Senior Research fellow
Computational Biology Group
The Institute of Mathematical Sciences
IV Cross Road, CIT Campus
Taramani
Chennai 600 113
Tamil Nadu, India
Phone: (+91)-044-2254-3106
Email: rakeshnetha AT imsc DOT res DOT in
About myself:
I am doctoral student working in computational biology group at The Institute of Mathematical Sciences with Prof. Rahul Siddharthan.
About my work:
It is fascinating that all of the cells within a multicellular organisms contain the same DNA, however they conatin many different cell types which arises from a single zygotic cell. The answer to this fundamental question lies in the way a particular combination of genes are turned on or off within the given cell type. There are various stages involved in the expression of genes starting right from signalling to the protein synthesis which can be regulated. These typically include signal transduction, chromatin remodelling, transcription, post-transcriptional modification, transport, translation, and post-translational modifications. My Ph.D. thesis work involves studying the interplay of two of above processes, that is, chromatin organization and regulation by transcription factors(TFs).
In this study, we tried to identify pairs of TFs which interact or avoid by binding to regions of genome which are proximal in 3D. We have developed a method and an associated tool, which we call it "ChromTogether" to comprehensively identify such TF pairs using the information about spatial proximity of chromatin regions and TF binding location on the genome from chromosome conformation capture techniques (ChIA-PET, Hi-C) and ChIP-seq respectively. We observe TFs segregate into two functionally distinct groups with enriched protein-protein interactions among co-occurring TF pairs.
Publications:
1. Transcription factors organize into functional groups on the linear genome and in 3D chromatin. Rakesh Netha Vadnala, Sridhar Hannenhalli, Leelavati Narlikar, Rahul Siddharthan. bioRxiv 2022.04.06.487423; doi: https://doi.org/10.1101/2022.04.06.487423
2. Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in Candida auris and a Chromosome Number Change in Related Species. Aswathy Narayanan, Rakesh Netha Vadnala, Promit Ganguly, Pavitra Selvakumar, Shivaprakash M. Rudramurthy, Rajendra Prasad, Arunaloke Chakrabarti, Rahul Siddharthan, Kaustuv Sanyal. 2021 May 11;12(3):e00905-21. doi: 10.1128/mBio.00905-21.
3. Loss of centromere function drives karyotype evolution in closely related Malassezia species, Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A Coelho, Md Hashim Reza, Bhagya C Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L Dawson, Joseph Heitman, Kaustuv Sanyal, eLife 9:e53944 (2020).
Under Construction!
