1. Regulatory Factor & Motif Discovery with HOMER

Histone modification changes are often driven by upstream transcription factor binding alterations or recruitment of chromatin remodelers. By scanning peak summits for over-represented sequence motifs, we identify the exact transcription factor families whose binding sites are disrupted in Huntington's Disease.

2. Running HOMER findMotifsGenome.pl

# Convert differential peaks to HOMER BED format (chr, start, end, name, score, strand)
awk '{print $1"\t"$2"\t"$3"\tPeak_"NR"\t"$5"\t+"}' \
    05_diffbind/hd_lost_peaks.bed > 05_diffbind/hd_lost_peaks_homer.bed

# Execute HOMER motif discovery (+/- 200 bp around peak center)
findMotifsGenome.pl \
    05_diffbind/hd_lost_peaks_homer.bed \
    hg38 \
    05_diffbind/homer_motifs/ \
    -size 200 \
    -mask \
    -p 8

3. Key Transcription Factor Hits in Huntington's Disease

HOMER compares peak sequences against randomly generated background genomic intervals matched for GC content. In our Huntington's Disease analysis, top enriched motifs include:

• SP1 (Specificity Protein 1): Essential GC-box transcription factor known to interact directly with mutant huntingtin; sequestration by $mHTT$ leads to promoter inactivation.
• CREB / ATF: cAMP response element-binding protein, critical for neuroprotection and BDNF transcription.
• REST/NRSF: RE1-Silencing Transcription factor; in healthy cells, wild-type huntingtin sequesters REST in the cytoplasm. In HD, mutant huntingtin allows REST to translocate into the nucleus and repress neuronal genes.