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Intrinsically Disordered Regions Define Unique Protein Interaction Networks in CHD Family Remodelers
Open accessPreprint — published as 10.1096/fj.202402808rr · Paper page
Abstract
Chromodomain helicase DNA-binding (CHD1-9) enzymes reposition nucleosomal DNA for transcription, recombination, and replication. They possess highly conserved ATPase domains flanked by poorly characterised N- and C-termini, which are enriched with intrinsically disordered regions (IDRs) and short aggregation-prone regions (APRs). The roles of IDRs and APRs in CHD function has remained elusive. Here, by integrating proteomics and AlphaFold Multimer analysis, we defined the protein-protein interaction (PPI) networks within the N- and C-termini of all CHDs. We generated a comprehensive map of CHD1-9-specific binding proteins, revealing dozens of novel interactions with transcription regulators. We identified APR regions that contribute to PPI formation and demonstrated that a highly conserved APR within the C-terminus of CHD4 is critical for its interaction with the nucleosome remodeling and deacetylase (NuRD), as well as the CHD, ADNP, and HP1 (ChAHP) complexes. Further analysis unravels a regulatory role for the CHD4 APR in gene transcription during erythrocyte formation. Our results emphasize that the N- and C-termini of CHD chromatin remodelers establish PPI networks that drive unique transcriptional programs.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
AlphaFold and Implications for Intrinsically Disordered Proteins
Ruff, K. M., & Pappu, R. V. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167208 · Cited by 635
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Metadata
- Authors
- Tabar, M. S., Parsania, C., Giardina, C., Feng, Y., Wong, A. C., Metierre, C., Nagarajah, R., Dhungel, B. P., Rasko, J. E., & Bailey, C. G.
- Affiliations
- The University of Sydney (AU)
- Royal Prince Alfred Hospital (AU)
- Corresponding author
- Rasko, John EJ
- Bailey, Charles G
- ORCID
- Venue
- The FASEB Journal
- Publisher
- openRxiv
- Published
- 2024-08-25
- Volume
- 39
- Issue
- 10
- Pages
- e70632-e70632
- ISSN
- 0892-6638 (ISSN-L)
- PMC
- PMC12080455
- OpenAlex
- W4410400478
- Cited by
- 7
- References
- 2
- Citations by year
- 2026: 6 · 2025: 1
- FWCI
- 2.10
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The FASEB Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Department of Health and Aged Care, Australian Government (#1128748, #1177305)
- National Health and Medical Research Council (1177305, 1128748)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- CHD4, intrinsically disordered regions, protein-protein interaction, protein termini, aggregation-prone regions, NuRD complex, ADNP, HP1γ, chromatin remodeling, gene transcription, erythroid differentiation, genome regulation
- MeSH terms
- DNA Helicases, DNA-Binding Proteins, Humans, Chromatin Assembly and Disassembly, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Protein Interaction Maps, Intrinsically Disordered Proteins
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