Location of SVP binding sites relative to nearby genes and analysis of SVP binding sites at the 3' UTR regions of target genes. (a) Promoter 3K refers to the 3,000 bp upstream of the transcription start site (TSS); transcribed refers to the transcript from the 5' UTR to 3' UTR. Promoter 3K and Transcribed refers to 3,000 bp upstream to the TSS until the 3'UTR region. Downstream 1K starts from the transcription termination site until 1,000 bp downstream. Intergenic is none of the above regions; (b) diagram representing distribution of SVP binding (peaks) sites within the transcribed regions with respect to transcription termination sites (0 on the × axis); (c) binding profiles in inflorescence tissue for selected target genes which are bound by SVP in the transcribed regions: AGL24, SEEDSTICK (STK), APETALA 3 (AP3), and FLC. TAIR annotation corresponds to TAIR8. Grey boxes represent the region validated by ChIP-PCR shown in (c); (d) ChIP-PCR validation for selected SVP target genes. ChIP assays were done using GFP antibodies and SVP::SVP-GFP svp-41 plants and compared with wild-type control plants. Error bars represent standard deviations of normalized data (SD).
Gregis et al. Genome Biology 2013 14:R56 doi:10.1186/gb-2013-14-6-r56