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

Abstract

19Gene expression programs determine cell fate in embryonic development and their 20 dysregulation results in disease. Transcription factors (TFs) control gene expression by 21 binding to enhancers, but how TFs select and activate their target enhancers is still unclear. 22HOX TFs share conserved homeodomains with highly similar sequence recognition 23properties, yet they impart the identity of different animal body parts. To understand how 24 HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and 25 HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with 26 TALE TFs and selectively target different subsets of a broad TALE chromatin platform. 27Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high 28 confidence, tissue-specific binding events, which bear the mark of active enhancers. We 29 propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate 30 tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected 31 enhancers. 32 33 Introduction 34 Gene expression programs instruct and maintain cell fate in embryonic development and 35 adult tissue homeostasis. Transcription factors (TFs) control gene expression by binding to 36 enhancers (Reiter et al., 2017; Spitz and Furlong, 2012). However, we still have no clear 37 idea of how TFs select their precise sets of target enhancers. While TFs contain DNA 38 binding domains which recognize DNA in a sequence-specific manner, these interactions 39 are typically insufficient to direct a TF to its functional targets. 40Transcriptional regulation is mediated by TFs working together, rather than in isolation. The 41 widespread occurrence of collaborative TF binding is imposed by chromatin. A single TF 42 cannot easily compete with nucleosomes to access DNA, but multiple TFs that recognize 43 closely spaced binding sites can effectively displace nucleosomes and indirectly facilitate 44 each other's binding (Mirny, 2010; Moyle-Heyrman et al., 2011). Such indirect cooperativity 45 can also result in TFs recognizing low affinity sites, i.e. sites that deviate from their optimal 46 3 consensus in vitro (Farley et al., 2015). Recent observations indicate that TF cooperativity 47 does not end at binding enhancers: clusters of enhancer-bound TFs concentrate co-48 activators and other nuclear factors via dynamic fuzzy interactions, driven by their 49 intrinsically disordered regions (IDRs). IDRs function in molecular recognition and mediate 50 the interaction with a diversity of regulatory proteins (Cumberworth et al., 2013; Staby et al., 51 2017) to promote the liquid-liquid phase transition associated with gene activation (Boija et 52 al., 2018). Thus, the formation, on DNA segments, of regulatory complexes made of different 53 combinations of factors, is key to activation of gene expression. These distinct combinations 54 of TFs produce virtually inexhaustible flavours of gene expression and cell fate (Spitz and 55 Furlong, 2012).56...