| Functional aspect | Key findings | Evidence type | Primary source(s) with year, DOI URL |
|---|---|---|---|
| Target identity / domain architecture | The literature matches **Saccharomyces cerevisiae Chd1**, the ATP-dependent chromatin remodeler encoded by **CHD1/YER164W**. Core architecture reported for yeast Chd1: tandem chromodomains, bilobal Snf2-family ATPase motor, and C-terminal SANT/SLIDE DNA-binding region; reviews also describe CHD-family flanking regulatory domains. This aligns with UniProt P32657 annotation as a SNF2/RAD54-family chromodomain helicase DNA-binding protein. (pqac-00000006, pqac-00000019) | Structural, review | Farnung et al., 2017, Nature, https://doi.org/10.1038/nature24046; Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840 |
| Primary biochemical activity | Chd1 is an **ATP-dependent chromatin remodeler** that repositions/slides nucleosomes and spaces nucleosomal arrays. Chd1 acts on nucleosomal DNA at **SHL2 (~20 bp from the dyad)** and can assemble/reposition nucleosomes into evenly spaced arrays. (pqac-00000012, pqac-00000017) | Biochemical, mechanistic | Park et al., 2023, Nucleic Acids Research, https://doi.org/10.1093/nar/gkad738 |
| In vitro spacing specificity | 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**. (pqac-00000011, pqac-00000020, pqac-00000021) | Review of primary spacing assays | Prajapati et al., 2020, Biology, https://doi.org/10.3390/biology9080190 |
| Structural mechanism on nucleosomes | Cryo-EM of **S. cerevisiae** Chd1 bound to the nucleosome shows the ATPase at **SHL +2**, the SANT/SLIDE DNA-binding region contacting linker DNA near **SHL −7**, and Chd1 **detaching/unwrapping two turns of DNA** from the histone octamer. This provides a direct structural explanation for ATP-coupled remodeling. (pqac-00000006) | Structural | Farnung et al., 2017, Nature, https://doi.org/10.1038/nature24046; Sundaramoorthy et al., 2018, eLife, https://doi.org/10.1101/290874 |
| Repositioning range / linker dependence | Text summarizing yeast Chd1 remodeling reports that Chd1 can reposition nucleosomes **23–39 bp into a 54 bp linker**, similar to ISW1a/ISW2, supporting active engagement of extranucleosomal linker DNA by the DNA-binding domain. (pqac-00000010, pqac-00000018) | Structural discussion with prior biochemical reference | Sundaramoorthy et al., 2018, eLife, https://doi.org/10.1101/290874 |
| Sliding directionality | Chd1 translocates DNA **unidirectionally toward the dyad** from a single SHL2 site, but because nucleosomes have two symmetric SHL2 sites, the net outcome can be **back-and-forth/bidirectional sliding**. DNA perturbations tend to localize about **one helical turn (~10 bp)** outside SHL2, and strong phasing can favor **~10 bp shifts**. (pqac-00000012, pqac-00000017) | Biophysical, sequencing-based mechanistic study | Park et al., 2023, Nucleic Acids Research, https://doi.org/10.1093/nar/gkad738 |
| DNA-sequence sensitivity / substrate preference | On the Widom 601 sequence, Chd1 preferentially shifts the dyad toward the **TA-poor side**; introducing long **poly(dA:dT)** tracts on that side reverses the preferred sliding direction. Similar principles were observed using the natural **S. cerevisiae SWH1 +1 nucleosome** sequence. (pqac-00000012, pqac-00000017) | Biophysical, substrate preference | Park et al., 2023, Nucleic Acids Research, https://doi.org/10.1093/nar/gkad738 |
| Cellular localization / chromatin context | Yeast Chd1 is enriched in the **nucleus on transcribed gene bodies/coding regions**, rather than promoters, and is associated with **active transcription**. It tracks especially well with highly transcribed genes and with RNAPII Ser5-phosphorylated occupancy patterns. (pqac-00000002, pqac-00000004, pqac-00000019) | Genome-wide, review | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636; Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840 |
| Recruitment by elongation machinery | Recruitment is strongly linked to **transcription elongation factors**. Chd1 association decreases in **Rtf1/PAF1C** mutants, supporting recruitment by PAF1C; **Spt4** can oppose/promote redistribution near 5′ ends depending on context. Chd1 also interacts functionally with **FACT (Spt16-Pob3)** and transcription elongation machinery. (pqac-00000002, pqac-00000004, pqac-00000005, pqac-00000019) | Genome-wide, genetic, review | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636; Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840 |
| Histone mark recognition / chromodomain function | 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. A **H3K36me3 mimic modestly stimulates** Chd1 activity, but the structural study did not support a stable direct H3K36-tail interaction in the captured state. (pqac-00000004, pqac-00000018) | Genome-wide, structural/biochemical | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636; Sundaramoorthy et al., 2018, eLife, https://doi.org/10.1101/290874 |
| Modulation by H2B ubiquitination | **H2BK120/K123 ubiquitination stimulates Chd1 activity ~2-fold** in vitro. In the Chd1-bound unwrapped nucleosome, ubiquitin is repositioned toward DNA; the unwrapped nucleosome state is estimated to have **~10% occupancy** in the absence of stabilizing factors, and ubiquitin is proposed to stabilize this transiently unwrapped state. Chd1 mutants also show reduced H2B ubiquitination. (pqac-00000006, pqac-00000010, pqac-00000018) | Structural, biochemical | Sundaramoorthy et al., 2018, eLife, https://doi.org/10.1101/290874 |
| Role in transcription-coupled chromatin restoration | 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. (pqac-00000004, pqac-00000012, pqac-00000019) | Genome-wide, mechanistic review | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636; Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840 |
| Cryptic transcription suppression | **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. (pqac-00000002, pqac-00000014, pqac-00000019) | Genetic, review | Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840; Prajapati et al., 2020, Biology, https://doi.org/10.3390/biology9080190 |
| Nucleosome organization phenotypes in mutants | Loss of both **ISW1 and CHD1** causes major chromatin disruption and formation of **close-packed dinucleosomes**. chd1Δ alone reduces phasing beyond the +1 nucleosome, whereas double loss causes much stronger disorganization, especially on highly transcribed genes. (pqac-00000008, pqac-00000014) | Genetic, review | Prajapati et al., 2020, Biology, https://doi.org/10.3390/biology9080190 |
| Effects on histone modification domains | Loss of CHD1 causes widespread, reciprocal disruption of **H3K4me3** and **H3K36me3** near the 5′ ends of genes, concentrated within **~1 kb of the TSS** and affecting approximately **half of the yeast genome**. (pqac-00000005, pqac-00000013, pqac-00000016) | Genome-wide ChIP-seq / RNA-seq | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636 |
| Effects on intron retention / splicing-linked transcription | RNA-seq showed **35 introns** significantly affected in chd1Δ, with **28/35 (80%)** showing **lower intron retention** (improved splicing). Reanalysis with deeper RNA-seq found **94% of introns** had lower retention in chd1Δ, with the effect especially clear in ribosomal protein genes where Chd1 is enriched. (pqac-00000013, pqac-00000016) | Genome-wide RNA-seq | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636 |
| Relationship with FACT / other partners | Chd1 functionally interacts with **FACT (Spt16-Pob3)**, **PAF1 complex/Rtf1**, and **Spt4-Spt5** elongation factors; these interactions place Chd1 in the transcription-coupled chromatin reassembly pathway rather than acting primarily by changing RNAPII processivity directly. (pqac-00000004, pqac-00000006, pqac-00000019) | Genome-wide, structural context, review | Lee et al., 2017, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx636; Sundaramoorthy et al., 2018, eLife, https://doi.org/10.1101/290874; Murawska & Brehm, 2011, Transcription, https://doi.org/10.4161/trns.2.6.17840 |


*Table: This table summarizes functional annotation evidence for Saccharomyces cerevisiae CHD1 (UniProt P32657), including biochemical activity, structural mechanism, recruitment, localization, mutant phenotypes, and key quantitative findings. It is useful as a compact evidence map linking specific claims to source types and DOI-resolved references.*