Taikichiro
Mori Memorial Research Fund Report
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Research
Project: |
System-wide model of
redox-regulated chromatin dynamics |
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Name: |
Cornelia
Amariei |
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Affiliation: |
Institute for Advanced
Biosciences, Graduate school of media and governance, Keio
University |
Research Project
Abstract
Previous studies using continuously-grown yeast have shown that the transcriptome can be highly oscillatory, hinting at a, yet to be elucidated, global transcription mechanism. A recent Fourier-based analysis method of oscillating transcriptome datasets identified 7 consensus clusters of gene expression. Further analyses of a large compendium of high-throughput data implicate differential promoter structures and nucleosome occupancy patterns (and the energetic requirements for remodelling) in the regulation of each of these clusters. Subsequent time-series experimental data on the metabolome and nucleosome positioning over several respiratory oscillations further implicates the energetics of the cell feeding back onto global nucleosome remodelling events to differentially regulate gene expression. Taken together our data provides a simplified view of the global transcription regulation mechanism driven by the energetic state of the cells shaping chromatin structure.
Progress
We have conducted a series of
Chromatin Immunoprecipitation experiments on time-series samples, aimed at
better understanding the dynamics of the transcription regulation with regard to
histone positioning and modifications. Although the results are still
preliminary and further work is needed, they suggest that:
(a) the waves of
mRNA quantities shown in previous studies are indeed regulated at
transcriptional level;
(b) histone acetylation shows differences over the
respiratory cycle and correlates with differentially expressed genes;
(c)
nucleosome positioning upstream of transcription start site (TSS) may be a
dynamic, global property, strongly linked to the respiratory cycle.
We have
further developed a simplified, reliable method for obtaining total nucleosomal
DNA and have conducted a 40-timepoint tiling array analysis of the nucleosomal
versus total DNA. We are currently processing this data and developing an R
package dedicated to analyzing and visualizing nucleosome dynamics on both
specific genomic regions and genome-wide changes.