ArticleBMC molecular biology2009
Quadruple 9-mer-based protein binding microarray with DsRed fusion protein.
Article in BMC molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice.Molecules and cells · 2024Article
- Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming.Nature communications · 2020Article
- Characterization of the CCAAT-binding transcription factor complex in the plant pathogenic fungus Fusarium graminearum.Scientific reports · 2020Article
- A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice.Molecules and cells · 2018Article
- Article
- Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice.Rice (New York, N.Y.) · 2017Article
- Article
- Expression of StMYB1R-1, a novel potato single MYB-like domain transcription factor, increases drought tolerance.Plant physiology · 2011Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionOur 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.
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