A chromatin-mediated mechanism for specification of conditional transcription factor targets

Abstract

Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that Rap1, a master regulator of yeast metabolism, binds to an expanded target set upon nutrient depletion despite decreasing protein levels and no evidence of posttranslational modification. Computational analysis predicted that proteins capable of recruiting the chromatin regulator Tup1 acted to restrict the binding distribution of Rap1 in the presence of nutrients. Deletions of TUP1, genes that encode recruiters of Tup1, or chromatin regulators recruited by Tup1, cause Rap1 to bind specifically and inappropriately to low-nutrient targets. These data, combined with whole-genome measurements of nucleosome occupancy and Tup1 distribution, provide evidence for a mechanism of dynamic target specification that coordinates the genome-wide distribution of intermediate-affinity DNA sequence motifs with chromatin-mediated regulation of accessibility to those sites. Main TextTo survive in fluctuating environments, organisms must respond to changes in their surroundings. One of the primary means of response at the cellular level is the adjustment of levels of gene transcription 1 . In some cases, new transcriptional programs are established by the binding of regulatory proteins to new gene targets under a given environmental condition 2 . These regulatory factors then act to either activate or repress transcription. Four straightforward mechanisms for the regulation of transcription-factor targeting have been demonstrated. These include altering the regulatory factor's concentration in the nucleus 3 , altering binding affinity by post-translational modification 4 or through an allosteric cofactor 5 , and altering binding properties by expression of a protein cofactor 6 . Here, we present experiments that provide evidence for a new mechanism of dynamic transcription factor target specification. In the proposed mechanism, the genome-wide distribution of DNA sequence motifs for which a factor has intermediate affinity is carefully coordinated with chromatinmediated regulation of accessibility to those sites. In this way, rather than through use of a specific cofactor or post-translational modification, the genome itself is remodeled to change the targeting and biological outcome of an unaltered transcription factor. Rap1 (Repressor-Activator Protein 1) directs a transcriptional program that is central to yeast metabolism, activating the transcription of genes encoding the ribosomal protein subunits and glycolytic enzymes [7][8][9] . Nearly 40% of the mRNA initiation events in mitotically growing yeast are activated by Rap1, yet Rap1 is also required for the repression of these same genes in

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

“…1). Such differential binding has also been reported for several other TFs between different cell types in human and mouse Palii et al 2011), different developmental stages in C. elegans (Zhong et al 2010), or different growth conditions in yeast (Zeitlinger et al 2003;Buck and Lieb 2006).…”

“…Context-specific binding appears to be a general property of TFs and has been observed for several TFs in different species (Zeitlinger et al 2003;Buck and Lieb 2006;Sandmann et al 2007;Zinzen et al 2009;Heinz et al 2010;Lin et al 2010;Verzi et al 2010;Zhong et al 2010;Palii et al 2011). (See Supplemental Tables S1 and S5 and the Supplemental Discussion for examples in C. elegans, mouse, and human, for which time-, cell-type-, or tissue-specific ChIP data sets were available.…”

“…Differential motif enrichment is predictive of context-specific binding Context-specific binding might result from other TFs facilitating or inhibiting binding (e.g., Zeitlinger et al 2003;Harbison et al 2004;Buck and Lieb 2006;Sandmann et al 2007;He et al 2011). We reasoned that the motifs for such putative (activating or inhibiting) partner factors should be differentially distributed between the binding sites in different contexts.…”

“…Context-specific binding might result from other TFs facilitating or inhibiting binding either directly or via changes to the chromatin structure and DNA accessibility (e.g., Zeitlinger et al 2003;Harbison et al 2004;Buck and Lieb 2006;Sandmann et al 2007;Heinz et al 2010;He et al 2011;John et al 2011;Kaplan et al 2011;Li et al 2011). Such a combinatorial model would be an elegant way to realize many gene regulatory states with a limited number of TFs and to achieve TF binding specificity within the context of a large genome.…”

“…For example, during Drosophila embryogenesis, the mesodermal TF Twist binds to only about a thousand of the roughly 1 million Twist motifs in the genome (Sandmann et al 2007;Zeitlinger et al 2007;Zinzen et al 2009). Second, in vivo TF binding appears to be highly contextspecific, and the same TF typically binds to different genomic binding sites in different conditions (e.g., Zeitlinger et al 2003;Buck and Lieb 2006;Sandmann et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Palii et al 2011). Twist-binding sites, for example, change dynamically between different time points during embryonic mesoderm development (2-8 h post-fertilization, hpf), which cannot be attributed to changes of Twist activity (e.g., by alternative splicing or post-translational modification) or concentration (Sandmann et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010; see also Fig.…”