Dr.Bhaswar Ghosh's Talk

Oct 11, 2012 - 12:00

Oct 11, 2012 - 13:00

Room 230 Department of Chemical Engineering.

Seminars

Dr.Bhaswar Ghosh Computational Systems Biology Lab Ecole Polytechnique Federale de Lausanne Lausanne Switzerland.

Abstract: The 137 genes encoding 78 different ribosomal proteins (RPs) in the budding yeast Saccharomyces cerevisiae are tightly co-regulated at the transcriptional level yet their promoters display relatively little sequence conservation. Here we describe how the transcriptional output and regulation of this suite of genes is encoded in their promoter DNA. By analyzing ChIP-seq data for four different factors (RAP1 FHL1 IFH1 and HMO1) we identify two general promoter classes characterized by the presence or absence of the HMG-box protein HMO1. The first class contains HMO1-bound promoters where we observe the absence of FHL1 DNA-binding sites which may imply that in these cases the HMO1 proteintethersFHL1 to the promoters. However at promoters not occupied by HMO1 we found the presence of FHL1 DNA-binding sites suggesting direct binding to DNA. To examine the effect of the different classes of promoter architectures on the transcriptional activities we further measured the promoter activities of 119 RP promoters. We first observed that the HMO1-boundpromoters are more tightly transcribed compared to other categories. In addition a linear model relating expression to promoter features such as binding strength of the regulators and nucleosome occupancy was able to capture a significant portion of the variance in promoter activities of HMO1-independent RP genes which was not the case forHMO1-associated promoters. This suggests that the HMO1-associated promoters are more robust to variability in the binding of different transcription factors compared to HMO1-independent cases. We further found that this robustness relates to higher sensitivities of HMO1-associated RP genes to some environmental perturbations compared to HMO1-independent classes.Brief Bio: By training I am a physicist now working on different bioinformatics and biophysical aspects of biological systems. I did my bachelor in Physics from Presidency College in Kolkata in 2000 and then went on to School of Physical Sciences at JNU to do my masters. In 2002 I joined TIFR as a graduate student but left TIFR after a year to join Bose Institute under the supervision of Prof Indrani Bose where for the first time I entered into biological systems. During my PhD I worked on applying the methods of nonlinear systems theory and stochastic processes to analyze the functions of different motifs starting from feedforward to feedback loops found in gene transcription regulatory networks in E. Coli and yeast as well as some signal transduction networks related to cell cycle and cancer. We have done a close collaboration with the lab of Prof Joyoti Basu at the Bose Institute to look at some aspects of persistence of mycobacterium through the integration of both mathematical modeling and experimental approaches. From 2009 to 2010 briefly for about a year I worked at Department of Crystallography and molecular Biology at the Saha Institute of Nuclear Physics Kolkata with Prof Rahul Banerjee on some protein bioinformatics problems related to protein-protein interactions. In 2010 I moved to EPFL Switzerland in the lab of Prof Felix Naef where I have been working on the Promoter architecture of ribosomal protein genes in yeast by analyzing and integrating genome wide binding transcriptional activity and microarray datasets with an experimental collaboration with David Shores lab at the University of Geneva.