DNA-dependent formation of transcription factor pairs alters their binding specificity

Abstract

Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.

Relationship between histone modifications and transcription factor binding is protein family specific

“…Hox proteins from the HD family, for instance, bind in close proximity to their cofactors from the same protein family to unleash their DNA binding specificities Abe et al 2015). It is possible that HM patterns explain the observation that cooperativity can occur promiscuously between TFs from diverse structural families (Jolma et al 2015). …”

Mapping genome-wide transcription-factor binding sites using DAP-seq

“…Alternative methods are needed for capturing genome-wide binding data for many organisms. In vitro TFBS identification methods such as Protein Binding Microarrays (PBM) and High Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX) have achieved the highest throughput for deducing TF binding specificities in vitro [9][10][11] , but these methods use short synthetic oligonucleotides lacking secondary DNA modifications and genomic context, both important determinants of selective TF binding in vivo [12][13][14][15][16] . The DAP-seq technique 15 described here employs an in vitro-expressed affinitytagged TF in combination with high-throughput sequencing of a genomic DNA library, allowing for the generation of genome-wide binding site maps reflective of both local sequence context and DNA methylation status.…”

A unique stylopod patterning mechanism by Shox2 controlled osteogenesis

“…However, because of the closely located binding centers of Shox2 and Pbx genome wide (Fig. S7), and the lack of a Pbx de novo motif -a phenomenon that is typical for cooperative binding of transcription factors (Jolma et al, 2015) -Shox2-TALE co-occupancy appears to be competitive. Moreover, since Hox9/Hox10 proteins were thought to interact with Meis/Pbx to pattern the proximal limb (Capellini et al, 2011;Zakany and Duboule, 2007), the fact that Shox2 interacted directly with Hoxa9 in co-IP assay (Fig.…”