ATP-dependent chromatin remodeler CHD1

Function

ATP-dependent chromatin-remodeling factor which functions as substrate recognition component for the transcription regulatory histone acetylation (HAT) complex SAGA. Recognizes H3K4me. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Negatively regulates DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.

Classification

Family (Pfam)

PF18196 Cdh1_DBD_1, PF13907 CHD1-like_C, PF00385 Chromo, PF00271 Helicase_C, PF23588 HTH_CHD1_Hrp3, PF00176 SNF2-rel_dom

InterPro

Cdh1_DBD, CHD1-2/Hrp3_HTH, CHD1-like_C, Chromo-like_dom_sf, Chromo/chromo_shadow_dom, Chromo_domain, Chromodomain_CS, Helicase_ATP-bd, Helicase_C-like, Homeodomain-like_sf, P-loop_NTPase, SNF2-like_sf, SNF2/RAD54-like_C, SNF2_N

Functional cluster

DEAD-Box RNA Helicases & Biogenesis Factors

Experimental structures · PDB · 18

• 2DY7 NMR
• 2DY8 NMR
• 2H1E X-ray 2.20A
• 2XB0 X-ray 2.00A
• 3MWY X-ray 3.70A
• 3TED X-ray 2.00A
• 5J70 X-ray 2.96A
• 5O9G EM 4.80A
• 6FTX EM 4.50A
• 6G0L EM 4.50A
• 7NKX EM 2.90A
• 7TN2 EM 2.30A
• … and 6 more

A predicted model is available from AlphaFold.

Gene Ontology · 31

• GO:0000785 chromatin
• GO:0005739 mitochondrion
• GO:0030874 nucleolar chromatin
• GO:0005634 nucleus
• GO:0000124 SAGA complex
• GO:0035861 site of double-strand break
• GO:0046695 SLIK (SAGA-like) complex
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0008094 ATP-dependent activity, acting on DNA
• GO:0140658 ATP-dependent chromatin remodeler activity
• GO:0003682 chromatin binding
• GO:0031490 chromatin DNA binding
• GO:0003677 DNA binding
• GO:0042393 histone binding
• GO:0140002 histone H3K4me3 reader activity
• GO:0140750 nucleosome array spacer activity
• GO:0000182 rDNA binding
• GO:0000976 transcription cis-regulatory region binding
• GO:0006338 chromatin remodeling
• GO:0000729 DNA double-strand break processing
• GO:0000724 double-strand break repair via homologous recombination
• GO:2000104 negative regulation of DNA-templated DNA replication
• GO:0034728 nucleosome organization
• GO:1902275 regulation of chromatin organization
• GO:0006357 regulation of transcription by RNA polymerase II
• GO:0001178 regulation of transcriptional start site selection at RNA polymerase II promoter
• GO:0007062 sister chromatid cohesion
• GO:0006363 termination of RNA polymerase I transcription
• GO:0006369 termination of RNA polymerase II transcription
• GO:0006368 transcription elongation by RNA polymerase II

Neighborhood · nearest proteins

Related proteins · sequence + function similarity

• ATP-dependent chromatin remodeler hrp1 0.95
• ATP-dependent chromatin remodeler hrp3 0.92
• CHD3-type chromatin-remodeling factor CHR7 0.87
• CHD3-type chromatin-remodeling factor PICKLE 0.85
• ISWI chromatin-remodeling complex ATPase ISW2 0.83
• ISWI chromatin-remodeling complex ATPase ISW2 0.83
• ISWI chromatin-remodeling complex ATPase CHR17 0.83
• ISWI chromatin-remodeling complex ATPase CHR11 0.81
• ATP-dependent chromatin remodeler CHD2 0.81
• Nuclear protein STH1/NPS1 0.81
• ATP-dependent chromatin remodeler CHD1 0.80
• ISWI chromatin-remodeling complex ATPase ISW1 0.79

Co-cited proteins · studied together in the literature

• ATP-dependent chromatin remodeler CHD1 2 shared papers
• Histone chaperone ASF1 1 shared papers
• ATP-dependent chromatin remodeler Chd3 1 shared papers
• Transcription elongation factor SPT5 1 shared papers
• Transcription elongation factor SPT4 1 shared papers
• FACT complex subunit POB3 2 shared papers
• FACT complex subunit SPT16 2 shared papers
• ATP-dependent chromatin remodeler CHD2 1 shared papers
• ATP-dependent chromatin remodeler CHD3 1 shared papers
• Transcription factor SPN1 1 shared papers
• RING finger protein PSH1 1 shared papers
• SAGA complex subunit HFI1 3 shared papers

Literature · 38 cited papers

• Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Mol. Cell · 2024
• Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nat. Struct. Mol. Biol. · 2022
• Structural basis of nucleosome transcription mediated by Chd1 and FACT. Nat. Struct. Mol. Biol. · 2021
• Yeast Chd1p unwraps the exit side DNA upon ATP binding to facilitate the nucleosome translocation occurring upon ATP hydrolysis. Biochemistry · 2020
• Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Elife · 2018
• Nucleosome-Chd1 structure and implications for chromatin remodelling. Nature · 2017
• Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns. Epigenetics Chromatin · 2014
• The reference genome sequence of Saccharomyces cerevisiae: Then and now. G3 (Bethesda) · 2014
• Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat. Struct. Mol. Biol. · 2012
• N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB. Proc. Natl. Acad. Sci. U.S.A. · 2012
• Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J. Biol. Chem. · 2011
• The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J. · 2011
• … and 26 more in the literature graph