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

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 procedu...

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Detalles Bibliográficos
Autores principales: Kong, Nikki Ruoxi, Chai, Li, Tenen, Daniel Geoffrey, Bassal, Mahmoud Adel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8379522/
https://www.ncbi.nlm.nih.gov/pubmed/34458869
http://dx.doi.org/10.1016/j.xpro.2021.100750
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author Kong, Nikki Ruoxi
Chai, Li
Tenen, Daniel Geoffrey
Bassal, Mahmoud Adel
author_facet Kong, Nikki Ruoxi
Chai, Li
Tenen, Daniel Geoffrey
Bassal, Mahmoud Adel
author_sort Kong, Nikki Ruoxi
collection PubMed
description 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).
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spelling pubmed-83795222021-08-27 A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines Kong, Nikki Ruoxi Chai, Li Tenen, Daniel Geoffrey Bassal, Mahmoud Adel STAR Protoc Protocol 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). Elsevier 2021-08-17 /pmc/articles/PMC8379522/ /pubmed/34458869 http://dx.doi.org/10.1016/j.xpro.2021.100750 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Kong, Nikki Ruoxi
Chai, Li
Tenen, Daniel Geoffrey
Bassal, Mahmoud Adel
A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title_full A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title_fullStr A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title_full_unstemmed A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title_short A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
title_sort modified cut&run protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8379522/
https://www.ncbi.nlm.nih.gov/pubmed/34458869
http://dx.doi.org/10.1016/j.xpro.2021.100750
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