Although the relationship between structural chromatin changes and cellular senescence is not well understood, one key protein required for SAHF formation is pRB, linking higher-order chromatin changes and replication (Narita et al., 2003).
Because hmo1Δ strains are slow growing, showing slower progression throughout the cell-cycle (Lu et al, 1996), and PCNA modifications with SUMO and ubiquitin are expected to be sensitive to cell-cycle changes and replication delays (Hoege et al, 2002), we established a conditional degron system (hmo1-AID), in which Hmo1 depletion is induced by addition of auxin (Nishimura et al, 2009).
Meanwhile, at 4 h after exposure, the top categories comprised nucleosome/chromatin assembly, DNA behavior involved in conformation change and DNA replication in up-regulated gene list, however most of the regulations involved in metabolic processes, nucleus and molecular binding were observed in the down-regulated genes (lower panel in Fig. 3).
Previous studies suggested a role for chromatin modifications in large-scale movement of loci away from heterochromatic regions and the subsequent changes in transcription and replication timing in the human β-globin locus [47] and the CFTR locus [48].
These new conformations may easily perturb, for example, protein-DNA binding and thereby induce changes in cellular transcription and replication.
As expected, newborn babies seem to have almost five-fold lower heart mtDNA copy numbers than adults and the copy number steadily increased concomitantly with the changes in mtDNA organization and replication.
In transcription and replication, changes in the chromatin structure are required in order to allow binding of the factors involved [ 4, 5].
Taken together, our results indicate that there is a correlation between changes in histone acetylation and replication timing with local modifications in origin architecture.
Based upon these analyses, which include changes to both structural and replication genes and their predicted gene products, we conclude that they are significantly different enough in genetic content and biology to be considered individual phages and not merely variants of one another.
The expression measurement for a gene for a specific array/protocol/sample can be broken down as X = Z + e, where X is the measured expression value Z is the "true" expression that does not change under replication, and e is the measurement error that does change under replication.
