btp101","article-title":"ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks","volume":"25","author":"Bindea","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib5","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1016\/j.cell.2018.10.008","article-title":"T helper cell cytokines modulate intestinal stem cell renewal and differentiation","volume":"175","author":"Biton","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib6","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/s42003-020-01625-6","article-title":"Mapping the immune environment in clear cell renal carcinoma by single-cell genomics","volume":"4","author":"Borcherding","year":"2021","journal-title":"Commun. Biol."},{"key":"10.1016\/j.neuron.2021.12.034_bib7","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib8","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.ccell.2019.08.008","article-title":"An evolutionarily conserved function of Polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer","volume":"36","author":"Burr","year":"2019","journal-title":"Cancer Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib9","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.neuron.2021.12.034_bib10","doi-asserted-by":"crossref","first-page":"4590","DOI":"10.1038\/s41467-018-07115-y","article-title":"Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity","volume":"9","author":"Chen","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2021.12.034_bib11","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/glia.20232","article-title":"Interferon-gamma inhibits cell cycle exit in differentiating oligodendrocyte progenitor cells","volume":"52","author":"Chew","year":"2005","journal-title":"Glia"},{"key":"10.1016\/j.neuron.2021.12.034_bib12","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib13","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1038\/s41588-020-00721-x","article-title":"Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer\u2019s and Parkinson\u2019s diseases","volume":"52","author":"Corces","year":"2020","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2021.12.034_bib14","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/s12859-018-2255-6","article-title":"BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization","volume":"19","author":"de Boer","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib15","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/ng.401","article-title":"Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci","volume":"41","author":"De Jager","year":"2009","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2021.12.034_bib16","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1074\/mcp.RA120.002102","article-title":"Changes in the oligodendrocyte progenitor cell proteome with ageing","volume":"19","author":"de la Fuente","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.neuron.2021.12.034_bib17","doi-asserted-by":"crossref","first-page":"e1004219","DOI":"10.1371\/journal.pcbi.1004219","article-title":"MAGMA: generalized gene-set analysis of GWAS data","volume":"11","author":"de Leeuw","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.neuron.2021.12.034_bib18","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib19","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/s41586-019-1362-5","article-title":"Single-cell analysis reveals T\u00a0cell infiltration in old neurogenic niches","volume":"571","author":"Dulken","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib20","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.cell.2020.03.002","article-title":"Cell type-specific intralocus interactions reveal oligodendrocyte mechanisms in MS","volume":"181","author":"Factor","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib21","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1038\/s41591-018-0236-y","article-title":"Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis","volume":"24","author":"Falc\u00e3o","year":"2019","journal-title":"Nat. Med."},{"key":"10.1016\/j.neuron.2021.12.034_bib22","doi-asserted-by":"crossref","first-page":"eaam7816","DOI":"10.1126\/scitranslmed.aam7816","article-title":"BCAS1 expression defines a population of early myelinating oligodendrocytes in multiple sclerosis lesions","volume":"9","author":"Fard","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.neuron.2021.12.034_bib23","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/s00401-019-02073-1","article-title":"The active contribution of OPCs to neuroinflammation is mediated by LRP1","volume":"139","author":"Fern\u00e1ndez-Casta\u00f1eda","year":"2020","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.neuron.2021.12.034_bib24","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/s41588-018-0081-4","article-title":"Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types","volume":"50","author":"Finucane","year":"2018","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2021.12.034_bib25","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/nrn.2017.136","article-title":"Regenerating CNS myelin\u2014from mechanisms to experimental medicines","volume":"18","author":"Franklin","year":"2017","journal-title":"Nat. Rev. Neurosci."},{"key":"10.1016\/j.neuron.2021.12.034_bib26","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1038\/s41588-019-0538-0","article-title":"Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations","volume":"51","author":"Fulco","year":"2019","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2021.12.034_bib27","article-title":"ArchR: an integrative and scalable software package for single-cell chromatin accessibility analysis","author":"Granja","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2021.12.034_bib82","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib28","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib29","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","article-title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression","volume":"459","author":"Heintzman","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib30","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib31","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.immuni.2009.09.002","article-title":"Cross-regulation of signaling pathways by interferon-gamma: implications for immune responses and autoimmune diseases","volume":"31","author":"Hu","year":"2009","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2021.12.034_bib32","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nri.2017.26","article-title":"BACH transcription factors in innate and adaptive immunity","volume":"17","author":"Igarashi","year":"2017","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.neuron.2021.12.034_bib33","doi-asserted-by":"crossref","first-page":"eaav7188","DOI":"10.1126\/science.aav7188","article-title":"Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility","volume":"365","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.neuron.2021.12.034_bib34","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1002\/glia.23129","article-title":"Mice lacking BCAS1, a novel myelin-associated protein, display hypomyelination, schizophrenia-like abnormal behaviors, and upregulation of inflammatory genes in the brain","volume":"65","author":"Ishimoto","year":"2017","journal-title":"Glia"},{"key":"10.1016\/j.neuron.2021.12.034_bib35","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/s41586-019-0903-2","article-title":"Altered human oligodendrocyte heterogeneity in multiple sclerosis","volume":"566","author":"J\u00e4kel","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib36","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1038\/s41467-019-09982-5","article-title":"CUT&Tag for efficient epigenomic profiling of small samples and single cells","volume":"10","author":"Kaya-Okur","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2021.12.034_bib37","doi-asserted-by":"crossref","first-page":"3887","DOI":"10.1038\/s41467-019-11638-3","article-title":"Oligodendrocyte precursor cells present antigen and are cytotoxic targets in inflammatory demyelination","volume":"10","author":"Kirby","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2021.12.034_bib83","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","author":"Korsunsky","year":"2019","journal-title":"Nature methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib38","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/s41586-020-2424-4","article-title":"Structural cells are key regulators of organ-specific immune responses","volume":"583","author":"Krausgruber","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib39","doi-asserted-by":"crossref","first-page":"D139","DOI":"10.1093\/nar\/gkw1064","article-title":"SNP2TFBS\u2014a database of regulatory SNPs affecting predicted transcription factor binding site affinity","volume":"45","author":"Kumar","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2021.12.034_bib40","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib41","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib42","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2021.12.034_bib43","doi-asserted-by":"crossref","first-page":"4211","DOI":"10.1128\/MCB.00327-10","article-title":"CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus","volume":"30","author":"Majumder","year":"2010","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.neuron.2021.12.034_bib44","doi-asserted-by":"crossref","first-page":"3925","DOI":"10.4049\/jimmunol.1303205","article-title":"B cell differentiation is associated with reprogramming the CCCTC binding factor-dependent chromatin architecture of the murine MHC class II locus","volume":"192","author":"Majumder","year":"2014","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.neuron.2021.12.034_bib45","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature03837","article-title":"Neural crest origins of the neck and shoulder","volume":"436","author":"Matsuoka","year":"2005","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib46","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2021.12.034_bib47","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.neuron.2021.12.034_bib86","article-title":"GSEABase: Gene set enrichment data structures and methods","volume":"R package version 1.56.0.","author":"Morgan","year":"2021","journal-title":"Bioconductor"},{"key":"10.1016\/j.neuron.2021.12.034_bib48","doi-asserted-by":"crossref","first-page":"2851","DOI":"10.1093\/emboj\/16.10.2851","article-title":"Expression of MHC class II molecules in different cellular and functional compartments is controlled by differential usage of multiple promoters of the transactivator CIITA","volume":"16","author":"Muhlethaler-Mottet","year":"1997","journal-title":"EMBO J."},{"key":"10.1016\/j.neuron.2021.12.034_bib49","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/nmeth.3999","article-title":"HiChIP: efficient and sensitive analysis of protein-directed genome architecture","volume":"13","author":"Mumbach","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib50","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0165-5728(99)00117-4","article-title":"Differential selectivity of CIITA promoter activation by IFN-gamma and IRF-1 in astrocytes and macrophages: CIITA promoter activation is not affected by TNF-alpha","volume":"99","author":"Nikcevich","year":"1999","journal-title":"J.\u00a0Neuroimmunol."},{"key":"10.1016\/j.neuron.2021.12.034_bib51","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib52","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1101\/gr.177881.114","article-title":"Tn5 transposase and tagmentation procedures for massively scaled sequencing projects","volume":"24","author":"Picelli","year":"2014","journal-title":"Genome Res."},{"key":"10.1016\/j.neuron.2021.12.034_bib53","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1016\/j.molcel.2018.06.044","article-title":"Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data","volume":"71","author":"Pliner","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib54","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib55","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.msard.2013.08.009","article-title":"Genetic evidence for a pathogenic role for the vitamin D3 metabolizing enzyme CYP24A1 in multiple sclerosis","volume":"3","author":"Ramasamy","year":"2014","journal-title":"Mult. Scler. Relat. Disord."},{"key":"10.1016\/j.neuron.2021.12.034_bib56","doi-asserted-by":"crossref","first-page":"W187","DOI":"10.1093\/nar\/gku365","article-title":"deepTools: a flexible platform for exploring deep-sequencing data","volume":"42","author":"Ram\u00edrez","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2021.12.034_bib57","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2021.12.034_bib58","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/j.neuron.2021.12.034_bib85","article-title":"Juicebox.js provides a cloud-based visualization system for Hi-C data","volume":"6","author":"Robinson","year":"2018","journal-title":"Cell Syst."},{"key":"10.1016\/j.neuron.2021.12.034_bib59","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1038\/nmeth.4401","article-title":"chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data","volume":"14","author":"Schep","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2021.12.034_bib60","first-page":"147","article-title":"ChIC and ChEC; genomic mapping of chromatin proteins","volume":"16","author":"Schmid","year":"2004","journal-title":"Mol. Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib61","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1093\/bioinformatics\/btv201","article-title":"GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach","volume":"31","author":"Schmidt","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib62","doi-asserted-by":"crossref","first-page":"572186","DOI":"10.3389\/fimmu.2020.572186","article-title":"Revisiting the pathoetiology of multiple sclerosis: has the tail been wagging the mouse?","volume":"11","author":"Sen","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.neuron.2021.12.034_bib63","doi-asserted-by":"crossref","first-page":"e21856","DOI":"10.7554\/eLife.21856","article-title":"An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites","volume":"6","author":"Skene","year":"2017","journal-title":"Elife"},{"key":"10.1016\/j.neuron.2021.12.034_bib64","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"10.1016\/j.neuron.2021.12.034_bib65","first-page":"i1","article-title":"Characterization of Nkx6-2-derived neocortical interneuron lineages. Cereb","volume":"19","author":"Sousa","year":"2009","journal-title":"Cortex"},{"key":"10.1016\/j.neuron.2021.12.034_bib66","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.neuron.2018.12.020","article-title":"Oligodendrocyte progenitor cells become regionally diverse and heterogeneous with age","volume":"101","author":"Spitzer","year":"2019","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2021.12.034_bib67","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41588-020-0643-0","article-title":"CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response","volume":"52","author":"Stik","year":"2020","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2021.12.034_bib68","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1242\/dev.01114","article-title":"Transcription factors Sox8 and Sox10 perform non-equivalent roles during oligodendrocyte development despite functional redundancy","volume":"131","author":"Stolt","year":"2004","journal-title":"Development"},{"key":"10.1016\/j.neuron.2021.12.034_bib69","article-title":"Multimodal single-cell chromatin analysis with Signac","author":"Stuart","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2021.12.034_bib70","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature11232","article-title":"The accessible chromatin landscape of the human genome","volume":"489","author":"Thurman","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib71","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/s41582-018-0082-z","article-title":"Treatment of multiple sclerosis - success from bench to bedside","volume":"15","author":"Tintore","year":"2019","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.neuron.2021.12.034_bib72","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1038\/nprot.2013.118","article-title":"Tagmentation-based whole-genome bisulfite sequencing","volume":"8","author":"Wang","year":"2013","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.neuron.2021.12.034_bib73","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1002\/glia.20912","article-title":"STAT1\/IRF-1 signaling pathway mediates the injurious effect of interferon-gamma on oligodendrocyte progenitor cells","volume":"58","author":"Wang","year":"2010","journal-title":"Glia"},{"key":"10.1016\/j.neuron.2021.12.034_bib74","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.cell.2014.08.009","article-title":"Determination and inference of eukaryotic transcription factor sequence specificity","volume":"158","author":"Weirauch","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2021.12.034_bib75","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1038\/s41593-019-0491-3","article-title":"Single-cell transcriptomic profiling of the aging mouse brain","volume":"22","author":"Ximerakis","year":"2019","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2021.12.034_bib76","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/s41586-018-0842-3","article-title":"Dynamics of oligodendrocyte generation in multiple sclerosis","volume":"566","author":"Yeung","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2021.12.034_bib77","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/s41593-021-00851-3","article-title":"Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer's disease","volume":"24","author":"Zalocusky","year":"2021","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2021.12.034_bib78","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1093\/bioinformatics\/btt145","article-title":"An accessible database for mouse and human whole transcriptome qPCR primers","volume":"29","author":"Zeisel","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2021.12.034_bib79","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2021.12.034_bib80","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/s41591-019-0695-9","article-title":"Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer\u2019s disease","volume":"26","author":"Zhou","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.neuron.2021.12.034_bib81","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1186\/s13059-019-1802-4","article-title":"CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis","volume":"20","author":"Zhu","year":"2019","journal-title":"Genome Biol."}],"container-title":["Neuron"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627321010898?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627321010898?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T12:44:15Z","timestamp":1778762655000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896627321010898"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4]]},"references-count":85,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2022,4]]}},"alternative-id":["S0896627321010898"],"URL":"https:\/\/doi.org\/10.1016\/j.neuron.2021.12.034","relation":{},"ISSN":["0896-6273"],"issn-type":[{"value":"0896-6273","type":"print"}],"subject":[],"published":{"date-parts":[[2022,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility","name":"articletitle","label":"Article Title"},{"value":"Neuron","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.neuron.2021.12.034","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}