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Yeast Chd1 is a monomeric, helicase-type ATP-dependent chromatin remodeler that
engages nucleosomal DNA at superhelix location 2 (SHL2, ~20 bp from the dyad) and
translocates DNA around the histone core through a stepwise cycle to reposition
nucleosomes.
"Yeast Chd1 is a **monomeric, helicase-type ATPase chromatin remodeller** that engages nucleosomal DNA with its ATPase motor at **superhelix location 2 (SHL2), ~20 bp from the dyad**, and shifts DNA around the histone core through a stepwise translocation cycle, repositioning nucleosomes along DNA."
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A cryo-EM structure of S. cerevisiae Chd1 bound to a nucleosome shows the ATPase at
SHL2, the SANT/SLIDE DNA-binding region contacting linker DNA, and Chd1 detaching/
unwrapping ~two turns of nucleosomal DNA, providing a structural basis for ATP-coupled
remodeling.
"A cryo-EM structure of *S. cerevisiae* Chd1 bound to a nucleosome indicates that Chd1 can **detach/unwrap ~two turns of nucleosomal DNA** and binds in a catalytically poised configuration."
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In comparative in vitro spacing assays CHD1 establishes the shortest average
nucleosome spacing (~160 bp) versus ~175 bp for ISW1/INO80 and ~200 bp for ISW2,
against a yeast in vivo average of ~165 bp.
"In comparative in vitro spacing assays, **CHD1 establishes the shortest average nucleosome spacing (~160 bp)**, compared with **~175 bp** for ISW1/INO80 and **~200 bp** for ISW2. Yeast average in vivo spacing is **~165 bp**."
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ISW1 and CHD1 are the major nucleosome-spacing enzymes in yeast and compete to set
spacing; loss of both causes major chromatin disruption with close-packed
dinucleosomes, indicating partially redundant roles.
"ISW1 and CHD1 are described as **major nucleosome-spacing enzymes** that can compete to set nucleosome spacing; loss of both produces major disruption partly due to **close-packed dinucleosomes**."
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Yeast Chd1 is enriched over transcribed gene bodies/coding regions of active genes
rather than at promoters, and is recruited by transcription elongation machinery.
The PAF1 complex is a key determinant of recruitment, with occupancy tracking
RNAPII Ser5-phosphorylated (early-elongation) patterns.
"Yeast Chd1 is associated with **transcribed gene bodies** rather than promoters and is enriched over coding regions of active genes."
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Chd1 functionally interacts with FACT (Spt16-Pob3), the PAF1 complex/Rtf1, and
Spt4-Spt5, placing it in the transcription-coupled chromatin reassembly pathway and
helping re-establish nucleosome organization after RNA Pol II passage to prevent
exposure of internal promoter-like DNA.
"Chd1 is thought to help **re-establish nucleosome organization after RNA polymerase II passage**, maintaining chromatin structure over coding regions and preventing inappropriate exposure of internal promoter-like DNA."
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chd1 mutants initiate transcription from cryptic internal promoters, a defect
strongly enhanced in chd1 isw1 double mutants, consistent with partially redundant
roles in preserving coding-region chromatin integrity.
"**chd1 mutants** show initiation from **cryptic internal promoters**; this defect is **strongly enhanced in chd1 isw1 double mutants**, indicating partially redundant roles of Chd1 and Isw1 in preserving coding-region chromatin integrity."
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Loss of CHD1 produces widespread, reciprocal disruption of H3K4me3/H3K36me3 patterns
across roughly half of the yeast genome, concentrated within ~1 kb of transcription
start sites. Importantly, unlike human CHD1, yeast Chd1 does not directly bind
H3K4me3; mark-boundary maintenance is indirect.
"In budding yeast, Chd1 contributes to maintaining **H3K4me3/H3K36me3 domain boundaries**, but Lee et al. report yeast Chd1 **does not directly bind H3K4me3** the way human CHD1 can."
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H2B K120 (yeast K123) ubiquitination, which is enriched in coding regions, stimulates
Chd1 activity ~2-fold in vitro; the transiently unwrapped nucleosome state is proposed
to be stabilized by ubiquitin repositioning upon Chd1 binding.
"**H2B K120 (yeast K123) ubiquitination** can **stimulate Chd1 activity ~2-fold** in vitro and is enriched in coding regions."
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Although Chd1 translocates DNA unidirectionally from a single SHL2 site, nucleosome
symmetry (two SHL2 sites) yields net back-and-forth bidirectional sliding, integrating
ATP-driven and intrinsic sequence-dependent positioning.
"although Chd1 action at one SHL2 site is unidirectional, nucleosome symmetry allows **back-and-forth (bi-directional) sliding** when the enzyme acts on either side."
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CHD1 deletion alters co-transcriptional RNA processing: in one RNA-seq analysis 35
introns were significantly affected, with 28/35 (80%) showing lower intron retention
(improved splicing) in chd1-delta, consistent with an indirect, elongation-coupled
effect on splicing.
"In one RNA-seq analysis, **35 introns** were significantly affected, with **28/35 (80%)** showing **lower intron retention** (improved splicing) in chd1Δ."
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A 2024/2025 bioRxiv preprint maps a direct Rtf1-Chd1 interaction in which a short
N-terminal region of Rtf1 (aa 1-30) contacts the Chd1 CHCT domain, proposed to help
distribute Chd1 across transcribed genes; this is provisional pending peer review.
"a short N-terminal region of Rtf1 (aa 1–30) interacts with the **Chd1 CHCT domain**, supported by yeast two-hybrid mapping and alanine-scan disruption of key residues."