While progressive striatal gene expression changes and epigenetic alterations are a prominent feature of Huntington's disease (HD), the mechanistic basis remains poorly understood. Using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that the huntingtin protein (HTT) reproducibly occupies specific locations in the mouse genome. Striatal HTT ChIP-seq peaks were enriched in coding regions of spiny projection neuron identity genes, which are found to have reduced expression in HD patients and mouse models, and had reduced occupancy in expanded polyglutamine HTT knock-in mice (HttQ111/Q111). Conversely, HTT occupancy was depleted near genes that are up-regulated in HD. ChIP-seq of striatal histone modifications revealed genotype-specific colocalization of HTT with active chromatin marks and enhancer of zeste homolog 2 (EZH2), a key enzymatic component of the PRC2 complex. Near genes that are differentially regulated in HD, greater HTT occupancy in HttQ111/Q111 vs. wildtype mice was associated with increased EZH2 binding, increased H3K4me3, and decreased H3K27me3. Our study suggests that huntingtin-chromatin interactions may play a role in organizing chromatin and promoting cell type-specific gene expression, with HTT occupancy predicting transcriptional dysregulation in HD.

Keywords:
Huntington's disease, Huntingtin, Chromatin, Epigenetics
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© 2025. Published by The Company of Biologists
2025
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First page of Altered Huntingtin-Chromatin Interactions Predict Transcriptional and Epigenetic Changes in Huntington's Disease Mouse Models

Supplementary information

Table S1.
Significant HTT peak calling results, including proximal gene names, including genotype category labels.

The “MACS Significant HTT Peaks” tab includes the MACS peak calling results - annotated with the most proximal gene and the distance to it. The “Peak.Label” column indicates whether each peak is in the category of “mHTT-specific”, “WT-specific”, or “WT-mHTTshared” - see text for details on these categories.

- xlsx file
Table S2.
HTT Peaks Per Gene.

A per-gene summary of HTT peaks across the categories of “mHTT-specific”, “WT-specific”, or “WT-mHTT-shared.”

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Table S3.
HTT DiffBind.

Differential HTT occupancy in HttQ111/Q111 vs. Htt+/+. Used to generate volcano plot Fig. 2A.

- xlsx file
Table S4.
HTT DiffBind Enrichr Results.

Geneset enrichment results for differential HTT peak occupancy in Figs. 2B, 2C.

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Table S5.
DiffBind Summary ActiveMotif.

Differential occupancy of EZH2, H3K27ac, H3K27me3, H3K4me3, and H3K9me3, peak regions. These results were used to generate Fig. 3A.

- xlsx file
Table S6.
H3K27me3 Enrichment.

Enrichment of H3K27me3 peaks with lower occupancy in HttQ111/+ vs. Htt+/+ striatum (p < 0.005) assessed for enrichment using Enrichr. Tabs correspond to terms for Gene Ontology Biological Process (GOBP), Gene Ontology Molecular Function (GOMF), and ENCODE and ChEA Consensus Transcription Factors (ENCODE-CHEA_tfs). Used to generate Figs. 3B-D.

- xlsx file
Table S7.
HTT Enrichment ActiveMotif Peaks.

Summary of GAT results testing the enrichment of HTT ChIP-seq peaksets amongst EZH2, H3K27ac, H3K27me3, H3K4me3, and H3K9me3, peak regions. These results were used to generate Fig. 3E.

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Table S8.
HTT Peaks, ActiveMotif and RNASeq Integration.

Includes integrated ChIP-seq and RNA-seq data for all intervals containing robust HTT peaks. For each HTT peak (“PeakRegion.ID”), available changes in RNA expression of included genes (“Langfelder et. al. RNA-Seq”) and our other ChIP-seq data (“Re-analysis of ActiveMotif ChIP-Seq”) are shown. These results were used to generate Fig. 5A-B and 6A-C.

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Table S9.
HTT HDSigDB Overlap.

Includes enrichments for HTT Peak sets and the genes included in each HDSigDB gene set. HDSigDB gene set meta information is included on the tab “HDSigDB.Genesets”. These results were used to generate Fig. 5C.

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