Deciphering gene regulatory circuitry governing cell fate changes
Date issued
Authors
Editors
Journal Title
Journal ISSN
Volume Title
Publisher
License
Abstract
During development, cellular differentiation is tightly controlled via integrating several regulatory layers such as signaling pathways as well as transcriptional and epigenetic mechanisms to guarantee precise spatio-temporal gene expression programs. In order to understand the gene regulatory circuitry governing cell fate changes, in this thesis I employed two established model systems that display defined cascades of phenotypic remodeling, i.e. Neurogenesis and Epithelial to Mesenchymal Transition (EMT). During brain development, the process of neurogenesis comprises a highly defined set of cell fate decisions that involves the transition of proliferative and multipotent neuroepithelial cells towards terminally differentiated post-mitotic neurons. A combinatorial analysis of genome-wide datasets during this process profiling the transcriptome, chromatin accessibility and the epigenome profiles, including H3K27ac, the mark for active enhancers and promoters, reveals the importance and highly dynamic nature of distal gene regulation during neurogenesis. We further show that terminally differentiated neurons also undergo remodeling of the distal regulatory landscape to ensure proper transcriptional output upon exposure to stimuli that induce neuronal activity. Interestingly, further such epigenetic and transcriptional response during neuronal activation conferring a transient loss of neuronal identity, gain of cellular plasticity and induction of pro-survival genes. Within another project we functionally characterized the radial glia cell specific transcription factor Tox3, and unravel its essential function during development of neocortex as it directly binds to the promoter of Nestin thereby ensuring its timely induction during embryonic neurogenesis.
The differentiation of static epithelial cells into motile mesenchymal cells, a process known as EMT, is integral in development and wound healing and it contributes pathologically to fibrosis and cancer progression. While studying this process, we uncovered a kinetically distinct role of the JNK signaling, which is not required for initiation, but progression of EMT. Furthermore, we identified FBXO32 as a key regulator of EMT that functions via ubiquitination of transcriptional corepressor protein CTBP1 to modulate its cellular localization. Such tight regulation of CtBP1 levels during EMT is required as epigenetic remodeling and transcriptional induction of CTBP1 target genes create a suitable microenvironment for EMT progression. We further identified the C2H2-zinc finger containing protein ZNF827, to be a critical player during EMT that modulates alternative splicing of numerous genes during EMT. ZNF827 mediates such stage specific transcript diversity by directly targeting these genomic loci, modulating their epigenetic landscape to alter RNA Pol II kinetics and also facilitates the recruitment of core splicing components to nascent RNA. Overall, this thesis delineates diverse gene regulatory mechanisms which cells utilize to orchestrate cell fate changes during development and disease.