Taikichiro
Mori Memorial Research Fund Report
Research
Project: |
System-wide model of
redox-regulated chromatin dynamics |
Name: |
Cornelia
Amariei |
Affiliation: |
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.
Progress 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.