Taikichiro Mori Memorial Research Fund Report



Research Project:

System-wide model of redox-regulated chromatin dynamics


Cornelia Amariei


Institute for Advanced Biosciences, Graduate school of media and governance, Keio University



Research Project Abstract

Histone modifications regulate the fundamental eukaryotic processes of DNA transcription, replication and repair. The growing amount of information on histone modification sites, enzymatic machineries and modification crosstalk reveal an involved and complex mechanism whose logic remains elusive. Numerous studies have shown that these dynamic events are intimately tied into cellular energetics (through ATP) and redox state. To further investigate this aspect, we have used continuously-grown yeast cultures that auto-synchronise their respiratory activity to produce stable oscillatory dynamics. Trancriptome and metabolome data indicate that cellular events are temporally separated into reductive and oxidative processes, that also correlate with gene DNA structure and nucleosome occupancy patterns. Key currency metabolites such as ATP, NAD(P)H, SAM and Acetyl-CoA required for nucleosome repositioning and histone modifications also show strong oscillatory behaviour, putatively regulating chromatin dynamics. Chromatin Immunoprecipitation experiments revealed several histone modification patterns supporting the idea of a nucleosome-mediated feedback on transcription.



Previously, 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. Preliminary results suggested 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 replicated these experiments over longer time-series covering three respiratory cycles, and have confirmed the occurrence of a global nucleosome remodeling event during oxidative phase, regardless of the position of the nucleosome along the gene or the transcriptional profile of the gene. We are currently performing for ChIP-on-chip experiments on both nucleosome occupancy and PolII occupancy, which will reveal the dynamics of nucleosomal occupancy and its relation to the transcriptional activity.


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