Raja Jothi, Ph.D.

Senior Investigator

Epigenetics & Stem Cell Biology Laboratory / Systems Biology Group


A-314 Rall Building
111 T W 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. 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.

  2. Pathania R, Ramachandran S, Elangovan S, Padia R, Yang P, Cinghu S, Veeranan-Karmegam R, Arjunan P, Gnana-Prakasam JP, Sadanand F, Pei L, Chang CS, Choi JH, Shi H, Manicassamy S, Prasad PD, Sharma S, Ganapathy V, Jothi R, Thangaraju M. DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nat Commun. 2015;6:6910.

  3. 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.

  4. Cinghu S, Yellaboina S, Freudenberg JM, Ghosh S, Zheng X, Oldfield AJ, Lackford BL, Zaykin DV, Hu G, Jothi R. Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis. Proc Natl Acad Sci U S A. 2014;111(16):E1581-90.

  5. Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R, Crabtree GR. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat Cell Biol. 2011;13(8):903-13.

This page was last updated on July 17th, 2018