This is in line with the ER binding data that is not centred over the CTCF binding summit.
This idea is consistent with recent PHF8 genome-wide binding data that showed it locating to the promoter regions of zinc finger-encoding genes [ 49].
To facilitate the interpretation of in vivo binding data that are shown as fold-enrichment of a bound DNA fragment, the corresponding data obtained with upstream and downstream fragments are also displayed; complementary expression data are available via the microarray data section in the report page.
We infer from the binding data that a relatively high affinity capsid binding site is located in the middle of the rod-shaped Soc, with the N and C termini facing the 2- and 3-fold symmetry axes of the capsid, respectively.
When comparing the list of genes differentially expressed in NANOGhigh and NANOGlow cells with the published promoter binding data, we found that 14 out of 32 gene promoters (44%) were bound by NANOG, indicating that they are direct transcriptional targets of NANOG.
On the basis of our ANS binding data, we infer that the 27 kDa 7B2 protein either contains a larger amount of tertiary structure than the 21 kDa form or has a higher degree of hydrophobic packing accessible to ANS, due to oligomerization.
However, as described above, when we analyzed the binding data for Puf3p, we found that binding motif matches in the 5′ UTR were also predictive of transcript binding.
Given the sensitivity and unambiguous binding data, artifacts that plague nearly every other binding assay can be avoided.
As more gene expression data and TF binding data become available, we believe that our method will be useful for reconstructing large-scale transcriptional regulatory networks.
As more gene expression and transcription factor binding data become available, we believe that our method is useful for reconstructing large-scale transcriptional regulatory networks in other species as well.
