{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:08:05Z","timestamp":1785424085820,"version":"3.56.0"},"reference-count":36,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["R01GM114142"],"award-info":[{"award-number":["R01GM114142"]}]},{"award":["R01GM114142"],"award-info":[{"award-number":["R01GM114142"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013030","name":"William & Ella Owens Medical Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013030","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/0101ppd69","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Aberrant H3K79 dimethylation (H3K79me2) by DOT1L is a defining feature of MLL-rearranged (MLLr) acute myeloid leukemia (AML), but whether this modification influences alternative splicing is unclear. We examined the relationship between H3K79me2 and exon skipping in primary MLLr AML. Methods: We performed H3K79me2 ChIP-seq and RNA-seq on primary samples from 24 MLLr AML patients, 4 wild-type MLL AML patients, and 4 healthy bone marrow donors, with matched profiling before and after DOT1L inhibition using EPZ5676. DOT1L co-immunoprecipitation with mass spectrometry (IP-MS) was performed in MV-4-11 and MOLM-14 cells, and an aggregate splicing score was evaluated in the TCGA-AML cohort. Results: A subset of exon skipping (SE) events was enriched at H3K79me2-occupied loci in MLLr samples. EPZ5676 remodeled SE patterns, and many switched events showed concurrent loss of local H3K79me2. Genes harboring these events were enriched for RNA processing, DNA repair, and apoptosis functions. Core spliceosomal and hnRNP proteins were prominent in the DOT1L interactome and were reduced after EPZ5676, and SRSF2 and hnRNPA1 binding motifs were enriched near the regulated exons. About two-thirds of the common switched events overlapped a local H3K79me2 peak, and an aggregate splicing score derived from these events stratified patients by overall survival in the TCGA-AML cohort, with higher scores associated with shorter survival. Conclusions: These data support a model in which H3K79me2 contributes to alternative splicing regulation in MLLr AML, linking the core epigenetic lesion of this disease to aberrant RNA processing with potential prognostic relevance.<\/jats:p>","DOI":"10.3390\/genes17080857","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T13:53:26Z","timestamp":1784901206000},"page":"857","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification of a Chromatin-Splicing Regulatory Axis Driven by DOT1L in MLL-Rearranged Acute Myeloid Leukemia"],"prefix":"10.3390","volume":"17","author":[{"given":"Qi","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Drylab Inc., Quincy, MA 02171, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5272-8349","authenticated-orcid":false,"given":"Bowen","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Diagnostic and Interventional Imaging, University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianbao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Drylab Inc., Quincy, MA 02171, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raven","family":"Garcia","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX 78229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7203-1143","authenticated-orcid":false,"given":"Shengtong","family":"Han","sequence":"additional","affiliation":[{"name":"School of Dentistry, Marquette University, Milwaukee, WI 53233, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8765-3471","authenticated-orcid":false,"given":"Victor X.","family":"Jin","sequence":"additional","affiliation":[{"name":"Data Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nrc2253","article-title":"MLL translocations, histone modifications and leukaemia stem-cell development","volume":"7","author":"Krivtsov","year":"2007","journal-title":"Nat. Rev. Cancer"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1038\/s41375-023-01877-1","article-title":"The KMT2A recombinome of acute leukemias in 2023","volume":"37","author":"Meyer","year":"2023","journal-title":"Leukemia"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41408-021-00557-6","article-title":"Predictors of outcomes in adults with acute myeloid leukemia and KMT2A rearrangements","volume":"11","author":"Issa","year":"2021","journal-title":"Blood Cancer J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1038\/leu.2011.90","article-title":"The heterogeneity of pediatric MLL-rearranged acute myeloid leukemia","volume":"25","author":"Balgobind","year":"2011","journal-title":"Leukemia"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.ccr.2011.06.010","article-title":"MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L","volume":"20","author":"Bernt","year":"2011","journal-title":"Cancer Cell"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"984","DOI":"10.3324\/haematol.2008.002436","article-title":"The molecular biology of mixed lineage leukemia","volume":"94","author":"Slany","year":"2009","journal-title":"Haematologica"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.cell.2005.02.020","article-title":"hDOT1L links histone methylation to leukemogenesis","volume":"121","author":"Okada","year":"2005","journal-title":"Cell"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3403","DOI":"10.1101\/gad.1741408","article-title":"Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia","volume":"22","author":"Guenther","year":"2008","journal-title":"Genes Dev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1101\/gad.1898410","article-title":"Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom)","volume":"24","author":"Mohan","year":"2010","journal-title":"Genes Dev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"15751","DOI":"10.1073\/pnas.1111498108","article-title":"Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes","volume":"108","author":"Biswas","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1182\/blood-2013-04-497644","article-title":"Potent inhibition of DOT1L as treatment of MLL-fusion leukemia","volume":"122","author":"Daigle","year":"2013","journal-title":"Blood"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.1182\/blood-2017-12-818948","article-title":"The DOT1L inhibitor pinometostat reduces H3K79 methylation and has modest clinical activity in adult acute leukemia","volume":"131","author":"Stein","year":"2018","journal-title":"Blood"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1124\/jpet.114.214577","article-title":"DOT1L inhibitor EPZ-5676 displays synergistic antiproliferative activity in combination with standard of care agents and hypomethylating agents in MLL-rearranged leukemia cells","volume":"350","author":"Klaus","year":"2014","journal-title":"J. Pharmacol. Exp. Ther."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1182\/blood-2015-11-684225","article-title":"DOT1L as a therapeutic target for the treatment of DNMT3A-mutant acute myeloid leukemia","volume":"128","author":"Rau","year":"2016","journal-title":"Blood"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1126\/science.1184208","article-title":"Regulation of alternative splicing by histone modifications","volume":"327","author":"Luco","year":"2010","journal-title":"Science"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/s41467-021-20979-x","article-title":"Splicing-associated chromatin signatures: A combinatorial and position-dependent role for histone marks in splicing definition","volume":"12","author":"Agirre","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4947","DOI":"10.1093\/nar\/gku151","article-title":"Sudemycin E influences alternative splicing and changes chromatin modifications","volume":"42","author":"Convertini","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nrc.2016.51","article-title":"RNA splicing factors as oncoproteins and tumour suppressors","volume":"16","author":"Dvinge","year":"2016","journal-title":"Nat. Rev. Cancer"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e1643","DOI":"10.1002\/wrna.1643","article-title":"Splicing alterations in healthy aging and disease","volume":"12","author":"Angarola","year":"2021","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev-biochem-060614-034242","article-title":"Regulation of alternative splicing through coupling with transcription and chromatin structure","volume":"84","author":"Naftelberg","year":"2015","journal-title":"Annu. Rev. Biochem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1016\/j.cell.2013.02.034","article-title":"Dynamic integration of splicing within gene regulatory pathways","volume":"152","author":"Braunschweig","year":"2013","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"110357","DOI":"10.1016\/j.celrep.2022.110357","article-title":"Histone marks regulate the epithelial-to-mesenchymal transition via alternative splicing","volume":"38","author":"Segelle","year":"2022","journal-title":"Cell Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/nature10496","article-title":"Frequent pathway mutations of splicing machinery in myelodysplasia","volume":"478","author":"Yoshida","year":"2011","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3616","DOI":"10.1182\/blood-2013-08-518886","article-title":"Clinical and biological implications of driver mutations in myelodysplastic syndromes","volume":"122","author":"Papaemmanuil","year":"2013","journal-title":"Blood"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1182\/blood-2018-04-843771","article-title":"Impact of spliceosome mutations on RNA splicing in myelodysplasia: Dysregulated genes\/pathways and clinical associations","volume":"132","author":"Pellagatti","year":"2018","journal-title":"Blood"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"6601","DOI":"10.1007\/s11033-023-08597-w","article-title":"Clinical and prognostic profile of SRSF2 and related spliceosome mutations in patients with acute myeloid leukemia","volume":"50","author":"Jia","year":"2023","journal-title":"Mol. Biol. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1042\/BJ20081501","article-title":"The SR protein family of splicing factors: Master regulators of gene expression","volume":"417","author":"Long","year":"2009","journal-title":"Biochem. J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1007\/s00439-016-1683-5","article-title":"The hnRNP family: Insights into their role in health and disease","volume":"135","author":"Geuens","year":"2016","journal-title":"Hum. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3145","DOI":"10.1038\/s41467-022-30960-x","article-title":"Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model","volume":"13","author":"Li","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_30","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":"ref_31","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":"ref_32","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"W367","DOI":"10.1093\/nar\/gkag470","article-title":"DAVID: A web server for functional annotation and functional enrichment analysis of gene lists (2025 update)","volume":"54","author":"Sherman","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"W361","DOI":"10.1093\/nar\/gku406","article-title":"RBPmap: A web server for mapping binding sites of RNA-binding proteins","volume":"42","author":"Paz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1038\/s41586-018-0623-z","article-title":"Functional genomic landscape of acute myeloid leukaemia","volume":"562","author":"Tyner","year":"2018","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13073-018-0538-1","article-title":"Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing","volume":"10","author":"Li","year":"2018","journal-title":"Genome Med."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/857\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T04:26:21Z","timestamp":1785039981000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/857"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,24]]},"references-count":36,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["genes17080857"],"URL":"https:\/\/doi.org\/10.3390\/genes17080857","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,24]]}}}