Systems Biology Group
Stem Cells, Epigenetics & Gene Regulation
Raja Jothi, Ph.D.
The Systems Biology Group seeks to elucidate mechanisms of gene regulation at various regulated stages of gene expression (Figure 1). In particular, the group is interested in understanding how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation. The group uses a combination of systems, molecular, and functional genomic approaches to map and characterize regulatory elements and epigenomes in human and mouse embryonic/hematopoietic stem cells, T cells, and cancer cells.
Chromatin remodeler esBAF both antagonizes and synergizes with Polycomb to promote pluripotency
Signaling by the cytokine LIF and its downstream transcription factor, STAT3, prevents differentiation of pluripotent embryonic stem cells (ESCs). This contrasts with most cell types where STAT3 signaling induces differentiation. In a collaborative effort with Gerald Crabtree's lab at Stanford, the group found that STAT3 binding across the pluripotent genome is dependent on Brg1, the ATPase subunit of a specialized chromatin remodelling complex (esBAF) found in ESCs. Brg1 is required to establish chromatin accessibility at STAT3 binding targets, preparing these sites to respond to LIF signalling. Brg1 deletion led to rapid polycomb (PcG) occupancy and H3K27me3-mediated silencing of many Brg1-activated targets genome wide, including the target genes of the LIF signaling pathway. This led to the conclusion that one crucial role of Brg1 in ESCs involves its ability to potentiate LIF signaling by opposing PcG. Contrary to expectations, Brg1 also facilitates PcG function at classical PcG targets, including all four Hox loci, reinforcing their repression in ESCs. Take together, it became evident that esBAF does not simply antagonize PcG. Rather, the two chromatin regulators act both antagonistically and synergistically with the common goal of supporting pluripotency.
Differential cell-fate outcome in fluctuating environment
To understand differential cell-fate outcome in response to the same stimulus, the group explored the link between regulatory network architecture and the genome-scale dynamics of the underlying entities (genes, mRNAs, and proteins). Integrating single-cell mRNA and protein expression datasets with the hierarchical architecture of gene regulatory networks, Jothi discovered that those transcription factors (TFs) that trigger/initiate regulatory cascades are relatively abundant, long-lived, and showed more cell-to-cell variability (due to inheret stochasticity) compared to the downstream TFs. This and other results led to the conclusion that the variability in expression of initiator TFs might confer a selective advantage as this may permit at least some members in a clonal cell population to initiate an effective response to fluctuating environments, whereas the tight regulation of the downstream TFs may minimize noise propagation and ensure fidelity in regulation. This dynamic variability in the expression of key regulatory proteins could permit differential sampling of the same underlying regulatory network governing different members in a clonal population, which might result in divergent cell-fate outcomes among different individuals in an otherwise identical cell population. This result is critical to understanding phenotypic variability in fluctuating environments, e.g., fractional survival or cell-death in clonal cell populations upon drug treatment in diseases such as cancer. The group's current research in this area is focused on identifying additional evidence supporting this notion, and understanding how cells adapt to changing environments, how different phenotypic outcomes are mediated in clonal cell populations, and how mutations that disrupt the dynamics of key regulatory proteins may influence disease conditions.
Major areas of research:
- Chromatin, epigenetics and gene regulatory networks
- Embryonic stem cell self-renewal and pluripotency
- Molecular interactions
- Identification and characterization of novel regulators of embryonic stem cell self-renewal and pluripotency
- CTCF's role in the global organization of chromatin architecture
- Epigenetic mechanisms of gene regulation
Raja Jothi, Ph.D., heads the Systems Biology Group within the Laboratory of Molecular Carcinogenesis. He also holds a secondary appointment in the Biostatistics Branch. He earned his Bachelors degree in 1998 from the University of Madras, and a Ph.D. in 2004 from the University of Texas at Dallas. He received his postdoctoral training in Computational Biology and Epigenetics from the laboratories of Teresa Przytycka (NCBI/NLM) and Keji Zhao (NHLBI), respectively, at the National Institutes of Health before joining NIEHS in 2009. He has published over 35 peer-reviewed articles and book chapters, and serves on the Editorial Boards for PLoS ONE and Frontiers in Bioinformatics and Computational Biology journals.