Preparation for the DNA Block

Chromatin accessibility

Important

You will need to review this material before class 17.

Papers we will discuss in the block

We’ll use data from the following studies in chromatin accessibility section.

Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res. 2015 PMID: 26314830; PMCID: PMC4617971 [Link]

Zentner GE, Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013 PMID: 24144978; PMCID: PMC3889552. [Link]

New software we will use in the block

GViz enables visualization of genomic signals in a “track” format. Review the GViz vignette, especially the “Basic Features” section, which provides an overview.

valr is a tool set for genome interval manipulation with R. Read over the “Getting Started” to get a sense of the tools and the types of analysis they enable.

ComplexHeatmap provides a flexible framework for generating heatmaps. Look over the “A Single Heatmap” section (section 2).