A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines

Nikki Ruoxi Kong; Li Chai; Daniel Geoffrey Tenen; Mahmoud Adel Bassal

doi:10.1016/j.xpro.2021.100750

A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines

STAR Protoc. 2021 Aug 17;2(3):100750. doi: 10.1016/j.xpro.2021.100750. eCollection 2021 Sep 17.

Authors

Nikki Ruoxi Kong^{1

2}, Li Chai^{1

2}, Daniel Geoffrey Tenen^{2

3}, Mahmoud Adel Bassal^{2

3}

Affiliations

¹ Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
² Harvard Stem Cell Institute, Boston, MA 02115, USA.
³ Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.

Abstract

CUT&RUN is a recently developed in situ chromatin profiling technique that enables high-resolution chromatin mapping and probing. Herein, we describe our adapted CUT&RUN protocol for transcription factors (TFs). Our protocol outlines all necessary steps for TF profiling including the procedure to obtain proteinA-Mnase, while also outlining the bioinformatic pipeline steps required to process, analyze, and identify novel binding sites and sequences. Due to the small number of cells required, this method will allow the elucidation of cell context-dependent functions of many TFs. For details on the use and execution of this protocol, please refer to Kong et al. (2021).

Keywords: Antibody; Bioinformatics; Cell Biology; Cell separation/fractionation; Genomics; In Situ Hybridization; Molecular Biology; Sequence analysis; Sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Cell Line
Computational Biology / methods*
Humans
Molecular Biology / methods*
Transcription Factors / genetics
Transcription Factors / metabolism*

Substances

Transcription Factors