Mechanistic analysis of enhancer sequences in the estrogen receptor transcriptional program.

Estrogen Receptor α (ERα) is a major lineage determining transcription factor (TF) in mammary gland development. Dysregulation of ERα-mediated transcriptional program results in cancer. Transcriptomic and epigenomic profiling of breast cancer cell lines has revealed large numbers of enhancers involved in this regulatory program, but how these enhancers encode function in their sequence remains poorly understood. A subset of ERα-bound enhancers are transcribed into short bidirectional RNA (enhancer RNA or eRNA), and this property is believed to be a reliable marker of active enhancers. We therefore analyze thousands of ERα-bound enhancers and build quantitative, mechanism-aware models to discriminate eRNAs from non-transcribing enhancers based on their sequence. Our thermodynamics-based models provide insights into the roles of specific TFs in ERα-mediated transcriptional program, many of which are supported by the literature. We use in silico perturbations to predict TF-enhancer regulatory relationships and integrate these findings with experimentally determined enhancer-promoter interactions to construct a gene regulatory network. We also demonstrate that the model can prioritize breast cancer-related sequence variants while providing mechanistic explanations for their function. Finally, we experimentally validate the model-proposed mechanisms underlying three such variants.

High Fat High Sugar Diet Reduces Small Intestinal Secretion by Sex-Dependent Mechanisms.

BACKGROUND/AIMS: The goal of this study was to determine the influence of high-fat high-sugar diet (Western diet) on intestinal function and subsequently to determine if there were any beneficial effects of exercise, genistein (a naturally occurring phytoestrogen) or both, on the intestine. METHODS: We measured transepithelial short circuit current (Isc), across freshly isolated segments of jejunum from male and female C57Bl/6J mice randomly assigned to one of the following groups for the 12-week study duration: high-fat high-sugar diet (HFS), HFS with genistein (Gen), HFS with exercise (Ex), or HFS with both genistein and exercise (Gen+Ex) and compared them to lean controls. Genistein concentration was 600 mg genistein/kg diet. Exercise comprised of moderate intensity treadmill running (150 min per week). At the completion of the study, segments of jejunum were frozen for western blot determination of key proteins involved in secretory and absorptive functions, as well as senescence. Intestinal morphology was assessed. Serum cytokine assays were performed. RESULTS: Basal Isc was significantly decreased (by 70%, P<0.05) in HFS females and males versus leans. This decrease was partially mitigated by exercise in both sexes. In females, the HFS-induced decrease in Isc was attributed to a significant loss of CLC2, NKCC1 and CFTR expression whereas in males this was due to a significant loss of Na/K-ATPase, KCa and NKCC1 expression (indicating sex-dependent mechanisms). Exercise mitigated most of the loss of Isc in both sexes. Our data suggested that A2BR levels were dysregulated in HFS fed mice and that concomitant treatment with Gen or Gen+Ex prevented this disruption in females only. Inflammatory state was associated with body weight changes. CONCLUSION: Our data suggests that the reduced basal jejunal Isc in HFS mice is attributed to sex-dependent mechanisms and while exercise partially mitigated this, it's mechanism of action was unclear. Improved understanding of Western diet induced intestinal dysfunctions may allow for the development of novel drug targets to treat gastrointestinal disturbances in diabetic obesity.

Major facilitator superfamily porters, LacY, FucP and XylE of Escherichia coli appear to have evolved positionally dissimilar catalytic residues without rearrangement of 3-TMS repeat units.

Based on alleged functional residue correspondences between FucP and LacY, a recent study has resulted in a proposed model of 3-TMS unit rearrangements [Madej et al.: Proc Natl Acad Sci USA 2013;110:5870-5874]. We rebut this theory, using 7 different lines of evidence. Our observations suggest that these two transporters are homologous throughout their lengths, having evolved from a common ancestor without repeat unit rearrangements. We exploit the availability of the high-resolution XylE crystal structures in multiple conformations including the inward-facing state to render possible direct comparisons with LacY. Based on a Δdistance map, we confirm the conclusion of Quistgaard et al. [Nat Struct Mol Biol 2013;20:766-768] that the N-terminal 6 TMS halves of these transporters are internally less mobile than the second halves during the conformational transition from the outward occluded state to the inward occluded state and inward occluded state to inward open state. These observations, together with those of Madej et al. [2013], lead to the suggestion that functionally equivalent catalytic residues involved in substrate binding and transport catalysis have evolved in dissimilar positions, but apparently often in similar positions in the putative 3-TMS repeat units, from a single structural scaffold without intragenic rearrangement.

Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA). Here we develop a computationally efficient implementation of DCA, which allows us to evaluate the accuracy of contact prediction by DCA for a large number of protein domains, based purely on sequence information. DCA is shown to yield a large number of correctly predicted contacts, recapitulating the global structure of the contact map for the majority of the protein domains examined. Furthermore, our analysis captures clear signals beyond intradomain residue contacts, arising, e.g., from alternative protein conformations, ligand-mediated residue couplings, and interdomain interactions in protein oligomers. Our findings suggest that contacts predicted by DCA can be used as a reliable guide to facilitate computational predictions of alternative protein conformations, protein complex formation, and even the de novo prediction of protein domain structures, contingent on the existence of a large number of homologous sequences which are being rapidly made available due to advances in genome sequencing.

Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.

Predictive understanding of the myriads of signal transduction pathways in a cell is an outstanding challenge of systems biology. Such pathways are primarily mediated by specific but transient protein-protein interactions, which are difficult to study experimentally. In this study, we dissect the specificity of protein-protein interactions governing two-component signaling (TCS) systems ubiquitously used in bacteria. Exploiting the large number of sequenced bacterial genomes and an operon structure which packages many pairs of interacting TCS proteins together, we developed a computational approach to extract a molecular interaction code capturing the preferences of a small but critical number of directly interacting residue pairs. This code is found to reflect physical interaction mechanisms, with the strongest signal coming from charged amino acids. It is used to predict the specificity of TCS interaction: Our results compare favorably to most available experimental results, including the prediction of 7 (out of 8 known) interaction partners of orphan signaling proteins in Caulobacter crescentus. Surveying among the available bacterial genomes, our results suggest 15∼25% of the TCS proteins could participate in out-of-operon "crosstalks". Additionally, we predict clusters of crosstalking candidates, expanding from the anecdotally known examples in model organisms. The tools and results presented here can be used to guide experimental studies towards a system-level understanding of two-component signaling.

Inference of direct residue contacts in two-component signaling.

Since the onset of the genomic era more than 1000 bacterial genomes have been sequenced and several fold more are expected to be completed in the near future. These genome sequences supply a wealth of information that can be exploited by statistical methods to gain significant insights into cellular processes. In Volume 422 of Methods in Enzymology we described a covariance-based method, which was able to identify coevolving residue pairs between the ubiquitous bacterial two-component signal transduction proteins, the sensor kinase and the response regulator. Such residue position pairs supply interaction specificity in the light of highly amplified but structurally conserved two-component systems in a typical bacterium and are enriched with interaction surface residue pairings. In this chapter we describe an extended version of this method, termed "direct coupling analysis" (DCA), which greatly enhances the predictive power of traditional covariance analysis. DCA introduces a statistical inference step to covariance analysis, which allows to distinguish coevolution patterns introduced by direct correlations between two-residue positions, from those patterns that arise via indirect correlations, that is, correlations that are introduced by covariance with other residues in the respective proteins. This method was shown to reliably identify residue positions in spatial proximity within a protein or at the interface between two interaction partners. It is the goal of this chapter to allow an experienced programmer to reproduce our techniques and results so that DCA can soon be applied to new targets.