Investigating gene expression regulation at the level of single genes and whole chromosomes

Abstract

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.