Where do proteins bind in the genome?

Jay Hesselberth

RNA Bioscience Initiative | CU Anschutz

2024-10-21

What to map and how to map it?

Targets

Transcription factors
Histone modifications
Chromatin remodelers
RNA polymerases
Other factors that bind chromatin

Methods

ChIP-seq
MNase-ChIP-seq
CUT&RUN
CUT&TAG

{fig-align=“center”}

Comparison of factor-centric methods

Method	Resolution	Sequencing cost
ChIP-seq	Low	High
MNase-ChIP-seq	High	High
CUT&RUN	High	Low

Workflow

FASTQ files

Adapter trimming
Aligning to the genome

Bed files

Generate read density genome-wide

Read density (wig/bedgraph)

Call peaks
Meta analysis
Identify motifs
Compare perturbations to control, compare to other datasets

Example data: CTCF CUT&RUN in K562 cells

Example data: CTCF CUT&RUN in K562 cells

(from Skene and Henikoff, eLIFE 2017)