Preparation for factor-centric chromatin analysis
You will need to review this material before class 20.
Experimental methods
Skene PJ, Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife. 2017 PMID: 28079019; PMCID: PMC5310842. [Link]
Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019 PMID: 31036827; PMCID: PMC6488672. [Link]
Software tools
MACS is the gold-standard in peak calling. It models read coverage as a Poisson process, enabling identification of regions of higher than expected coverage (i.e., peaks) to be identified using a single parmaeter (lambda) that captures the mean and variance of read coverage. Read over the paper to get a sense of how it works.
We’ll use the motifRG R library, which implements a discriminative (i.e., foreground / background) approach for motif discovery and answer the question, “Which sequences drive factor association to DNA?”.