Kranthi Varala

Active Mentor - currently hosting PULSe students for laboratory rotations and recruiting PULSe students into the laboratory; serves on preliminary exam committees

Current Research Interests:

The Varala lab focuses on how plants perceive abiotic stress and alter their transcriptional programs as a response to the specific stress. We aim to capture natural genetic variation and the resultant transcriptional states leading to plant adaptation and resilience by using a combination of genomic, systems biology and phylogenetic tools. The research aims to understand how plants alter their transcriptional program immediately in response to thermal stress in the short term. We apply systems biology approaches in the model plants to understand transcriptional reprogramming in response to environmental stimuli such as temperature, nutrition etc. In the long term, we want to understand how plants change their overall gene expression regime on evolutionary scales to adapt to colder and warmer climates. We routinely use phylogenomic approaches to identify gene-to-trait association by tracking recurring changes in plant genomes that co-occur with the gain/loss of a trait. The broader question we aim to address, is whether the transient changes in the plant transcriptome offer insights into plant adaptation to diverse environments.

Selected Publications:

Doidy, J., Li, Y., Neymotin, B., Edwards, M. B., Varala, K., Gresham, D., & Coruzzi, G. M. (2016). "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run" BMC GENOMICS, 17. doi:10.1186/s12864-016-2410-2

Varala, K., Li, Y., Marshall-Colon, A., Para, A., & Coruzzi, G. M. (2015). "Hit-and-Run" leaves its mark: Catalyst transcription factors and chromatin modification. BIOESSAYS, 37(8), 851-856. doi:10.1002/bies.201400205

Li, Y., Varala, K., & Coruzzi, G. M. (2015). From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks. 31(9), 509-515. doi:10.1016/j.tig.2015.05.005

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution. (2014) PM Delaux, K Varala, PP Edger, GM Coruzzi, JC Pires, JM Ané. PLoS genetics 10 (7), e1004487.

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. (2014) A Para, Y Li, A Marshall-Colón, K Varala, NJ Francoeur, TM Moran,MB Edwards, C Hackley, BOR Bargmann, KD Birnbaum,WR McCombie, G Krouk, GM Coruzzi. Proceedings of the National Academy of Sciences 111 (28), 10371-10376.

Findley, S. D., Cannon, S., Varala, K., Du, J., Ma, J., Hudson, M. E., . . . Stacey, G. (2010). A Fluorescence in Situ Hybridization System for Karyotyping Soybean. GENETICS, 185(3), 727-744. doi:10.1534/genetics.109.113753

Toth, A. L., Varala, K., Henshaw, M. T., Rodriguez-Zas, S. L., Hudson, M. E., & Robinson, G. E. (2010). Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 277(1691), 2139-2148. doi:10.1098/rspb.2010.0090

Tuteja, J. H., Zabala, G., Varala, K., Hudson, M., & Vodkin, L. O. (2010). Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats (vol 21, pg 3063, 2009) PLANT CELL, 22(5), 1647-1647. doi:10.1105/tpc.110.220560

Swaminathan, K., Alabady, M. S., Varala, K., De Paoli, Emanuele, Ho, I., Rokhsar, D. S., . . . Hudson, M. E. (2010). Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. GENOME BIOLOGY, 11(2). doi:10.1186/gb-2010-11-2-r12

Swaminathan, K., Varala, K., & Hudson, M. E. (2007). Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC GENOMICS, 8. doi:10.1186/1471-2164-8-132

Toth, A. L., Varala, K., Newman, T. C., Miguez, F. E., Hutchison, S. K., Willoughby, D. A., . . . Robinson, G. E. (2007). Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. SCIENCE, 318(5849), 441-444. doi:10.1126/science.1146647