Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses, and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here, we have developed ‘enhancer-FACS-Seq’ (eFS) technology for highly parallel identification of active, tissue-specific enhancers in Drosophila embryos. Analysis of enhancers identified by eFS to be active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, novel mesodermal transcription factors (TFs). Naïve Bayes classifiers using TF binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded within them

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression by identifying their trans-regulatory inputs. Here, we present the generation of a mouse-specific transcription factor (TF) open-reading frame clone library and its implementation in yeast one-hybrid assays to enable large-scale protein–DNA interaction detection with mouse regulatory elements. Once specific interactions are identified, we then use a microfluidics-based method to validate and precisely map them within the respective DNA sequences. Using well-described regulatory elements as well as orphan enhancers, we show that this cross-platform pipeline characterizes known and uncovers many novel TF–DNA interactions. In addition, we provide evidence that several of these novel interactions are relevant in vivo and aid in elucidating the regulatory architecture of enhancers

Quantitative analysis of gene regulation in Drosophila

In this project, characterization of the MAPK signaling cascade was done using the terminal patterning of Drosophila embryo as an experimental system. MAPK acts downstream of the Torso receptor tyrosine kinase (RTK) whose activation is limited to the poles of the embryo. This results in a localized activation of MAPK which is essential for the specification of the embryonic termini. Active MAPK controls the expression of the tailless (tll) and huckebein (hkb) gap genes by downregulating a transcriptional repressor, Capicua (Cic). In this work we are interested in understanding the mechanisms that allow differential specification and precise positioning of gene expression boundaries. We quantitatively analyzed information flow from MAPK to Cic and the two target genes, tll and hkb, by constructing input-output maps in wild type embryos. Our results show that the sharp MAPK activation is translated into a graded gradient of Cic concentration and switch-like responses of tll and hkb genes. This indicates that the ultrasensitive response occurs at the level of the Cic repression which led us to test the hypothesis that Cic alone could be sufficient for tll and hkb boundary specification. However, data from mutants containing lower levels of Cic showed that boundaries of two genes become indistinguishable in terms of Cic concentration while still clearly different in terms of position. This suggests that MAPK downregulation of Cic alone is not sufficient to explain the observed localization and that, other factors are required for the robust patterning of the termini of the Drosophila embryo. To find the missing components of this regulatory system we have started an in vitro Yeast One Hybrid screen. This technique, allowing detection of protein-DNA interaction, was optimized for high-throughput screening. Together with a library Drosophila transcription factors we hope to identify the missing regulators of tll and hkb genes

Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo

Terminal regions of the Drosophila embryo are patterned by the localized activation of Mitogen Activated Protein Kinase (MAPK), which induces zygotic genes through relief of their repression by transcriptional repressor Capicua. The levels of MAPK activation at the anterior and posterior termini are close to each other, but the expression patterns of MAPK-target genes, such as zerknullt (zen) and tailless (tll), display strong anterior-posterior (AP) asymmetry. This region-specific response to MAPK activation provides a clear example of context-dependent interpretation of inductive signaling, a common developmental effect that remains poorly understood. In the past, the AP asymmetry of zen expression was attributed to a mechanism that depends on MAPK substrate competition. We present data suggesting that the asymmetric expression of tll is generated by a different mechanism, based on feedforward control and multiple enhancers of the tll gene. A simple mathematical model of this mechanism correctly predicts how the wild-type expression pattern of tll changes in mutants affecting the anterior, dorsoventral, and terminal patterning systems and some of their direct targets. (C) 2013 AIP Publishing LLC