Joshua Fletcher and Bing He will present their research on March 21 2013
Bing He’s research abstract
Identify enhancer-promoter associations in human
Transcriptional enhancers play an essential role in establishing cell type and developmental stage specific gene expression patterns in metazoans. They typically comprise multiple transcription factor (TF) binding sites (TFBS) located in DNA regions of a few hundred base pairs. To date, mechanisms of enhancer action are still poorly understood and a key gap in our knowledge is how enhancers select specific promoters for activation. To fill this gap we aim to develop an integrative approach to computationally predict enhancer-promoter associations followed by experimental validation in human. Our preliminary results based on a set of experimentally supported enhancer-promoter pairs show that several features can be extracted from ENCODE data and are effective in discriminating between real and random enhancer-promoter associations. These features include activity profile correlation, TF-target expression correlation, evolutionary constraint, and distance constraint between enhancers and target promoters. They can be integrated to construct a computational framework for robust prediction of enhancer-promoter pairs. This work will have significant impact on multiple aspects of enhancer research such as the basic mode of action of enhancers and their involvement in disease etiology.
Joshua Fletcher’s research abstract
Functional Genomics and Immunological Approaches to Understanding Francisella tularensis Virulence Mechanisms
Bacterial pathogens often subvert host immune function by effector proteins that are delivered through sophisticated secretion systems. Unlike other intracellular pathogens such asLegionella and Salmonella, the Francisella genome does not encode common secretion systems (Type III, Type IV, etc.) or their associated effectors, although evidence exists for a putative Type VI apparatus encoded in the Francisella Pathogenicity Island. Subversion of the host response (inhibition of oxidative burst, degradation of the phagosome, etc.) is an active process requiring live bacteria, indicating that while LPS and capsule contribute to immune evasion, other undiscovered Francisella factors may also be important. To identify these factors a combined bioinformatics and transposon mutagenesis approach was used to generate a list of candidate virulence factors. The amino acid sequences of the proteins encoded by the Schu S4 genome were analyzed for functional domains. We sought to identify eukaryotic-like domains, prokaryotic domains associated with virulence, and domains of unknown function. Candidate genes were compared to previously published TraSH screen data generated by our lab. Site-directed mutants for FTL0881c, FTL0784, and FTL0177 were generated for three candidates in the Live Vaccine Strain (LVS) strain of Francisella tularensis subsp. holartica. FTL0881c is predicted to be a homolog of a secreted protein found primarily in plant pathogens and Legionella; FTL0784 has numerous SEL1 domains, originally identified in C. elegans and thought to mediate protein-protein interactions; FTL0177 is predicted to be a member of the alpha hemolysin family of proteins. The ability of the mutants to survive and replicate intracellularly was tested by infecting the murine macrophage-like J774 cell line. Preliminary data indicates that none of the mutants are defective for intracellular growth over 24 hours, however subtle decreases in fitness are detectable for FTL0881c and FTL0177 in competition infections. Future work includes in vitro infections with these and other candidate mutants generated in the fully virulent Schu S4 strain.