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(A – B ) IGV images of ChIP-seq data revealing high infection-dependent WRKY33 binding at the promoters of AMT1 (A ) and CYP71A12 (B ).
In addition, we observed low levels of NdgR binding at the promoters of metH (SCO1657) and leuA (SCO5559) relative to the other binding peaks.
Notwithstanding its direct binding at the promoters of genes in the BCAA biosynthetic pathway, NdgR was not essential for BCAA biosynthesis under the growth conditions used here.
(B, C ) Integrative Genomics Viewer (IGV) images of ChIP-seq data revealing high infection-dependent WRKY33 binding at the promoters of Arabidopsis WRKY33 (B ) and WRKY41 (C ).
Twenty-four hours after KSHV reactivation, we found a significant increase in SUMO-2/3 binding at the promoters of genes with high expression (~15%) and medium expression (~10%).
Following the reviewers' suggestion, we performed ChIP analyses of H3 and H4 acetylation and BRD4 binding at the promoters of MYC, a transiently repressed gene, and HEXIM1, an example of a "permanently" repressed gene (see Figure 3 figure supplement 2), at early time points (0, 1 and 2 hr) of the i-CDK9 treatment.
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Over multiple iterations of clustering, we identified 2404 genes that have strong H3K27me3 binding at the promoter region of WT CD71+Ter119+ erythroblasts, which is virtually eliminated in CD71+Ter119+ erythroblasts lacking Mtf2 (Supplementary Table S1).
This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.
Physical binding at the promoter is a crucial evidence for a transcription factor to regulate transcription of a gene directly in yeast.
In order to investigate the effect of Compound A on ERRα binding at the promoter region of ERRα target genes (ESRRA, ACADM, and TFF1), chromatin Immunoprecipitation (ChIP) assays were performed after MCF-7 cells were treated with DMSO, 3 pM 17β-estradiol (E2), or 5 uM Compound A for 24 and 48 hours.
Thus, increasing the RNA polymerase (RNAP) binding at the promoter site would effectively activate transcription of the target genes.
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