Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

Abstract

The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is encoded in the cis-regulatory DNA sequence has, however, remained unclear. We computationally dissect context-specific TF binding sites in Drosophila, Caenorhabditis elegans, mouse, and human and find distinct combinations of sequence motifs for partner factors, which are predictive and reveal specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself depend on Vielfaltig motifs, suggesting that Vielfaltig is more generally important for early transcription. Our finding that the motif content can predict contextspecific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes (cis-regulatory signatures), which appear to be conserved during evolution. Taken together, this study establishes a novel approach to derive predictive cis-regulatory motif requirements for individual TF binding sites and enhancers. Importantly, the method is generally applicable across different cell types and organisms to elucidate cis-regulatory sequence determinants and the corresponding trans-acting factors from the increasing number of tissue-and cell-type-specific TF binding studies.

Atoh1 in sensory hair cell development: constraints and cofactors

“…These 'combinatorial codes' of transcription factors help to explain context-dependence of transcription factor binding in many different cell types (40,41). Therefore, the cell-type-specific cooperation between transcription factors at enhancer regions could explain, at least in part, why Atoh1 exhibits a distinct DNA-binding profile in neurons compared with intestinal cells.…”

A conserved role for Snail as a potentiator of active transcription

“…5C) based solely on differences in their motif content using the 15 most discriminative TF motifs ( Fig. 5D; Supplemental Table S9; see Yanez-Cuna et al 2012). When we repeated the predictions after randomizing the class membership for each binding site, the predictions dropped to 56.8% (AUC: 0.56).…”

“…To determine which TF motifs were the most important for the correct prediction of each enhancer, we performed in silico mutations (Yanez-Cuna et al 2012). The confidence of the prediction was scored by bootstrapping the data selected in model training for each individual binding site in wild-type and mutant CRMs after all instances of a given motif were computationally ablated (Supplemental Material).…”

“…To determine whether differential motif content is sufficient to predict the regulatory output of Snail, we used an established machine learning method (a support vector machine [SVM]) for predictive discriminatory sequence analysis (Yanez-Cuna et al 2012) based on 429 known or predicted TF PWMs ( Fig. 5B; Stark et al 2007).…”

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

“…Broadly expressed transcription factors can regulate multiple, distinct developmental processes, but whether they do so through context-specific DNA-binding events, or through activities subsequent to DNA binding, remains an open question. Based on the relatively limited number of studies that have elucidated transcription factor binding over multiple stages of development, it has been suggested that functional binding events are temporally dynamic (Jakobsen et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Spitz and Furlong 2012;Yanez-Cuna et al 2012;Slattery et al 2013Slattery et al , 2014. These changes in binding site occupancy by sequence-specific transcription factors are regulated largely through alterations in chromatin structure that modulate the accessible regions of the genome Li et al 2011).…”