HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.
Author summary The different anatomical features that develop along the animal body axis are determined by HOX transcription factors. Each member of the HOX family appears in a well-defined territory of the developing embryo, and instruct a specific gene expression program. In stark contrast to their specificity in vivo, which is central to developmental programs, HOX transcription factors display highly similar sequence recognition properties in vitro. To understand how HOX transcription factors control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. We find that HOXA2 and HOXA3 occupy a large set of high-confidence, non-overlapping genomic regions, that are also bound by three aminoacid loop extension (TALE) transcription factors. We identify three main determinants of HOX paralog-selective binding: recognition of unique variants of the HOX-PBX motif, differential affinity at shared HOX-PBX motifs and, additionally, contribution of tissue-specific transcription factors. These mechanisms result in high-confidence, cooperative HOX-TALE binding at different genomic locations, which bear the mark of active enhancers. We propose that HOX paralogs operate, alone and in concert with tissue-specific transcription factors, to switch on TALE function at selected enhancers.