Developmental regulation of replication fork pausing in Xenopus laevis ribosomal RNA genes

Maric, Chrystelle; Levacher, Béatrice; Hyrien, Olivier

doi:10.1006/jmbi.1999.3017

Cited by 22 publications

(17 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Speci®c attachment of the rDNA chromatin domain after the MBT may permit it to be structurally insulated for both transcription and replication. Signi®cantly, after the MBT, both transcription and replication termination sites in the rDNA domain are located within the intergenic spacer (Maric et al, 1999;Meissner et al, 1991).…”

Section: Dna Loop Domains and Organization Of Replicationmentioning

confidence: 99%

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

2001

View full text Add to dashboard Cite

Organization of DNA into chromatin is likely to participate in the control of the timing and selection of DNA replication origins. Reorganization of the chromatin is carried out by chromatin remodelling machines, which may a ect the choice of replication origins and e ciency of replication. Replication itself causes a profound rearrangement in the chromatin structure, from nucleosomes to DNA loop domains, allowing to retain or switch an epigenetic state. The present review considers the e ects of chromatin remodelling on replication and vice versa. Oncogene (2001) 20, 3086 ± 3093.

show abstract

Section: Dna Loop Domains and Organization Of Replicationmentioning

confidence: 99%

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

2001

View full text Add to dashboard Cite

show abstract

“…The mere existence of such contrahelicases strongly suggests a requirement to protect transcription of important genes from DNA replication. Replication fork barriers were also observed in such diverse eukaryotes as the pea (28), the mouse (29), Xenopus laevis (33), Tetrahymena thermophila (49), and fission yeast (44).…”

mentioning

confidence: 98%

Mechanisms of Transcription-Replication Collisions in Bacteria

Mirkin

2005

Molecular and Cellular Biology

166

153

View full text Add to dashboard Cite

While collisions between replication and transcription in bacteria are deemed inevitable, the fine details of the interplay between the two machineries are poorly understood. In this study, we evaluate the effects of transcription on the replication fork progression in vivo, by using electrophoresis analysis of replication intermediates. Studying Escherichia coli plasmids, which carry constitutive or inducible promoters in different orientations relative to the replication origin, we show that the mutual orientation of the two processes determines their mode of interaction. Replication elongation appears not to be affected by transcription proceeding in the codirectional orientation. Head-on transcription, by contrast, leads to severe inhibition of the replication fork progression. Furthermore, we evaluate the mechanism of this inhibition by limiting the area of direct contact between the two machineries. We observe that replication pausing zones coincide exactly with transcribed DNA segments. We conclude, therefore, that the replication fork is most likely attenuated upon direct physical interaction with the head-on transcription machinery.In bacteria, DNA replication and transcription continue throughout the life cycle. The speed of the replication fork progression in Escherichia coli is ϳ1,000 bp per s (16), while the elongation rate for RNA polymerase is just 50 nucleotides (nt) per s (15); i.e., replication is approximately 20-fold faster than transcription. Since the two processes proceed simultaneously, frequent collisions between replication and transcription seem unavoidable (3, 38). Given that both processes are polar, the collisions can occur either head-on or codirectionally (Fig. 1). In the case of head-on collisions, the front edge of RNA polymerase meets the hexameric DNA helicase DnaB that moves along the lagging strand template. In the codirectional case, by contrast, the front edge of the leading strand DNA polymerase collides with the rear edge of RNA polymerase.While it is unclear a priori which type of collision is more damaging for DNA metabolism, the data on the organization of bacterial genomes point to selection against head-on collisions. Sequencing of the E. coli genome revealed that there is a bias towards codirectional alignment of transcription units with replication (2). Most strikingly, all seven ribosomal operons face the direction of their replichores. For other genes, however, this bias is much less pronounced: ϳ62% of tRNA genes and ϳ55% of protein-coding genes are aligned codirectionally with replication. Similar principles of gene arrangement were observed for other bacteria, such as Bacillus subtilis, Borrelia burgdorferi, Treponema pallidum, Haemophilus influenzae, Helicobacter pylori, Mycoplasma genitalium, and Mycoplasma pneumoniae (36), as well as for bacteriophages T7 and lambda (3).Experimental data on transcription-replication collision are relatively scarce. This problem was addressed in vitro by studying interactions between bacterial RNA polymerases and phage repl...

show abstract

“…In several eukaryotic systems, any DNA sequence can function as a replicator (17,29). In early embryos of Xenopus and Drosophila melanogaster, replication initiates with no regard for specific sequences, whereas later in development origins are progressively restricted to more specific sequences (33,46,58). In differentiated cells, nevertheless, there is evidence that defined cis-acting elements are required for origin function.…”

mentioning

confidence: 99%

Replication of the Chicken β-Globin Locus: Early-Firing Origins at the 5′ HS4 Insulator and the ρ- and β^A-Globin Genes Show Opposite Epigenetic Modifications

Prioleau

Gendron

Hyrien

2003

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

Chromatin structure is believed to exert a strong effect on replication origin function. We have studied the replication of the chicken ␤-globin locus, whose chromatin structure has been extensively characterized. This locus is delimited by hypersensitive sites (HSs) that mark the position of insulator elements. A stretch of condensed chromatin and another HS separate the ␤-globin domain from an adjacent folate receptor (FR) gene. We demonstrate here that in erythroid cells that express the FR but not the globin genes, replication initiates at four sites within the ␤-globin domain, one at the 5 HS4 insulator and the other three near theand ␤ A -globin genes. Three origins consist of G؉C-rich sequences enriched in CpG dinucleotides. The fourth origin is A؉T rich. Together with previous work, these data reveal that the insulator origin has unmethylated CpGs, hyperacetylated histones H3 and H4, and lysine 4-methylated histone H3. In contrast, opposite modifications are observed at the other G؉C-rich origins. We also show that the whole region, including the stretch of condensed chromatin, replicates early in S phase in these cells. Therefore, different early-firing origins within the same locus may have opposite patterns of epigenetic modifications. The role of insulator elements in DNA replication is discussed.The replicon model (35) hypothesized two essential components for replication initiation: the initiator, a trans-acting factor, and the replicator, a cis-acting element. The initiator would bind the replicator, and appropriate signals would direct DNA unwinding and recruitment of additional factors at a replication origin that, in the simplest case, would coincide with the replicator. This model has been confirmed in bacteria and viruses, which use a single origin to duplicate their genome. In the genomes of eukaryotic cells, replication initiates at multiple origins that have been more difficult to identify. Studies with Saccharomyces cerevisiae led to the identification of replicators, the so-called autonomously replicating sequences (ARSs) that share an essential 11-bp ARS consensus sequence (for reviews see references 49 and 61) and to a single initiator, the origin recognition complex (ORC) (8,19). The discovery that ORC and additional factors required for initiation are highly conserved suggested that the replicon model might be directly applicable to all eukaryotes (7).However, no element with properties similar to those of the yeast ARS consensus sequence has been identified to date in any other eukaryote. In several eukaryotic systems, any DNA sequence can function as a replicator (17,29). In early embryos of Xenopus and Drosophila melanogaster, replication initiates with no regard for specific sequences, whereas later in development origins are progressively restricted to more specific sequences (33,46,58). In differentiated cells, nevertheless, there is evidence that defined cis-acting elements are required for origin function. For example, an 8-kb deletion encompassing the initiation region locat...

show abstract

Developmental regulation of replication fork pausing in Xenopus laevis ribosomal RNA genes

Cited by 22 publications

References 56 publications

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

Mechanisms of Transcription-Replication Collisions in Bacteria

Replication of the Chicken β-Globin Locus: Early-Firing Origins at the 5′ HS4 Insulator and the ρ- and β^A-Globin Genes Show Opposite Epigenetic Modifications

Contact Info

Product

Resources

About

Developmental regulation of replication fork pausing in Xenopus laevis ribosomal RNA genes

Cited by 22 publications

References 56 publications

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

Chromatin remodelling and DNA replication: from nucleosomes to loop domains

Mechanisms of Transcription-Replication Collisions in Bacteria

Replication of the Chicken β-Globin Locus: Early-Firing Origins at the 5′ HS4 Insulator and the ρ- and βA-Globin Genes Show Opposite Epigenetic Modifications

Contact Info

Product

Resources

About

Replication of the Chicken β-Globin Locus: Early-Firing Origins at the 5′ HS4 Insulator and the ρ- and β^A-Globin Genes Show Opposite Epigenetic Modifications