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Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation
Open accessPreprint — published as 10.1093/nar/gkaf918 · Paper page
Abstract
Histone deacetylase 1 and 2 (HDAC1/2) are highly related enzymes that regulate histone acetylation levels in all cells, as catalytic and structural components of six unique multiprotein complexes: SIN3, NuRD, CoREST, MIDAC, MIER and RERE. Co-immunoprecipitation of HDAC1-Flag followed by mass spectrometry revealed that 92% of HDAC1 in mouse embryonic stem cells resides in 3 complexes, NuRD (49%), CoREST (28%) and SIN3 (15%). We compared the structures of MTA1:HDAC1 and MIDAC:HDAC1 to identify critical binding residues on the surface of HDAC1. Surprisingly, a single mutation, Y48E, disrupts binding to all complexes except SIN3. Rescue experiments performed with HDAC1-Y48E in HDAC1/2 double-knockout cells, showed that retention of SIN3 binding alone is sufficient for cell viability. Gene expression and histone acetylation patterns were perturbed in both Y48E and a second mutant cell line, HDAC1-E63R, indicating that cells require a full repertoire of the HDAC1/2 complexes to regulate their transcriptome appropriately. Comparative analysis of MTA1/HDAC1 and SIN3B/HDAC2 structures confirmed the differential modes of HDAC1 recruitment, such that Y48 interacts with ELM2/SANT domain-containing proteins, but not SIN3. The E63R mutation shows markedly reduced binding to NuRD and MiDAC complexes, but retains some CoREST binding. We provide novel molecular insights into the abundance, co-factors and assemblies of this crucial family of chromatin modifying machines.
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Metadata
- Authors
- Alshehri, A., Baker, I.-M., English, D. M., Fairall, L., Collins, M. O., Schwabe, J. W., & Cowley, S. M.
- Affiliations
- University of Leicester (GB)
- University of Sheffield (GB)
- Corresponding author
- Schwabe, John WR
- Cowley, Shaun M
- Venue
- Nucleic Acids Research
- Publisher
- openRxiv
- Published
- 2025-02-27
- Volume
- 53
- Issue
- 17
- ISSN
- 0305-1048 (ISSN-L)
- PMC
- PMC12448893
- OpenAlex
- W4414346486
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 4 · 2025: 1
- FWCI
- 1.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Funders
- Wellcome Trust (222493/Z/21/Z, 222493, MR/W00190X/1)
- UK Research and Innovation
- Musculoskeletal Research Center, Washington University in St. Louis (MR/W00190X/1, MR/X012220/1)
- Biotechnology and Biological Sciences Research Council (BB/P021689/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- HDAC1, histone deacetylase, protein complex formation, NuRD complex, CoREST complex, MTA1, SANT domain, histone acetylation, chromatin regulation, gene expression, mouse embryonic stem cells, protein-protein interaction
- MeSH terms
- Mouse Embryonic Stem Cells, Acetylation, Animals, Gene Expression Regulation, Histone Deacetylases, Histones, Humans, Models, Molecular, Mutation, Protein Binding, Repressor Proteins, Trans-Activators, Mice, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Sin3 Histone Deacetylase and Corepressor Complex, Histone Deacetylase 1, Histone Deacetylase 2, Co-Repressor Proteins
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