The vertebrate gastrointestinal tract is a flexible system that is highly responsive to internal (host) and external (environment) dynamics. Our understanding of this plasticity, both biomedically relevant and in the context of ecology and evolution, has largely been studied without considering the gut microbiome – the diverse microbial communities that perform vital physiological and metabolic functions. Diet induces changes in the form and function of the gastrointestinal tract, and the microbial community within. However, the microbial contribution to the rapid and reversible changes in the physiology of the gastrointestinal tract remains unexplored. The products of bacterial fermentation, also known as short-chain fatty acids, act as energy sources, histone deacetylase (HDAC) inhibitors, and G-protein coupled receptor molecules in various cells. I hypothesize that short-chain fatty acids modulate gene expression via epigenetic controls to alter rapid adaptations in the gastrointestinal tract. For my dissertation research, I will test whether the microbiome (via the production of short-chain fatty acids) alters host plasticity and gene expression. I plan to integrate aspects of protein activity and expression, host transcriptomics, and microbial metagenomics, and epigenetics to understand the relationship between diet, microbiome, and host in the gastrointestinal tract system with a focus on animal’s ecology and evolution.
Investigating the functional role of Spt5 on transcription elongation complex assembly (Sanchirmaa)
Transcription elongation by RNA polymerase II (RNAPII) is a highly dynamic and regulated process. RNAPII requires the assistance of accessory factors to transcribe the chromatin template. Chromatin poses a barrier to RNAPII due to its organization into nucleosomes, ~147 bp of DNA wrapped around an octamer of histones. A transcription elongation factor that assists RNAPII to maintain its processivity and speed is Spt5. Spt5 is the only transcription elongation factor conserved in all three domains of life and is essential for viability. It associates with RNAPII (and I) during early elongation until transcription termination and serves as an interaction platform for protein complexes that regulate RNA polymerase processivity, RNA processing and histone modifications. The C-terminal region (CTR) of Spt5 contains multiple copies of a very characteristic peptide repeat that is involved in the recruitment of factors to the elongation complex (EC) in a phosphorylation-dependent manner. Nonetheless, the roles of Spt5 and its CTR phosphorylation on transcription elongation are mostly unknown. I hypothesized that Spt5 is an integral part of EC, and the depletion of Spt5 would result in the dissociation of other elongation factors from EC. I tested this hypothesis by using a plant-derived auxin-inducible degron (AID) system to rapidly deplete S. cerevisae Spt5 while avoiding the accumulation of secondary effects arising from its functional loss. I performed chromatin immunoprecipitation (ChIP) qPCR and ChIP-seq to investigate the effects of Spt5 depletion on the localization of several elongation factors across gene bodies. The results revealed that the occupancy of Spt5 and its known associated factors decreased genome-wide. Interestingly, the results suggest a functional role of Spt5 in the retention of Spt6 to the EC, which has not been reported previously. In addition, consistent with published observations made in S. pombe, my ChIP-seq results showed an accumulation of RNAPII over the 5’ region of gene bodies upon Spt5 depletion, suggesting a conserved role for Spt5 in facilitating progress of RNAPII past a potential “barrier” during elongation.