Shilpa Nadimpalli will present her research seminar/general exam on Thursday May 9 at 1PM in Room 402. The members of her committee are: Mona Singh, advisor, Olga Troyanskaya, and Kai Li. Everyone is invited to attend her talk and those faculty wishing to remain for the oral exam following are welcome to do so. Her abstract and reading list follow below. ------------------ Abstract ======== Gene regulatory networks control where, when, and in what amount genes are expressed. Interestingly, these networks appear to be highly malleable, despite the fact that changes in gene regulation hugely impact organisms' phenotypic characteristics. For instance, gene regulation changes can explain the differentiation between closely-related species, such as humans and chimps, or among subpopulations of the same species. How do regulatory networks change? We explore one hypothesis, that changes can occur in transcription factors (TFs), which bind to DNA to change the expression of groups of genes. We have curated a high-quality dataset of Cys2-His2 zinc finger (ZF) genes, the largest group of TFs in tetrapods, across the 12 sequenced Drosophila species. Somewhat surprisingly, we see evidence of significant change due to transcription factors. Analysis of the DNA-binding ZF domains within these genes reveals patterns of divergence related to phylogeny, gene conservation, domain organization, and gene function. We also show that the ZF domains within these TF genes are functionally important, and that sections of these genes are under positive selective pressure. This suggests that the ZF transcription factors are a source of new regulatory activity in Drosophila. Reading List ========== [1] Jones, NC & Pevsner, PA (2004). "An Introduction to Bioinformatics Algorithms (Computional Molecular Biology). 1st ed. MIT Press, Cambridge, MA. [2] Przytycka, TM, Singh, M, & Slonim, DK (2009). "Toward the dynamic interactome: it's about time." Briefings in Bioinformatics, 2(1): 15-29. [3] Johnson, AD & Li, H (2010). "Evolution of Transcription Networks -- Lessons from Yeast." Current Biology, 20(17): R746-R753. [4] Wagner, GP & Lynch, VJ (2008). "The gene regulatory logic of transcription factor evolution." Trends in Ecology and Evolution, 23: 377-385. [5] Hsia, CC & McGinnis, W (2003). "Evolution of transcription factor function." Current Opinion in Genetics and Development, 13(2): 199-206. [6] Emerson, RO & Thomas, JH (2009). "Adaptive Evolution in Zinc Finger Transcription Factors." PLoS Genetics, 5(1). [7] Singh, LN & Hannenhalli, S (2008). "Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression." PLoS ONE, 3(6): e2345. [8] Persikov, AV, Osada, R, & Singh, M (2009). "Predicting DNA recognition by Cys2-His2 zinc finger proteins." Bioinformatics, 25(1): 22-29. [9] Enuameh, SE et al. (2013). "Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants." Genome Research. [10] Tadepally, HD, Burger, G, & Aubry, M (2008). "Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes, and effector domains." BMC Evolutionary Biology, 8: 176.