Relationship of eukaryotic DNA replication to committed gene expression: general theory for gene control.

Abstract

Promoter Occlusion by Nucleosomes and Other Chromatin Proteins Occlusion of promoters by bound nucleosomes also appears to be stable in vitro and refractory to factor competition (377; for reviews, see references 138 and 395). Stable DNA-bound nucleosomes are reported not to be displaced by high-affinity DNA-binding molecules such as heparin (295), nuclear factor 1 (NF1) (62), the glucocorticoid receptor (288), or the general transcription factor TFIID (400). There is a general consensus that nucleosomes will prevent

Enhancer dependence of polyomavirus persistence in mouse kidneys

“…We used a mixed-virus infection of mice with three different strains of Py enhancer variants and established that the organs of mice specifically replicate Py DNA and can sort the viral replicon with the compatible enhancer during both the acute and the persistent phases of a viral infection. These results further establish that organspecific DNA replication is a major determinant of cellspecific virus replication, as previously proposed (30,31,33,35). Of specific interest was the ability of PyACR and PyMLV (but not PyA2) to replicate efficiently in the neonatal mouse pancreas.…”

“…We recently proposed the existence of two types of DNA replication, cell cycle-regulated and unregulated runaway DNA replication, which could represent persistent and highlevel DNA replication, respectively (35). Although we currently have no direct evidence that low-level persistent Py DNA replication is cell cycle regulated (as is bovine papillomavirus and Epstein-Barr virus replication), simian virus 40 origin-directed DNA replication can be cell cycle regulated (6), and arguments in support of this view have been presented for Py (35). These considerations may be relevant to recent observations with JC virus and BK virus.…”

Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos.

“…Not only are new associations formed during S-phase, but results suggest that the association of transcriptionally active sequences with the matrix may be temporarily abrogated since there is an increase in atypical nuclei in which a transcriptionally active sequence becomes distended on loops. These observations are consistent with the idea that the DNA may be in dynamic flux as it moves relative to replication complexes (Berezney and Coffey, 1975; for review see Cook, 1991;Jackson, 1991;Berezney, 1991) and with studies suggesting that some functionally significant structural rearrangement of DNA may occur during replication, so as to effectuate heritable changes in cell commitment or gene expression (for review see Bodnar et al, 1989a;Villarreal, 1991). Finally, a marked difference in the structural associations of specific genes in mitotic and interphase cells is revealed by this assay, such that sequences which remain tightly condensed within residual interphase nuclei are freely distended from the residual scaffold of mitotic chromosomes.…”

The region encompassing the procyclic acidic repetitive protein (PARP) gene promoter plays a role in plasmid DNA replication inTrypanosoma brucei

“…The association between elements that support transcription and DNA replication in an ancient eukaryotic lineage such as T.brucei mirrors observations in several higher eukaryotes and their viruses, and suggests evolutionary conservation of this feature (for reviews see [25][26][27][28][29]; see also [30][31][32]. Transcription per se, either through or into an ori, may not be critical (33,34).…”