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Abstract
Epigenomics offers a genome-wide perspective on how changes in chromatin regulate gene expression and cellular phenotype. This course introduces the underlying biological notions through a hands-on exploration of such data, providing an introduction to (R-based) tools necessary to explore, visualize and interpret it.
Objective
The objective of the course is two-fold: 1) to enable students, if not to be wholly independent with respect to NGS chromatin data analysis, at least to be able to autonomously explore, visualize and interpret such data; 2) to understand and critically appraise, from a genomics perspective and through hands-on data exploration, the key concepts underlying chromatin regulation of transcription and its impact on various biological phenomena.
Content
- Introduction to the Bioconductor ecosystem for genomic data analysis, with a focus on flexible and re-usable tools (e.g. standard data structures and visualization techniques) - How to find and re-use data from the literature - Basic analysis pipelines for ATAC-seq, ChIP-seq, and related assays, with a focus on data manipulation, exploration and visualization, motif analysis, etc. (Single-cell ATAC-seq is presented but not included in the practicals) - Introduction to regulatory genomics, with critical discussions of some of its conceptual issues: types of functional elements, the histone code, sequence recognition and binding specificity, transcriptor factor (TF) activation and binding, DNA accessibility, topological domains and chromatin loops, etc. - Importance of chromatin regulation in differentiation and neurological conditions