High-Resolution Replication Bands Compared with Morphologic G- and R-bands

Drouin, Régen; Holmquist, Gerald P.; Richer, Claude‐Lise

doi:10.1007/978-1-4757-9062-7_2

Cited by 54 publications

(66 citation statements)

References 251 publications

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“…ToR and the global structure of a genomic region were observed to be associated as a corollary of the finding that late-replicating regions tend to colocalize with dark Giemsa bands (G bands), whereas early regions are associated with R bands (Drouin et al 1994;Latt 1975;Hand 1978). Similarly, it was noticed that the early replicating regions are rich in genes (Cohen et al 1998).…”

Section: Genetic and Epigenetic Characteristics Of The Replication Zonesmentioning

confidence: 93%

Genome-wide analysis of the replication program in mammals

Farkash-Amar¹,

Simon²

2009

Chromosome Res

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Microarray technology has facilitated the research of eukaryotic DNA replication on a genomewide scale. Recent studies have shed light on the association between time of replication and chromosome structure, on the organization principles of the replication program, and on the correlation between replication timing and transcription. In this review, we summarize various genomic measurement approaches and the biological insights achieved through applying them in the study of the mammalian replication program.

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Section: Genetic and Epigenetic Characteristics Of The Replication Zonesmentioning

confidence: 93%

Genome-wide analysis of the replication program in mammals

Farkash-Amar¹,

Simon²

2009

Chromosome Res

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“…Microscopic analysis of metaphase chromosomes suggested that gene-rich R bands replicate early and gene-poor G bands replicate late (5,6). Although the exact nature of G and R band staining is unclear, R bands tend to be GC rich, and G bands tend to be GC poor.…”

mentioning

confidence: 99%

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states

White

Emanuelsson

Scalzo

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

130

138

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Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific sequences can change during development; however, the determinants of this dynamic process are poorly understood. To gain insights into the contribution of developmental state, genomic sequence, and transcriptional activity to replication timing, we investigated the timing of DNA replication at high resolution along an entire human chromosome (chromosome 22) in two different cell types. The pattern of replication timing was correlated with respect to annotated genes, gene expression, novel transcribed regions of unknown function, sequence composition, and cytological features. We observed that chromosome 22 contains regions of early-and late-replicating domains of 100 kb to 2 Mb, many (but not all) of which are associated with previously described chromosomal bands. In both cell types, expressed sequences are replicated earlier than nontranscribed regions. However, several highly transcribed regions replicate late. Overall, the DNA replication-timing profiles of the two different cell types are remarkably similar, with only nine regions of difference observed. In one case, this difference reflects the differential expression of an annotated gene that resides in this region. Novel transcribed regions with low coding potential exhibit a strong propensity for early DNA replication. Although the cellular function of such transcripts is poorly understood, our results suggest that their activity is linked to the replication-timing program. E ukaryotic chromosomes initiate DNA replication from origins that fire at different times during the S phase of the cell cycle. Autoradiography experiments have revealed that mammalian DNA replication origins are spaced from 50 to 330 kb apart (1-3). Moreover, cytological and molecular studies have established that different chromosomal regions replicate at different times throughout the S phase (reviewed in ref. 4).Several studies have correlated the timing of DNA replication with chromosomal features. Microscopic analysis of metaphase chromosomes suggested that gene-rich R bands replicate early and gene-poor G bands replicate late (5, 6). Although the exact nature of G and R band staining is unclear, R bands tend to be GC rich, and G bands tend to be GC poor. Thus, the differential replication timing of G and R bands is consistent with a recent report that replication timing correlates with GC content (7). However, it is not known whether R and G bands always correlate with DNA replication timing.Analysis of a few mammalian loci has revealed that alterations in transcriptional activity can coincide with changes in replication timing (4). Thus, it has been speculated that replication timing and gene expression are functionally linked. A more comprehensive correlation of the timing of DNA replication with gene expression by using DNA microarrays has been performed in Drosophila and human cells...

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“…These include gene density and DNA sequence composition, since gene dense/GC-rich DNA generally replicates early and gene-poor/ AT-rich DNA replicates late during S phase. 2 The clearest manifestation of this relationship is seen on metaphase chromosomes where clustered early-and late-firing replicons form replication bands that are usually at the positions of R-and G-bands. 3,4 The best-studied correlate of replication timing, however, is transcriptional status.…”

Section: Abbreviationsmentioning

confidence: 99%

Replication Timing Profile Reflects the Distinct Functional and Genomic Features of the MHC Class II Region

Takousis

Johonnett²,

Williamson³

et al. 2007

Cell Cycle

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The timing of DNA replication generally correlates with transcription, gene density and sequence composition. How is the timing affected if a genomic region has a combination of features that individually correlate with either early or late replication? The major histocompatibility complex (MHC) class II region is an AT-rich isochore that would be expected to replicate late, but it also contains coordinately regulated genes that are highly expressed in antigen-presenting cells and are strongly inducible in other cell types. Using cytological and biochemical assays, we find that the entire MHC replicates within the first half of S-phase, and that the class II region replicates slightly later than the adjacent regions irrespective of gene expression. These data suggest that despite ATrichness, an early-to-middle replication time in the class II region is defined by an open chromatin conformation that allows rapid transcriptional activation as a defence against pathogens.

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High-Resolution Replication Bands Compared with Morphologic G- and R-bands

Cited by 54 publications

References 251 publications

Genome-wide analysis of the replication program in mammals

Genome-wide analysis of the replication program in mammals

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states

Replication Timing Profile Reflects the Distinct Functional and Genomic Features of the MHC Class II Region

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