1. Introduction to Chromatin Biology & ChIP-Seq

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the gold standard for surveying genome-wide protein-DNA interactions, transcription factor binding sites, and histone modifications. Within eukaryotic nuclei, genomic DNA is wrapped around octamers of core histone proteins ($H2A$, $H2B$, $H3$, $H4$) to form nucleosomes. Covalent post-translational modifications (PTMs) occurring on histone amino-terminal tails dynamically dictate chromatin architecture, determining whether specific genomic loci are transcriptionally permissive (euchromatin) or silenced (heterochromatin).

2. Case Study: Chromatin Dysregulation in Huntington's Disease (HD)

Huntington's Disease is an autosomal-dominant, fatal neurodegenerative disorder caused by an expanded $CAG$ trinucleotide repeat in the huntingtin (HTT) gene, translating into an expanded polyglutamine tract. While mutant huntingtin protein ($mHTT$) forms toxic cytoplasmic and nuclear aggregates, an early pathological hallmark in the human striatum and cortex is massive, coordinated transcriptional dysregulation.

Biochemically, mutant huntingtin directly binds and sequesters essential histone acetyltransferases (such as CBP/p300 and PCAF) while disrupting histone methyltransferase complexes (including MLL/SET domain complexes) and derepressing the transcriptional silencer REST/NRSF. This leads to profound loss of the permissive mark H3K4me3 at critical neuroprotective genes, such as BDNF (Brain-Derived Neurotrophic Factor) and striatal medium spiny neuron markers such as PPP1R1B / DARPP-32.

3. The 4-Phase Curriculum Architecture

Throughout this hands-on course, you will analyze real post-mortem prefrontal cortex and striatal tissue datasets from Huntington's Disease patients and matched neurotypical controls (based on NCBI GEO accessions such as GSE68952 / GSE108503). You will execute the complete production pipeline:

• Phase 1 (Modules 1–2): Experimental design, input controls, SRA data retrieval, and raw FASTQ quality control (FastQC & fastp).
• Phase 2 (Modules 3–4): Splice-unaware alignment with Bowtie2, SAMtools MAPQ filtering, Sambamba duplicate marking, ENCODE blacklist masking, and cross-correlation QC (phantompeakqualtools).
• Phase 3 (Modules 5–6): Statistical peak calling with MACS3 (narrowPeak format) and quantitative differential binding analysis with DiffBind + DESeq2.
• Phase 4 (Modules 7–10): Peak annotation with ChIPseeker, pathway enrichment with clusterProfiler, transcription factor motif discovery with HOMER, deepTools TSS heatmaps, and IGV desktop verification.