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Fig. 4 | Molecular Horticulture

Fig. 4

From: Genome-wide binding analysis of the tomato transcription factor SlDof1 reveals its regulatory impacts on fruit ripening

Fig. 4

Chromatin immunoprecipitation sequencing reveals SlDof1 binding sites in tomato fruit. (A) Western blot analysis of the affinity-purified SlDof1 polyclonal antibody used for the chromatin immunoprecipitation assay. Nuclear proteins from the wild-type fruit at 38 days post-anthesis were hybridized with the purified SlDof1 antibody or preimmune serum. (B) Venn diagram depicting the numbers of SlDof1 binding peaks in three biological replicates of chromatin immunoprecipitation sequencing (ChIP-seq). Peaks were obtained by the MACS program with a P-value cut-off of 1E-5. (C) Genome-scale view of SlDof1 binding sites across the 12 chromosomes of tomato. The SlDof1 target genes are depicted as red bars, whereas normally expressed genes are depicted as green bars. (D) Distribution of SlDof1 binding peaks across genomic features. Peaks found within 2 kb upstream of a transcription start site and downstream of a translation termination site were categorized as upstream and downstream sites, respectively. Peaks that were found further upstream or downstream were categorized as intergenic sites. (E) Distribution of SlDof1 binding peaks relative to the genic region. SlDof1 binding sites are highly enriched in the region proximal to the transcriptional start site. (F) Binding motifs identified in the SlDof1 binding peaks. The top three motifs identified using the DREME software are shown

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