{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T01:54:46Z","timestamp":1768528486249,"version":"3.49.0"},"posted":{"date-parts":[[2025,10,31]]},"group-title":"Molecular Biology","reference-count":52,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T00:00:00Z","timestamp":1761868800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"NIH","award":["R35GM122519"],"award-info":[{"award-number":["R35GM122519"]}]},{"name":"NIH","award":["R01HL140471"],"award-info":[{"award-number":["R01HL140471"]}]},{"name":"NIH","award":["R03HD095088"],"award-info":[{"award-number":["R03HD095088"]}]},{"name":"NIH","award":["R01GM134130"],"award-info":[{"award-number":["R01GM134130"]}]},{"DOI":"10.13039\/100000968","name":"American Heart Association","doi-asserted-by":"crossref","award":["16SDG31400009"],"award-info":[{"award-number":["16SDG31400009"]}],"id":[{"id":"10.13039\/100000968","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,31]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Craniofacial Developmental Protein 1 (CFDP1) is a member of the evolutionarily conserved family of Bucentaur (BCNT) proteins and was originally classified as a protein required for cell survival and differentiation during tooth development. Yeast Swc5, a BCNT family member, is an essential subunit of the yeast SWR1C chromatin remodeling complex that catalyzes the deposition of histone variant H2A.Z. Direct connections between CFDP1, H2A.Z deposition, and the mammalian SWR1 homolog, Snf2-Related CREBBP Activator Protein (SRCAP), have not been identified. Here, we perform detailed biochemical reconstitution and characterization of the human SRCAP complex (SRCAP-C). We find that CFDP1 weakly interacts with SRCAP-C in a salt concentration-dependent manner. SRCAP-C purified under a high-salt condition does not co-purify with CFDP1 and is inactive in H2A.Z dimer exchange reaction, but the addition of exogeneous CFDP1 restores the H2A.Z deposition activity of SRCAP-C, demonstrating that CFDP1 is required for H2A.Z dimer exchange by SRCAP-C. We show that CFDP1 stimulates the basal ATPase activity of reconstituted SRCAP-C, suggesting a requirement for CFDP1 in regulating intrinsic catalytic ATPase activity. Consistent with this idea, CFDP1 deficiency in human induced pluripotent stem cells (hiPSCs) leads to a genome-wide reduction of H2A.Z, H3K27me3, and H3K4me3 deposition, accompanied by the upregulation of developmental genes normally marked by these modifications. Taken together, our results provide mechanistic insights into how CFDP1 regulates histone variant H2A.Z deposition by SRCAP-C. Given mutations in the SRCAP gene cause Floating-Harbor syndrome (FHS), a rare, dominant developmental disorder, our study provides an additional link between craniofacial defects and SRCAP-mediated H2A.Z deposition.<\/jats:p>","DOI":"10.1101\/2025.10.30.685587","type":"posted-content","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T21:10:28Z","timestamp":1761945028000},"source":"Crossref","is-referenced-by-count":0,"title":["CFDP1 is required for histone variant H2A.Z deposition by the human SRCAP chromatin remodeling complex"],"prefix":"10.64898","author":[{"given":"Naoe","family":"Moro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dandan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1173-2429","authenticated-orcid":false,"given":"Vincent L.","family":"Butty","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7363-562X","authenticated-orcid":false,"given":"Stuart S.","family":"Levine","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig L.","family":"Peterson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3491-4962","authenticated-orcid":false,"given":"Laurie A.","family":"Boyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8842-6716","authenticated-orcid":false,"given":"Shinya","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025110401500627000_2025.10.30.685587v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(99)00220-6"},{"key":"2025110401500627000_2025.10.30.685587v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(01)00868-X"},{"key":"2025110401500627000_2025.10.30.685587v1.3","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.yexcr.2017.10.022","article-title":"Functional analysis of the cfdp1 gene in zebrafish provides evidence for its crucial role in craniofacial development and osteogenesis","volume":"361","year":"2017","journal-title":"Experimental cell research"},{"key":"2025110401500627000_2025.10.30.685587v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb1023"},{"key":"2025110401500627000_2025.10.30.685587v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2011.12.001"},{"key":"2025110401500627000_2025.10.30.685587v1.6","doi-asserted-by":"crossref","first-page":"3196","DOI":"10.1002\/ajmg.a.35635","article-title":"Floating-Harbor syndrome and polycystic kidneys associated with SRCAP mutation","volume":"158A","year":"2012","journal-title":"Am J Med Genet A"},{"key":"2025110401500627000_2025.10.30.685587v1.7","doi-asserted-by":"publisher","DOI":"10.1111\/cge.12199"},{"key":"2025110401500627000_2025.10.30.685587v1.8","doi-asserted-by":"publisher","DOI":"10.1186\/1750-1172-8-63"},{"key":"2025110401500627000_2025.10.30.685587v1.9","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/s12881-014-0127-0","article-title":"Expanded spectrum of exon 33 and 34 mutations in SRCAP and follow-up in patients with Floating-Harbor syndrome","volume":"15","year":"2014","journal-title":"BMC Med Genet"},{"key":"2025110401500627000_2025.10.30.685587v1.10","doi-asserted-by":"publisher","DOI":"10.1007\/BF02079072"},{"key":"2025110401500627000_2025.10.30.685587v1.11","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1002\/ajmg.a.33294","article-title":"The phenotype of Floating-Harbor syndrome in 10 patients","volume":"152A","year":"2010","journal-title":"Am J Med Genet A"},{"key":"2025110401500627000_2025.10.30.685587v1.12","doi-asserted-by":"publisher","DOI":"10.1097\/MCD.0b013e32834af5a7"},{"key":"2025110401500627000_2025.10.30.685587v1.13","doi-asserted-by":"publisher","DOI":"10.1101\/sqb.2010.75.063"},{"key":"2025110401500627000_2025.10.30.685587v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-018-0102-y"},{"key":"2025110401500627000_2025.10.30.685587v1.15","doi-asserted-by":"crossref","first-page":"115767","DOI":"10.1016\/j.celrep.2025.115767","article-title":"Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements","volume":"44","year":"2025","journal-title":"Cell Rep"},{"key":"2025110401500627000_2025.10.30.685587v1.16","doi-asserted-by":"crossref","unstructured":"C. L. Lin et al., Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex. Nucleic Acids Res, (2017).","DOI":"10.1093\/nar\/gkx414"},{"key":"2025110401500627000_2025.10.30.685587v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2016.166"},{"key":"2025110401500627000_2025.10.30.685587v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(01)00329-3"},{"key":"2025110401500627000_2025.10.30.685587v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-021-00589-3"},{"key":"2025110401500627000_2025.10.30.685587v1.20","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/s41421-023-00640-1","article-title":"Structural insights into histone exchange by human SRCAP complex","volume":"10","year":"2024","journal-title":"Cell Discov"},{"key":"2025110401500627000_2025.10.30.685587v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1036"},{"key":"2025110401500627000_2025.10.30.685587v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/srep45022"},{"key":"2025110401500627000_2025.10.30.685587v1.23","doi-asserted-by":"publisher","DOI":"10.1021\/bi060043d"},{"key":"2025110401500627000_2025.10.30.685587v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms8108"},{"key":"2025110401500627000_2025.10.30.685587v1.25","doi-asserted-by":"crossref","unstructured":"O. Willhoft et al., Structure and dynamics of the yeast SWR1-nucleosome complex. Science 362, (2018).","DOI":"10.1126\/science.aat7716"},{"key":"2025110401500627000_2025.10.30.685587v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/ng.409"},{"key":"2025110401500627000_2025.10.30.685587v1.27","doi-asserted-by":"publisher","DOI":"10.1021\/bi00193a013"},{"key":"2025110401500627000_2025.10.30.685587v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.10.019"},{"key":"2025110401500627000_2025.10.30.685587v1.29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx589"},{"key":"2025110401500627000_2025.10.30.685587v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.08.015"},{"key":"2025110401500627000_2025.10.30.685587v1.31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M703418200"},{"key":"2025110401500627000_2025.10.30.685587v1.32","doi-asserted-by":"publisher","DOI":"10.1101\/gad.303784.117"},{"key":"2025110401500627000_2025.10.30.685587v1.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2012.11.003"},{"key":"2025110401500627000_2025.10.30.685587v1.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.09.056"},{"key":"2025110401500627000_2025.10.30.685587v1.35","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M601443200"},{"key":"2025110401500627000_2025.10.30.685587v1.36","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-013-1343-z"},{"key":"2025110401500627000_2025.10.30.685587v1.37","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.celrep.2017.04.001","article-title":"KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency","volume":"19","year":"2017","journal-title":"Cell Rep"},{"key":"2025110401500627000_2025.10.30.685587v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.10.039"},{"key":"2025110401500627000_2025.10.30.685587v1.39","doi-asserted-by":"crossref","unstructured":"A. S. Baier et al., Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C. Elife 13, (2024).","DOI":"10.7554\/eLife.94869.3"},{"key":"2025110401500627000_2025.10.30.685587v1.40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1221"},{"key":"2025110401500627000_2025.10.30.685587v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.08.002"},{"key":"2025110401500627000_2025.10.30.685587v1.42","doi-asserted-by":"publisher","DOI":"10.1385\/1592596819"},{"key":"2025110401500627000_2025.10.30.685587v1.43","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.21.6.2098-2106.2001"},{"key":"2025110401500627000_2025.10.30.685587v1.44","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2016.01.015"},{"key":"2025110401500627000_2025.10.30.685587v1.45","doi-asserted-by":"publisher","DOI":"10.1126\/science.1229758"},{"key":"2025110401500627000_2025.10.30.685587v1.46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003725"},{"key":"2025110401500627000_2025.10.30.685587v1.47","doi-asserted-by":"crossref","unstructured":"M. P. Meers , T. D. Bryson , J. G. Henikoff , S. Henikoff , Improved CUT&RUN chromatin profiling tools. Elife 8, (2019).","DOI":"10.7554\/eLife.46314"},{"key":"2025110401500627000_2025.10.30.685587v1.48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"2025110401500627000_2025.10.30.685587v1.49","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-019-0287-4"},{"key":"2025110401500627000_2025.10.30.685587v1.50","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2025110401500627000_2025.10.30.685587v1.51","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1630"},{"key":"2025110401500627000_2025.10.30.685587v1.52","doi-asserted-by":"crossref","first-page":"e1010378","DOI":"10.1371\/journal.pcbi.1010378","article-title":"WhichTF is functionally important in your open chromatin data?","volume":"18","year":"2022","journal-title":"PLoS computational biology"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.10.30.685587","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:56:08Z","timestamp":1768470968000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.10.30.685587"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,31]]},"references-count":52,"URL":"https:\/\/doi.org\/10.1101\/2025.10.30.685587","relation":{},"subject":[],"published":{"date-parts":[[2025,10,31]]},"subtype":"preprint"}}