Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.
Project description:In this study we used DNA affinity purification sequencing (DAP-seq) to identify genome-wide binding of allele-specific RAP2-7 transcription factor variants in five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including low-alkaloid iucundus line (83A:476), high-alkaloid Iucundus line (P27255) and three Bryansk low-alkaloid lines (95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83)).
Project description:To elucidate the molecular landscape of NAC103-mediated transcriptional regulation in Arabidopsis, we combined chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) to capture the comprehensive cistrome of NAC103. In this project, we employed the transgenic plants of 35S:NAC103-GFP as the material for ChIP. For DAP-seq, NAC103 protein tagged with Halo (NAC103-Halo) was expressed using Promega’s wheat germ system. These results indicate that NAC103 can directly target promoter regions of ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1 (ASA1, AT5G05730) and Acetyl-coenzyme A Carboxylase 2 (ACC2, AT1G36180).
Project description:To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.
Project description:To better understand FvSEP3-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to uncover FvSEP3 directly binding sites at the genome level. For DAP-seq analysis, the recombinant FvSEP3 fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.
Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.
Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).
