Raja Jothi, Ph.D.

Senior Investigator

Epigenetics & Stem Cell Biology Laboratory / Systems Biology Group


David P Rall Building
111 Tw Alexander Dr
Research Triangle Park, NC 27709



Research Topics

Identification of gene networks and signaling pathways associated with specific biological phenotypes is an essential step toward understanding the molecular basis of development and pathogenesis. Research in our laboratory is focused on transcriptional and epigenetic control of cell fate decisions. Using integrative interdisciplinary approaches, such as merging bioinformatics, functional genomics, and molecular biology, we reconstruct and characterize gene regulatory networks and epigenomes that underline cell states during development, differentiation, and homeostasis.


Dr. Jothi received his Bachelor’s degree from the University of Madras in 1998, and his Ph.D. from the University of Texas at Dallas in 2004. Following postdoctoral training in Systems Biology and Epigenetics at the National Center for Biotechnology Information and the National Heart, Lung, and Blood Institute, respectively, he was recruited to NIEHS in 2009 and promoted to Senior Investigator with tenure in 2015. Dr. Jothi is the recipient of the NIEHS Early Career "Rising Star" Award in 2009 and the Ruth L. Kirschstein Mentoring Award in 2016.

Selected Publications

  1. Kumar D, Cinghu S, Oldfield AJ, Yang P, Jothi R. Decoding the function of bivalent chromatin in development and cancer. Genome Res. 2021.
  2. Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nat Commun. 2019;10(1):3072.
  3. Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R. Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency. Cell Syst. 2019;8(5):427-445.e10.
  4. Cinghu S, Yang P, Kosak JP, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R. Intragenic Enhancers Attenuate Host Gene Expression. Mol Cell. 2017;68(1):104-117.e6.
  5. Oldfield AJ, Yang P, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R. Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors. Mol Cell. 2014;55(5):708-22.

Related Scientific Focus Areas

This page was last updated on Tuesday, July 17, 2018