Visit the Somarowthu Lab

We are an interdisciplinary research group that integrates techniques from biochemistry, cell biology and computational biology to understand the mechanisms of important cellular pathways.

Understanding the role of long non-coding RNAs in gene regulation

LncRNAs have recently emerged as key players in many biological processes and diseases including cancer. As of 2015, the LNCipedia database holds 90,000 human lncRNAs sequences, which represents a five-fold increase in the number of sequences deposited within the last three years. Despite increasing evidence suggesting that lncRNAs play a myriad of critical roles in biology, the molecular mechanisms by which they function remain poorly understood. My laboratory aims to investigate the molecular mechanisms by which lncRNAs regulate gene expression, with a special focus on those conserved across mammalian genomes.

Viral non-coding RNAs

In addition to the mammalian lncRNAs, we plan to work on viral non-coding RNAs. Specifically, we are interested in understanding how viral ncRNAs interact and recruit host proteins. By characterizing both mammalian and viral non-coding RNAs, we can compare structural elements that are important for recruiting protein partners, and we will add to our knowledge of RNA structural elements.

RNA modeling

Determining experimental structures of RNA is extremely challenging. As of July 2015, there are only 1,114 (<2%) RNA-only structures deposited in the PDB. In the absence of crystal structures, computational models can provide valuable insights and guide the experiments. In recent years, progress has been made in all areas of RNA tertiary structure prediction; however, current tools are limited to small RNAs (~100 nts). My laboratory aims to build a pipeline of computational tools for modeling large RNAs (>200 nts), which will be provided to the scientific community as webservers or plugins.

Commonwealth of Pennsylvania Announces Recent CURE Grant Recipients
(August 14, 2023)

Selected Publications

View all of Dr. Somarowthu's publications in PubMed

"Progress and Current Challenges in Modeling Large RNAs"
Somarowthu S 
J Mol Biol.; 736-47, 2016

"HOTAIR forms an intricate and modular secondary structure"
Somarowthu S, Legiewicz M, Chillon I, Marci M, Liu F and Pyle AM
Mol Cell 58, 353-61, 2015

"Native Purification and Analysis of Long RNAs"
Chillon I, Marcia M, Legiewicz M, Liu F, Somarowthu S and Pyle AM
Methods Enzymol 558, 3-37, 2015

"Prediction of distal residue participation in enzyme catalysis"
Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D and Ondrechen MJ 
Protein Sci 24, 762-78, 2015

"Visualizing the ai5gamma group IIB intron"
Somarowthu S, Legiewicz M, Keating KS and Pyle AM
Nucleic Acids Res 42, 1947-58, 2014

"Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)"
Wang Z, Yin P, Lee JS, Parasuram R, Somarowthu S and Ondrechen MJ
BMC Bioinformatics 14 Suppl 3, S13, 2013

"Now on display: a gallery of group II intron structures at different stages of catalysis"
Marcia M, Somarowthu S and Pyle AM
Mob DNA 4, 14, 2013

"Solving nucleic acid structures by molecular replacement: examples from group II intron studies"
Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K and Pyle AM
Acta Crystallogr D Biol Crystallogr 69, 2174-85, 2013

"POOL server: machine learning application for functional site prediction in proteins"
Somarowthu S and Ondrechen MJ
Bioinformatics 28, 2078-9, 2012

"High-performance prediction of functional residues in proteins with machine learning and computed input features"
Somarowthu S, Yang H, Hildebrand DG and Ondrechen MJ
Biopolymers 95, 390-400, 2011

"A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase"
Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ and Beuning PJ
Biochemistry 50, 9283-95, 2011

"Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity"
Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA and Ondrechen MJ
Proteins 79, 2146-60, 2011

"Functional classification of protein 3D structures from predicted local interaction sites"
Parasuram R, Lee JS, Yin P, Somarowthu S and Ondrechen MJ
J Bioinform Comput Biol 8 Suppl 1, 1-15, 2010