Description
- Abstract:
- In this thesis we provide evidence that the FAIRE method can reveal interesting and relevant changes in genome-wide chromatin organization as cells undergo replicative senescence, providing a potential mechanism to account for the widespread changes in gene expression that have already been documented. Our study is one of the first to investigate these changes at the chromatin level.<br/> The analysis of the unique fraction of the genome on whole genome tiling arrays revealed a general loss of FAIRE signal in senescent cells. Loss of FAIRE signal has previously been shown to correlate with higher nucleosome occupancy. This loss of signal can thus be inferred to correspond to a more closed chromatin structure. The loss of signal affected both TSS and enhancers, two of the most important cis-regulatory elements for the regulation of transcription. Senescent cells had fewer open TSS, and those that were open had a quantitatively lower signal. This loss of FAIRE openness was correlated with reduced gene expression. A subset of TSS were shown to gain FAIRE signal in senescent cells (and also increase their transcription), but this was a small effect relative to the overall trend.<br/> In contrast to what was observed in the unique fraction of the genome on the tiling arrays, FAIRE accessibility in the repetitive fraction of the genome increased, as determined by dot blot analysis. Although we have not comprehensively examined all regions of the repetitive genome, the same trend was observed for Alu and L1 elements, which between them comprise a very significant fraction of the repetitive genome. Increased FAIRE signal was accompanied by increased Alu and L1 RNA transcription, further reinforcing the overall positive correlation between FAIRE accessibility and permissiveness for transcription. The overall effect on genome organization in senescent cells is thus one of remarkable homogenization: the repetitive fraction of the genome, which is typically more heterochromatic becomes more accessible, and the unique fraction of the genome, which is typically more euchromatic becomes more closed.<br/>
- Notes:
- Thesis (Ph.D. -- Brown University (2012)
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Citation
Peckham, Edward Joseph,
"Changes in Chromatin Conformation During Replicative Senescence of Normal Human Diploid Fibroblasts"
(2012).
Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations.
Brown Digital Repository. Brown University Library.
https://doi.org/10.7301/Z0MC8X9P
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Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations
Theses and Dissertations for the Molecular Biology, Cell Biology, and Biochemistry department....