[talks] S Nadimpalli general exam

[Melissa M. Lawson]

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.
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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.