MersV1, Main, Exploration, bibRecord, 002770

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

Identifieur interne : 002770 ( Main/Exploration ); précédent : 002769; suivant : 002771

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

Auteurs : Min-Jeong Kim [Corée du Sud] ; Tae-Ho Lee [Corée du Sud] ; Yoon-Mok Pahk [Corée du Sud] ; Yul-Ho Kim [Corée du Sud] ; Hyang-Mi Park [Corée du Sud] ; Yang Do Choi [Corée du Sud] ; Baek Hie Nahm [Corée du Sud] ; Yeon-Ki Kim [Corée du Sud]

Source :

BMC Molecular Biology [ 1471-2199 ] ; 2009.

RBID : PMC:2754467

Descripteurs français

KwdFr :
- Analyse par réseau de protéines (), Liaison aux protéines, Motifs d'acides aminés, Oligonucléotides (génétique), Oligonucléotides (métabolisme), Oryza (), Oryza (génétique), Oryza (métabolisme), Protéines luminescentes (génétique), Protéines luminescentes (métabolisme), Protéines végétales (), Protéines végétales (génétique), Protéines végétales (métabolisme), Sites de fixation.
MESH :
- génétique : Oligonucléotides, Oryza, Protéines luminescentes, Protéines végétales.
- métabolisme : Oligonucléotides, Oryza, Protéines luminescentes, Protéines végétales.
- Analyse par réseau de protéines, Liaison aux protéines, Motifs d'acides aminés, Oryza, Protéines végétales, Sites de fixation.

English descriptors

KwdEn :
- Amino Acid Motifs, Binding Sites, Luminescent Proteins (genetics), Luminescent Proteins (metabolism), Oligonucleotides (genetics), Oligonucleotides (metabolism), Oryza (chemistry), Oryza (genetics), Oryza (metabolism), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Protein Array Analysis (methods), Protein Binding.
MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : Luminescent Proteins, Oligonucleotides, Plant Proteins.
- chemical , metabolism : Luminescent Proteins, Oligonucleotides, Plant Proteins.
- chemistry : Oryza.
- genetics : Oryza.
- metabolism : Oryza.
- methods : Protein Array Analysis.
- Amino Acid Motifs, Binding Sites, Protein Binding.

Abstract

Background

The interaction between a transcription factor and DNA motif (cis-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.

Results

We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the cis-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified cis-acting element of the OsNAC6 rice transcription factor.

Conclusion

Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754467

DOI: 10.1186/1471-2199-10-91
PubMed: 19761621
PubMed Central: 2754467

Affiliations:

Le document en format XML

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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The interaction between a transcription factor and DNA motif (<italic>cis</italic>
-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.</p>
</sec>
<sec><title>Results</title>
<p>We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the <italic>cis</italic>
-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified <italic>cis</italic>
-acting element of the OsNAC6 rice transcription factor.</p>
</sec>
<sec><title>Conclusion</title>
<p>Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.</p>
</sec>
</div>
</front>
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<name sortKey="Nahm, Baek Hie" sort="Nahm, Baek Hie" uniqKey="Nahm B" first="Baek Hie" last="Nahm">Baek Hie Nahm</name>
<name sortKey="Nahm, Baek Hie" sort="Nahm, Baek Hie" uniqKey="Nahm B" first="Baek Hie" last="Nahm">Baek Hie Nahm</name>
<name sortKey="Pahk, Yoon Mok" sort="Pahk, Yoon Mok" uniqKey="Pahk Y" first="Yoon-Mok" last="Pahk">Yoon-Mok Pahk</name>
<name sortKey="Pahk, Yoon Mok" sort="Pahk, Yoon Mok" uniqKey="Pahk Y" first="Yoon-Mok" last="Pahk">Yoon-Mok Pahk</name>
<name sortKey="Park, Hyang Mi" sort="Park, Hyang Mi" uniqKey="Park H" first="Hyang-Mi" last="Park">Hyang-Mi Park</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002770 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002770 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     PMC:2754467
   |texte=   Quadruple 9-mer-based protein binding microarray with DsRed fusion protein
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:19761621" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

Source :

Descripteurs français

English descriptors

Abstract

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

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.