{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:57:23Z","timestamp":1791824243420,"version":"4.3.4"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T00:00:00Z","timestamp":1715731200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R35GM128822"],"award-info":[{"award-number":["1R35GM128822"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000008","name":"David and Lucile Packard Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000008","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005508","name":"Boettcher Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005508","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Discovery Boost","award":["DBG-23-1155983-01-DMC"],"award-info":[{"award-number":["DBG-23-1155983-01-DMC"]}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn\u2019s disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.<\/jats:p>","DOI":"10.1093\/hmg\/ddae084","type":"journal-article","created":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T08:24:53Z","timestamp":1715243093000},"page":"1454-1464","source":"Crossref","is-referenced-by-count":8,"title":["An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140"],"prefix":"10.1093","volume":"33","author":[{"given":"Adam K","family":"Dziulko","sequence":"first","affiliation":[{"name":"Department of Molecular , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"},{"name":"University of Colorado Boulder , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holly","family":"Allen","sequence":"additional","affiliation":[{"name":"Department of Molecular , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"},{"name":"University of Colorado Boulder , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5392-937X","authenticated-orcid":false,"given":"Edward B","family":"Chuong","sequence":"additional","affiliation":[{"name":"Department of Molecular , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"},{"name":"University of Colorado Boulder , Cellular, and Developmental Biology and BioFrontiers Institute, , 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,15]]},"reference":[{"key":"2024080722303794500_ref1","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1063127","article-title":"Translating the histone code","volume":"293","author":"Jenuwein","year":"2001","journal-title":"Science"},{"key":"2024080722303794500_ref2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.molcel.2006.12.014","article-title":"Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark","volume":"25","author":"Ruthenburg","year":"2007","journal-title":"Mol Cell"},{"key":"2024080722303794500_ref3","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.it.2020.04.007","article-title":"The speckled protein (SP) family: Immunity\u2019s chromatin readers","volume":"41","author":"Fraschilla","year":"2020","journal-title":"Trends Immunol"},{"key":"2024080722303794500_ref4","doi-asserted-by":"crossref","first-page":"29198","DOI":"10.1074\/jbc.271.46.29198","article-title":"Identification and characterization of a leukocyte-specific component of the nuclear body","volume":"271","author":"Bloch","year":"1996","journal-title":"J Biol Chem"},{"key":"2024080722303794500_ref5","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1182\/blood.V88.4.1423.bloodjournal8841423","article-title":"LYSP100-associated nuclear domains (LANDs): description of a new class of subnuclear structures and their relationship to PML nuclear bodies","volume":"88","author":"Dent","year":"1996","journal-title":"Blood"},{"key":"2024080722303794500_ref6","doi-asserted-by":"crossref","first-page":"11133","DOI":"10.1128\/JVI.76.21.11133-11138.2002","article-title":"Implication of the lymphocyte-specific nuclear body protein Sp140 in an innate response to human immunodeficiency virus type 1","volume":"76","author":"Madani","year":"2002","journal-title":"J Virol"},{"key":"2024080722303794500_ref7","doi-asserted-by":"crossref","first-page":"3232","DOI":"10.1016\/j.cell.2022.06.048","article-title":"Epigenetic reader SP140 loss of function drives Crohn\u2019s disease due to uncontrolled macrophage topoisomerases","volume":"185","author":"Amatullah","year":"2022","journal-title":"Cell"},{"key":"2024080722303794500_ref8","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aag3160","article-title":"Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140","volume":"2","author":"Mehta","year":"2017","journal-title":"Sci Immunol"},{"key":"2024080722303794500_ref9","first-page":"4012","article-title":"SP140 regulates the expression of immune-related genes associated with multiple sclerosis and other autoimmune diseases by NF-\u03baB inhibition","volume":"27","author":"Karaky","year":"2018","journal-title":"Hum Mol Genet"},{"key":"2024080722303794500_ref10","doi-asserted-by":"crossref","first-page":"a000034","DOI":"10.1101\/cshperspect.a000034","article-title":"The NF-\u03baB family of transcription factors and its regulation","volume":"1","author":"Oeckinghaus","year":"2009","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2024080722303794500_ref11","doi-asserted-by":"crossref","first-page":"4228","DOI":"10.3390\/cimb45050269","article-title":"The epigenetic reader protein SP140 regulates dendritic cell activation, maturation and Tolerogenic potential","volume":"45","author":"Ghiboub","year":"2023","journal-title":"Curr Issues Mol Biol"},{"key":"2024080722303794500_ref12","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.67290","article-title":"Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons","volume":"10","author":"Ji","year":"2021","journal-title":"elife"},{"key":"2024080722303794500_ref13","doi-asserted-by":"crossref","first-page":"5536","DOI":"10.1016\/j.cell.2023.11.002","article-title":"Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis","volume":"186","author":"Kotov","year":"2023","journal-title":"Cell"},{"key":"2024080722303794500_ref14","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/89675","article-title":"The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation","volume":"8","author":"Bottomley","year":"2001","journal-title":"Nat Struct Biol"},{"key":"2024080722303794500_ref15","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.tibs.2005.11.001","article-title":"The PHD finger, a nuclear protein-interaction domain","volume":"31","author":"Bienz","year":"2006","journal-title":"Trends Biochem Sci"},{"key":"2024080722303794500_ref16","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.bbagen.2018.11.011","article-title":"Sp140 is a multi-SUMO-1 target and its PHD finger promotes SUMOylation of the adjacent Bromodomain","volume":"1863","author":"Zucchelli","year":"2019","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2024080722303794500_ref17","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.cell.2012.02.013","article-title":"Histone recognition and large-scale structural analysis of the human bromodomain family","volume":"149","author":"Filippakopoulos","year":"2012","journal-title":"Cell"},{"key":"2024080722303794500_ref18","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1038\/s41467-020-15448-w","article-title":"Dual functions of Aire CARD multimerization in the transcriptional regulation of T cell tolerance","volume":"11","author":"Huoh","year":"2020","journal-title":"Nat Commun"},{"key":"2024080722303794500_ref19","doi-asserted-by":"crossref","first-page":"E11053","DOI":"10.1073\/pnas.1815912115","article-title":"Evolution of weak cooperative interactions for biological specificity","volume":"115","author":"Gao","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024080722303794500_ref20","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf4382","article-title":"Liquid phase condensation in cell physiology and disease","volume":"357","author":"Shin","year":"2017","journal-title":"Science"},{"key":"2024080722303794500_ref21","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1126\/science.aad9964","article-title":"Phase separation of signaling molecules promotes T cell receptor signal transduction","volume":"352","author":"Su","year":"2016","journal-title":"Science"},{"key":"2024080722303794500_ref22","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar3958","article-title":"Coactivator condensation at super-enhancers links phase separation and gene control","volume":"361","author":"Sabari","year":"2018","journal-title":"Science"},{"key":"2024080722303794500_ref23","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"Jostins","year":"2012","journal-title":"Nature"},{"key":"2024080722303794500_ref24","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1038\/ng.717","article-title":"Genome-wide meta-analysis increases to 71 the number of confirmed Crohn\u2019s disease susceptibility loci","volume":"42","author":"Franke","year":"2010","journal-title":"Nat Genet"},{"key":"2024080722303794500_ref25","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1038\/ng.2770","article-title":"Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis","volume":"45","author":"International Multiple Sclerosis Genetics Consortium (IMSGC)","year":"2013","journal-title":"Nat Genet"},{"key":"2024080722303794500_ref26","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1038\/ng.219","article-title":"A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia","volume":"40","author":"Di Bernardo","year":"2008","journal-title":"Nat Genet"},{"key":"2024080722303794500_ref27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0029632","article-title":"Post-GWAS functional characterization of susceptibility variants for chronic lymphocytic leukemia","volume":"7","author":"Sill\u00e9","year":"2012","journal-title":"PLoS One"},{"key":"2024080722303794500_ref28","doi-asserted-by":"crossref","first-page":"5619","DOI":"10.1093\/hmg\/ddv256","article-title":"A functional variant that affects exon-skipping and protein expression of SP140 as genetic mechanism predisposing to multiple sclerosis","volume":"24","author":"Matesanz","year":"2015","journal-title":"Hum Mol Genet"},{"key":"2024080722303794500_ref29","doi-asserted-by":"crossref","first-page":"e005088","DOI":"10.1136\/jitc-2022-005088","article-title":"SP140 inhibits STAT1 signaling, induces IFN-\u03b3 in tumor-associated macrophages, and is a predictive biomarker of immunotherapy response","volume":"10","author":"Tanagala","year":"2022","journal-title":"J Immunother Cancer"},{"key":"2024080722303794500_ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.immuni.2013.07.012","article-title":"Oncology meets immunology: the cancer-immunity cycle","volume":"39","author":"Chen","year":"2013","journal-title":"Immunity"},{"key":"2024080722303794500_ref31","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1038\/s41598-023-49770-2","article-title":"A CIC-related-epigenetic factors-based model associated with prediction, the tumor microenvironment and drug sensitivity in osteosarcoma","volume":"14","author":"Yu","year":"2024","journal-title":"Sci Rep"},{"key":"2024080722303794500_ref32","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: from conflicts to benefits","volume":"18","author":"Chuong","year":"2017","journal-title":"Nat Rev Genet"},{"key":"2024080722303794500_ref33","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","article-title":"Ten things you should know about transposable elements","volume":"19","author":"Bourque","year":"2018","journal-title":"Genome Biol"},{"key":"2024080722303794500_ref34","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome assembly from long-read RNA-seq alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol"},{"key":"2024080722303794500_ref35","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1093\/bioinformatics\/btx547","article-title":"Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples","volume":"34","author":"Wilks","year":"2018","journal-title":"Bioinformatics"},{"key":"2024080722303794500_ref36","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/s41586-019-1186-3","article-title":"Next-generation characterization of the cancer cell line Encyclopedia","volume":"569","author":"Ghandi","year":"2019","journal-title":"Nature"},{"key":"2024080722303794500_ref37","doi-asserted-by":"crossref","first-page":"D201","DOI":"10.1093\/nar\/gkaa1056","article-title":"RJunBase: a database of RNA splice junctions in human normal and cancerous tissues","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024080722303794500_ref38","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1126\/science.aad5497","article-title":"Regulatory evolution of innate immunity through co-option of endogenous retroviruses","volume":"351","author":"Chuong","year":"2016","journal-title":"Science"},{"key":"2024080722303794500_ref39","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1101\/gr.276241.121","article-title":"Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity","volume":"32","author":"Kelly","year":"2022","journal-title":"Genome Res"},{"key":"2024080722303794500_ref40","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.82617","article-title":"Mouse B2 SINE elements function as IFN-inducible enhancers","volume":"12","author":"Horton","year":"2023","journal-title":"elife"},{"key":"2024080722303794500_ref41","doi-asserted-by":"crossref","article-title":"Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.","author":"Ivancevic","DOI":"10.1126\/sciadv.ado1218"},{"key":"2024080722303794500_ref42","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nmeth.4556","article-title":"GIGGLE: a search engine for large-scale integrated genome analysis","volume":"15","author":"Layer","year":"2018","journal-title":"Nat Methods"},{"key":"2024080722303794500_ref43","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/s41594-023-00960-6","article-title":"Regulation of human trophoblast gene expression by endogenous retroviruses","volume":"30","author":"Frost","year":"2023","journal-title":"Nat Struct Mol Biol"},{"key":"2024080722303794500_ref44","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1101\/gr.277150.122","article-title":"Regulation of endogenous retrovirus-derived regulatory elements by GATA2\/3 and MSX2 in human trophoblast stem cells","volume":"33","author":"Du","year":"2023","journal-title":"Genome Res"},{"key":"2024080722303794500_ref45","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/s41556-023-01169-x","article-title":"Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal-fetal interface following SARS-CoV-2 infection","volume":"25","author":"Gao","year":"2023","journal-title":"Nat Cell Biol"},{"key":"2024080722303794500_ref46","doi-asserted-by":"crossref","first-page":"4745","DOI":"10.1093\/nar\/gkad109","article-title":"Endogenous retrovirus-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization","volume":"51","author":"Yu","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024080722303794500_ref47","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024080722303794500_ref48","doi-asserted-by":"crossref","first-page":"D729","DOI":"10.1093\/nar\/gky1094","article-title":"Cistrome data browser: expanded datasets and new tools for gene regulatory analysis","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024080722303794500_ref49","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nrc2694","article-title":"Signal integration by JNK and p38 MAPK pathways in cancer development","volume":"9","author":"Wagner","year":"2009","journal-title":"Nat Rev Cancer"},{"key":"2024080722303794500_ref50","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12915-022-01380-6","article-title":"Modulation of macrophage inflammatory function through selective inhibition of the epigenetic reader protein SP140","volume":"20","author":"Ghiboub","year":"2022","journal-title":"BMC Biol"},{"key":"2024080722303794500_ref51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2015\/526518","article-title":"SP140L, an evolutionarily recent member of the SP100 family, is an autoantigen in primary biliary cirrhosis","volume":"2015","author":"Saare","year":"2015","journal-title":"J Immunol Res"},{"key":"2024080722303794500_ref52","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1038\/s41592-018-0048-5","article-title":"An enhanced CRISPR repressor for targeted mammalian gene regulation","volume":"15","author":"Yeo","year":"2018","journal-title":"Nat Methods"},{"key":"2024080722303794500_ref53","doi-asserted-by":"crossref","first-page":"17023","DOI":"10.1038\/sigtrans.2017.23","article-title":"NF-\u03baB signaling in inflammation","volume":"2","author":"Liu","year":"2017","journal-title":"Signal Transduct Target Ther"},{"key":"2024080722303794500_ref54","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/nm.2129","article-title":"Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma","volume":"16","author":"Lamprecht","year":"2010","journal-title":"Nat Med"},{"key":"2024080722303794500_ref55","first-page":"E4630","article-title":"Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma","volume":"112","author":"Lock","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024080722303794500_ref56","doi-asserted-by":"crossref","first-page":"2542","DOI":"10.1038\/onc.2015.308","article-title":"Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma","volume":"35","author":"Babaian","year":"2016","journal-title":"Oncogene"},{"key":"2024080722303794500_ref57","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1038\/s41588-019-0416-9","article-title":"Author correction: transposable elements drive widespread expression of oncogenes in human cancers","volume":"51","author":"Jang","year":"2019","journal-title":"Nat Genet"},{"key":"2024080722303794500_ref58","doi-asserted-by":"crossref","first-page":"3506","DOI":"10.1038\/s41467-020-17206-4","article-title":"Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia","volume":"11","author":"Deniz","year":"2020","journal-title":"Nat Commun"},{"key":"2024080722303794500_ref59","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1038\/s41467-023-41081-4","article-title":"Transposable elements as tissue-specific enhancers in cancers of endodermal lineage","volume":"14","author":"Karttunen","year":"2023","journal-title":"Nat Commun"},{"key":"2024080722303794500_ref60","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1158\/2159-8290.CD-23-0331","article-title":"Transposable elements are Co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer","volume":"13","author":"Grillo","year":"2023","journal-title":"Cancer Discov"},{"key":"2024080722303794500_ref61","doi-asserted-by":"crossref","first-page":"317","DOI":"10.2174\/156800907780809723","article-title":"AP-1 a target for cancer prevention","volume":"7","author":"Matthews","year":"2007","journal-title":"Curr Cancer Drug Targets"},{"key":"2024080722303794500_ref62","doi-asserted-by":"crossref","first-page":"3279","DOI":"10.1038\/sj.onc.1210421","article-title":"MAP kinase signalling pathways in cancer","volume":"26","author":"Dhillon","year":"2007","journal-title":"Oncogene"},{"key":"2024080722303794500_ref63","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.46314","article-title":"Improved CUT&RUN chromatin profiling tools","volume":"8","author":"Meers","year":"2019","journal-title":"elife"},{"key":"2024080722303794500_ref64","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1021\/acschembio.7b00549","article-title":"CRISPR-mediated tagging of endogenous proteins with a luminescent peptide","volume":"13","author":"Schwinn","year":"2018","journal-title":"ACS Chem Biol"},{"key":"2024080722303794500_ref65","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2024080722303794500_ref66","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"}],"container-title":["Human Molecular Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/33\/16\/1454\/58758651\/ddae084.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/33\/16\/1454\/58758651\/ddae084.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T20:34:39Z","timestamp":1723062879000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hmg\/article\/33\/16\/1454\/7673981"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,15]]},"references-count":66,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2024,5,15]]},"published-print":{"date-parts":[[2024,8,6]]}},"URL":"https:\/\/doi.org\/10.1093\/hmg\/ddae084","relation":{},"ISSN":["0964-6906","1460-2083"],"issn-type":[{"value":"0964-6906","type":"print"},{"value":"1460-2083","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,8,15]]},"published":{"date-parts":[[2024,5,15]]}}}