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To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer.
We explored the reasons for this by mutagenizing putative binding sites in three cis-regulatory modules.
A recent study uses data on binding sites in three yeast species and deduces the rates of sequence evolution [ 42].
CpG coverage distribution within regions [-50 bp, +50 bp] of the center of CTCF-A, CTCF-B and CTCF-C binding sites in three cell lines (GM12878, K562 and HeLaS3).
DNA methylation distribution within regions [-50 bp, +50 bp] of the center of CTCF-A, CTCF-B and CTCF-C binding sites in three cell lines (GM12878, K562 and HeLaS3).
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The presence of at least two functional binding sites in one single trimerbody molecule was further demonstrated in bispecific trimerbodies.
The strategy used here could also be applied to the independent modification of binding sites in single chain avidin (scAvd), which has four binding sites in one polypeptide chain [18].
In addition to E2F family members that warrant investigation (above), we have identified c/EBPβ, FOXC1, FOXJ2, GATA-3, POU2F1/AP-2γ, RARA, TFAP2C, and TFE3 as estrogen-responsive transcription factors with predicted binding sites in one or both promoter regions of the PCNA gene.
To address this question, we assessed statistically significant functions of genes within flanking regions of STAT binding sites in six different cell types using the GREAT program [ 28].
The comparative content analysis of DtxR binding sites in four corynebacterial genome sequences provided further insights into the topology of the DtxR regulon of C. glutamicum.
Having demonstrated the functional significance of Slou-preferred binding sites in two FC enhancers, we next asked whether FCI-HD-preferred binding sequences are more generally involved in the regulation of FC gene expression.
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