Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.

Immunoprecipitated crosslinked protein-DNA fragments typically range in size from several hundred to several thousand base pairs, with a significant part of chromatin being much longer than the optimal length for next-generation sequencing (NGS) procedures. Because these larger fragments may be non-...

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Autores principales:	Michal Mokry, Pantelis Hatzis, Ewart de Bruijn, Jan Koster, Rogier Versteeg, Jurian Schuijers, Marc van de Wetering, Victor Guryev, Hans Clevers, Edwin Cuppen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/68b3e00bcb334a91b78ef370c1399ac7
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id	oai:doaj.org-article:68b3e00bcb334a91b78ef370c1399ac7
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spelling	oai:doaj.org-article:68b3e00bcb334a91b78ef370c1399ac72021-11-18T07:02:18ZEfficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.1932-620310.1371/journal.pone.0015092https://doaj.org/article/68b3e00bcb334a91b78ef370c1399ac72010-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21152096/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Immunoprecipitated crosslinked protein-DNA fragments typically range in size from several hundred to several thousand base pairs, with a significant part of chromatin being much longer than the optimal length for next-generation sequencing (NGS) procedures. Because these larger fragments may be non-random and represent relevant biology that may otherwise be missed, but also because they represent a significant fraction of the immunoprecipitated material, we designed a double-fragmentation ChIP-seq procedure. After conventional crosslinking and immunoprecipitation, chromatin is de-crosslinked and sheared a second time to concentrate fragments in the optimal size range for NGS. Besides the benefits of increased chromatin yields, the procedure also eliminates a laborious size-selection step. We show that the double-fragmentation ChIP-seq approach allows for the generation of biologically relevant genome-wide protein-DNA binding profiles from sub-nanogram amounts of TCF7L2/TCF4, TBP and H3K4me3 immunoprecipitated material. Although optimized for the AB/SOLiD platform, the same approach may be applied to other platforms.Michal MokryPantelis HatzisEwart de BruijnJan KosterRogier VersteegJurian SchuijersMarc van de WeteringVictor GuryevHans CleversEdwin CuppenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 11, p e15092 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michal Mokry Pantelis Hatzis Ewart de Bruijn Jan Koster Rogier Versteeg Jurian Schuijers Marc van de Wetering Victor Guryev Hans Clevers Edwin Cuppen Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
description	Immunoprecipitated crosslinked protein-DNA fragments typically range in size from several hundred to several thousand base pairs, with a significant part of chromatin being much longer than the optimal length for next-generation sequencing (NGS) procedures. Because these larger fragments may be non-random and represent relevant biology that may otherwise be missed, but also because they represent a significant fraction of the immunoprecipitated material, we designed a double-fragmentation ChIP-seq procedure. After conventional crosslinking and immunoprecipitation, chromatin is de-crosslinked and sheared a second time to concentrate fragments in the optimal size range for NGS. Besides the benefits of increased chromatin yields, the procedure also eliminates a laborious size-selection step. We show that the double-fragmentation ChIP-seq approach allows for the generation of biologically relevant genome-wide protein-DNA binding profiles from sub-nanogram amounts of TCF7L2/TCF4, TBP and H3K4me3 immunoprecipitated material. Although optimized for the AB/SOLiD platform, the same approach may be applied to other platforms.
format	article
author	Michal Mokry Pantelis Hatzis Ewart de Bruijn Jan Koster Rogier Versteeg Jurian Schuijers Marc van de Wetering Victor Guryev Hans Clevers Edwin Cuppen
author_facet	Michal Mokry Pantelis Hatzis Ewart de Bruijn Jan Koster Rogier Versteeg Jurian Schuijers Marc van de Wetering Victor Guryev Hans Clevers Edwin Cuppen
author_sort	Michal Mokry
title	Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
title_short	Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
title_full	Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
title_fullStr	Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
title_full_unstemmed	Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
title_sort	efficient double fragmentation chip-seq provides nucleotide resolution protein-dna binding profiles.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/68b3e00bcb334a91b78ef370c1399ac7
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Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.

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