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CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast ma...

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Autores principales: Savic, Daniel, Partridge, E. Christopher, Newberry, Kimberly M., Smith, Sophia B., Meadows, Sarah K., Roberts, Brian S., Mackiewicz, Mark, Mendenhall, Eric M., Myers, Richard M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579343/
https://www.ncbi.nlm.nih.gov/pubmed/26355004
http://dx.doi.org/10.1101/gr.193540.115
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author Savic, Daniel
Partridge, E. Christopher
Newberry, Kimberly M.
Smith, Sophia B.
Meadows, Sarah K.
Roberts, Brian S.
Mackiewicz, Mark
Mendenhall, Eric M.
Myers, Richard M.
author_facet Savic, Daniel
Partridge, E. Christopher
Newberry, Kimberly M.
Smith, Sophia B.
Meadows, Sarah K.
Roberts, Brian S.
Mackiewicz, Mark
Mendenhall, Eric M.
Myers, Richard M.
author_sort Savic, Daniel
collection PubMed
description Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable data sets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIP-quality antibodies are not available.
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spelling pubmed-45793432016-04-01 CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins Savic, Daniel Partridge, E. Christopher Newberry, Kimberly M. Smith, Sophia B. Meadows, Sarah K. Roberts, Brian S. Mackiewicz, Mark Mendenhall, Eric M. Myers, Richard M. Genome Res Method Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable data sets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIP-quality antibodies are not available. Cold Spring Harbor Laboratory Press 2015-10 /pmc/articles/PMC4579343/ /pubmed/26355004 http://dx.doi.org/10.1101/gr.193540.115 Text en © 2015 Savic et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Method
Savic, Daniel
Partridge, E. Christopher
Newberry, Kimberly M.
Smith, Sophia B.
Meadows, Sarah K.
Roberts, Brian S.
Mackiewicz, Mark
Mendenhall, Eric M.
Myers, Richard M.
CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title_full CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title_fullStr CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title_full_unstemmed CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title_short CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
title_sort cetch-seq: crispr epitope tagging chip-seq of dna-binding proteins
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579343/
https://www.ncbi.nlm.nih.gov/pubmed/26355004
http://dx.doi.org/10.1101/gr.193540.115
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