Transcription regulation ensures appropriate gene expression allowing cells to undergo
cell differentiation. Gene expression is controlled at multiples levels: locally, through the
binding of activating (e.g. RNA Polymerases, RNAPII) or repressive (e.g. Polycomb
repressive complexes) proteins; at large‐scale levels where chromosomes occupy discrete
territories with implications on nuclear functions. Chromosome reorganisation has been
implicated in disease and altered gene expression.
In this thesis, I explored two aspects of gene expression regulation. In mouse ES cells, I
investigated RNAPII occupancy genome‐wide and compared with Lamin B1 occupancy,
reflecting association to the repressive nuclear lamina compartment. I used DamID
mapping to determine RNAPII occupancy independently of its post‐translational
modifications. Presence of RNAPII at promoter regions of Polycomb‐repressed genes was
observed using DamID mapping of Polr2F subunit with the same levels as at active genes,
although overall levels of enrichment were low. Comparison with extent of Ser5
phosphorylation at the two groups of genes, suggest that RNAPII at PRC‐repressed genes
may be less phosphorylated than at active genes. ChIP experiments using newly available
pan‐phospho RNAPII antibodies also suggest that phosphorylation levels at PRC‐repressed
genes is lower than that found at active genes.
In blood cells from Huntington’s disease (HD) patients and normal individuals, I
investigated whether gene deregulation, identified across large genomic regions using
Chromowave, is related with changes in chromosome structure. I selected four
chromosomes (4, 5, 19 and 22) and performed cryoFISH to study their position, shape and
volume. I found that chromosomes structure, especially chromosome 22, is altered in HD.
I also selected and measured the expression of a novel set of genes located in genomic
regions that have concerted changes in gene expression with HD. I showed that STAG2,
encoding a cohesin component, is misexpressed in blood from HD, in both Early and
Moderate stages, opening new avenues for HD research.