PoplarV1, Main, Exploration, bibRecord, 002390

A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue.

Identifieur interne : 002390 ( Main/Exploration ); précédent : 002389; suivant : 002391

A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue.

Auteurs : Wei Li [États-Unis] ; Ying-Chung Lin [États-Unis] ; Quanzi Li [République populaire de Chine] ; Rui Shi [États-Unis] ; Chien-Yuan Lin [États-Unis] ; Hao Chen [États-Unis] ; Ling Chuang [États-Unis] ; Guan-Zheng Qu [République populaire de Chine] ; Ronald R. Sederoff [États-Unis] ; Vincent L. Chiang [États-Unis]

Source :

Nature protocols [ 1750-2799 ] ; 2014.

RBID : pubmed:25144269

Descripteurs français

KwdFr :
- ADN (métabolisme), Analyse de séquence d'ADN (MeSH), Bois (cytologie), Données de séquences moléculaires (MeSH), Facteurs de transcription (métabolisme), Fragmentation de l'ADN (MeSH), Histone (métabolisme), Immunoprécipitation (MeSH), Immunoprécipitation de la chromatine (méthodes), Populus (cytologie), Populus (métabolisme), Séquence nucléotidique (MeSH), Xylème (génétique), Xylème (métabolisme).
MESH :
- cytologie : Bois, Populus.
- génétique : Xylème.
- métabolisme : ADN, Facteurs de transcription, Histone, Populus, Xylème.
- méthodes : Immunoprécipitation de la chromatine.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Fragmentation de l'ADN, Immunoprécipitation, Séquence nucléotidique.

English descriptors

KwdEn :
- Base Sequence (MeSH), Chromatin Immunoprecipitation (methods), DNA (metabolism), DNA Fragmentation (MeSH), Histones (metabolism), Immunoprecipitation (MeSH), Molecular Sequence Data (MeSH), Populus (cytology), Populus (metabolism), Sequence Analysis, DNA (MeSH), Transcription Factors (metabolism), Wood (cytology), Xylem (genetics), Xylem (metabolism).
MESH :
- chemical , metabolism : DNA, Histones, Transcription Factors.
- cytology : Populus, Wood.
- genetics : Xylem.
- metabolism : Populus, Xylem.
- methods : Chromatin Immunoprecipitation.
- Base Sequence, DNA Fragmentation, Immunoprecipitation, Molecular Sequence Data, Sequence Analysis, DNA.

Abstract

Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.

DOI: 10.1038/nprot.2014.146
PubMed: 25144269

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<term>Histones (metabolism)</term>
<term>Immunoprecipitation (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Populus (cytology)</term>
<term>Populus (metabolism)</term>
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<term>Fragmentation de l'ADN (MeSH)</term>
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<term>Immunoprécipitation (MeSH)</term>
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<term>Populus (métabolisme)</term>
<term>Séquence nucléotidique (MeSH)</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term>
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<term>Données de séquences moléculaires</term>
<term>Fragmentation de l'ADN</term>
<term>Immunoprécipitation</term>
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<front><div type="abstract" xml:lang="en">Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.</div>
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<Abstract><AbstractText>Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.</AbstractText>
</Abstract>
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<AffiliationInfo><Affiliation>1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Forest Biotechnology Group, Department of Forestry &Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA.</Affiliation>
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A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue.

A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue.

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