Our study does reveal differences with the canonical TRE site identified by Chatonnet and coworkers, who observed a DR-4 like consensus in neural cells rather than the half-site seen here. We do not understand whether this difference is related to technical aspects of our study versus that of Chatennet, including TR expression levels. This issue will also require further investigation. Our findings also reveal unexpected features of TR binding site architecture. T3-induced genes are often associated with clusters of TRb peaks rather than single elements, and there is enrichment of TRb binding both 59 and 39 of transcribed genes and binding sites can be seen within untranscribed regions and within introns. It is not clear whether TRs play distinct roles in gene expression when bound to different locations with TH-302 respect to the transcription unit; this issue will require further investigation. It is also intriguing that computerized analysis of consensus TREs throughout the genome indicates that they are not obviously over-represented near TR target genes, implying that actual TRb binding events are dependent on other factors, possibly local states of chromatin modification or binding events of partner TFs. It will be important to understand mechanisms that underlie TRb binding site selection within the milieu of living cells. A large proportion of TRb peaks exhibit some apparent T3dependency, but we do not believe that this reflects large scale redistribution of TRs in response to hormone. Overall genomic localization of TRs is similar in the absence and presence of T3 and reanalysis of data with altered stringency of peak calling did not change our conclusion that overall TR distribution does not change after hormone treatment. Close investigation of TRb peaks near target genes revealed relatively modest alterations in TRb peak position and footprint size rather than large scale appearance or disappearance of TRs from the vicinity of target genes. We found some examples in which apparent changes in footprint size could not be verified with standard ChIP. More commonly, however, we were able to verify at least some degree of hormone-dependency of Tofacitinib TRb binding at selected peaks with conventional ChIP. Thus, we favor the idea that there are modest redistributions in TRb binding after hormone treatment and think that this effect accounts for the large apparent change in TRb peak distribution after hormone treatment. Functional significance of verifiable hormone-dependent changes, if any, remains unclear. T3 may promote relocalization of TRb from inactive DNA pools near a negatively regulated target gene to nearby functional regulatory elements. Our observations suggest, however, that T3-dependent changes in TRb footprint and peak position are complex and gene-specific with no obvious pattern. We recently showed that hormone-dependent TRb binding to a TRE within the glucose-6-phosphatase promoter requires TRb interactions with a gene specific cofactor, the NAD+-dependent deacetylase Sirtuin 1. Clearly, more investigation will be needed to understand the potential importance of this unexpected phenomenon in the context of T3dependent TRb binding. Finally, our results allow us to define possibilities for TR crosstalk with other TFs.