scholarly journals Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009714
Author(s):  
Eric J. Foss ◽  
Smitha Sripathy ◽  
Tonibelle Gatbonton-Schwager ◽  
Hyunchang Kwak ◽  
Adam H. Thiesen ◽  
...  
Keyword(s):  
Binding Sites ◽  
Budding Yeast ◽  
Replication Timing ◽  
S Phase ◽  
Genome Replication ◽  
Sequence Specificity ◽  
Chromosomal Distribution ◽  
Chromosomal Replication ◽  
Inactive X Chromosome ◽  
Spatio Temporal

The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed similar individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution: Footprints in budding yeast were more sharply focused compared to the other three organisms, consistent with the relative sequence specificity of replication origins in S. cerevisiae. Nonetheless, with some clear exceptions, most notably the inactive X-chromosome, much of the fluctuation in replication timing along the chromosomes in all four organisms reflected uneven chromosomal distribution of pre-replication complexes.

scholarly journals Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

2019 ◽  
Author(s):  
Eric J. Foss ◽  
Smitha Sripathy ◽  
Tonibelle Gatbonton-Schwager ◽  
Hyunchang Kwak ◽  
Adam H. Thiesen ◽  
...  
Keyword(s):  
Fission Yeast ◽  
X Chromosome ◽  
Budding Yeast ◽  
Gc Content ◽  
Replication Timing ◽  
S Phase ◽  
Genome Replication ◽  
Chromosomal Distribution ◽  
Inactive X Chromosome ◽  
Genomic Regions

AbstractThe spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S-phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed identical MCM double-hexamer footprints across the species, but notable differences in their distribution: In budding yeast, complexes were present in sharp peaks comprised largely of single double-hexamers; in fission yeast, corresponding peaks typically contained 4 to 8 double-hexamers, were more disperse, and showed a striking correlation with AT content. In mouse and humans, complexes were even more disperse, with a preference for regions of high GC content. Nonetheless, most fluctuations in replication timing in all four organisms could be accounted for by differences in chromosomal MCM distribution. This analysis also identified genomic regions whose replication timing was clearly not attributable to MCM density. The most notable was the inactive X-chromosome, which replicates late in S phase despite the fact that both MCM abundance and chromosomal distribution were comparable to those on the early replicating active X-chromosome. We conclude that, although certain genomic regions, most notably the inactive X-chromosome, are subject to post-licensing regulation, most differences in replication timing along the chromosome reflect uneven chromosomal distribution of stochastically firing pre-replication complexes.

scholarly journals Developmental differences in genome replication program and origin activation

2020 ◽  
Vol 48 (22) ◽  
pp. 12751-12777
Author(s):  
Cathia Rausch ◽  
Patrick Weber ◽  
Paulina Prorok ◽  
David Hörl ◽  
Andreas Maiser ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Embryonic Stem ◽  
S Phase ◽  
Developmental Differences ◽  
Centromeric Heterochromatin ◽  
Genome Replication ◽  
Origin Activation ◽  
Spatio Temporal ◽  
Mes Cells

Abstract To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.

scholarly journals Temporal regulation of dUTP biosynthesis limits uracil incorporation during early DNA replication

2015 ◽  
Author(s):  
Jay R. Hesselberth ◽  
Debra Suzi Bryan
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribonucleotide Reductase ◽  
Chromosomal Instability ◽  
Budding Yeast ◽  
Replication Timing ◽  
S Phase ◽  
Concomitant Increase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nucleotide Biosynthesis ◽  
Temporal Regulation

Antimetabolite chemotherapies increase uracil levels in DNA, and thus identification of factors that influence the uracil content in DNA may have implications for understanding uracil-mediated chromosomal instability. We previously showed in the budding yeast Saccharomyces cerevisiae that uracil content in DNA correlates with replication timing, where the earliest and latest replicating regions are depleted in uracil. Here, we manipulated nucleotide biosynthesis enzymes in budding yeast to determine whether the pattern of uracil incorporation could be altered. In strains with high levels of uracil incorporation, deletion of dCMP deaminase (Dcd1) accelerated uracil incorporation at early-firing origins, likely due to rapid dTTP pool depletion. In contrast, increasing the activity of ribonucleotide reductase, which is required for the synthesis of all dNTPs via ribonucleotide diphosphates, lead to dUTP and dTTP pool equilibration and a concomitant increase in uracil content throughout the genome. These data suggest that uracil availability and the dUTP:dTTP ratio are temporally regulated during S phase and govern uracil incorporation into the genome. Therapeutic manipulation of nucleotide biosynthesis in human cells to either increase the dUTP pool or deplete the dTTP pool in early S phase may therefore improve the efficacy of antimetabolite chemotherapies.

scholarly journals Cell cycle–dependent localization of macroH2A in chromatin of the inactive X chromosome

2002 ◽  
Vol 157 (7) ◽  
pp. 1113-1123 ◽  
Author(s):  
Brian P. Chadwick ◽  
Huntington F. Willard
Keyword(s):  
Cell Cycle ◽  
X Chromosome ◽  
Degradation Pathway ◽  
S Phase ◽  
Histone H2a ◽  
The Core ◽  
Inactive X Chromosome ◽  
Inactivation Center ◽  
Chromatin Proteins ◽  
Cycle Dependent

One of several features acquired by chromatin of the inactive X chromosome (Xi) is enrichment for the core histone H2A variant macroH2A within a distinct nuclear structure referred to as a macrochromatin body (MCB). In addition to localizing to the MCB, macroH2A accumulates at a perinuclear structure centered at the centrosome. To better understand the association of macroH2A1 with the centrosome and the formation of an MCB, we investigated the distribution of macroH2A1 throughout the somatic cell cycle. Unlike Xi-specific RNA, which associates with the Xi throughout interphase, the appearance of an MCB is predominantly a feature of S phase. Although the MCB dissipates during late S phase and G2 before reforming in late G1, macroH2A1 remains associated during mitosis with specific regions of the Xi, including at the X inactivation center. This association yields a distinct macroH2A banding pattern that overlaps with the site of histone H3 lysine-4 methylation centered at the DXZ4 locus in Xq24. The centrosomal pool of macroH2A1 accumulates in the presence of an inhibitor of the 20S proteasome. Therefore, targeting of macroH2A1 to the centrosome is likely part of a degradation pathway, a mechanism common to a variety of other chromatin proteins.

scholarly journals Long-Distance Control of Origin Choice and Replication Timing in the Human β-Globin Locus Are Independent of the Locus Control Region

2000 ◽  
Vol 20 (15) ◽  
pp. 5581-5591 ◽  
Author(s):  
Daniel M. Cimbora ◽  
Dirk Schübeler ◽  
Andreas Reik ◽  
Joan Hamilton ◽  
Claire Francastel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Control Region ◽  
Globin Gene ◽  
Replication Timing ◽  
S Phase ◽  
Chromatin Conformation ◽  
Erythroid Cells ◽  
Long Distance ◽  
Targeted Deletion ◽  
Globin Gene Expression

ABSTRACT DNA replication in the human β-globin locus is subject to long-distance regulation. In murine and human erythroid cells, the human locus replicates in early S phase from a bidirectional origin located near the β-globin gene. This Hispanic thalassemia deletion removes regulatory sequences located over 52 kb from the origin, resulting in replication of the locus from a different origin, a shift in replication timing to late S phase, adoption of a closed chromatin conformation, and silencing of globin gene expression in murine erythroid cells. The sequences deleted include nuclease-hypersensitive sites 2 to 5 (5′HS2-5) of the locus control region (LCR) plus an additional 27-kb upstream region. We tested a targeted deletion of 5′HS2-5 in the normal chromosomal context of the human β-globin locus to determine the role of these elements in replication origin choice and replication timing. We demonstrate that the 5′HS2-5-deleted locus initiates replication at the appropriate origin and with normal timing in murine erythroid cells, and therefore we conclude that 5′HS2-5 in the classically defined LCR do not control replication in the human β-globin locus. Recent studies also show that targeted deletion of 5′HS2-5 results in a locus that lacks globin gene expression yet retains an open chromatin conformation. Thus, the replication timing of the locus is closely correlated with nuclease sensitivity but not globin gene expression.

scholarly journals MRX (Mre11/Rad50/Xrs2) Mutants Reveal Dual Intra-S-Phase Checkpoint Systems in Budding Yeast

Cell Cycle ◽  
2005 ◽  
Vol 4 (8) ◽  
pp. 4073-4077 ◽  
Author(s):  
Catherine A. Andrews ◽  
Duncan J. Clarke
Keyword(s):  
Budding Yeast ◽  
S Phase ◽  
S Phase Checkpoint

Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase

1992 ◽  
Vol 12 (6) ◽  
pp. 2872-2883
Author(s):  
J H de Winde ◽  
L A Grivell
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cytochrome C ◽  
Mitochondrial Biogenesis ◽  
Binding Sites ◽  
Promoter Region ◽  
S Phase ◽  
Negative Regulator ◽  
Global Regulation ◽  
Two Factors ◽  
Efficient Induction

The multifunctional DNA-binding proteins ABF1 and CPF1 bind in a mutually exclusive manner to the promoter region of the QCR8 gene, which encodes 11-kDa subunit VIII of the Saccharomyces cerevisiae mitochondrial ubiquinol-cytochrome c oxidoreductase (QCR). We investigated the roles that the two factors play in transcriptional regulation of this gene. To this end, the overlapping binding sites for ABF1 and CPF1 were mutated and placed in the chromosomal context of the QCR8 promoter. The effects on transcription of the QCR8 gene were analyzed both under steady-state conditions and during nutritional shifts. We found that ABF1 is required for repressed and derepressed transcription levels and for efficient induction of transcription upon escape from catabolite repression, independently of DNA replication. CPF1 acts as a negative regulator, modulating the overall induction response. Alleviation of repression through CPF1 requires passage through the S phase. Implications of these findings for the roles played by ABF1 and CPF1 in global regulation of mitochondrial biogenesis are discussed.

scholarly journals Structural Changes in Mcm5 Protein Bypass Cdc7-Dbf4 Function and Reduce Replication Origin Efficiency in Saccharomyces cerevisiae

2007 ◽  
Vol 27 (21) ◽  
pp. 7594-7602 ◽  
Author(s):  
Margaret L. Hoang ◽  
Ronald P. Leon ◽  
Luis Pessoa-Brandao ◽  
Sonia Hunt ◽  
M. K. Raghuraman ◽  
...  
Keyword(s):  
Structural Changes ◽  
S Phase ◽  
Minichromosome Maintenance ◽  
Chromosomal Replication ◽  
Origin Firing ◽  
Highly Active ◽  
Mcm Complex ◽  
Alternate States ◽  
Firing Efficiency ◽  
Intrinsic Firing

ABSTRACT Eukaryotic chromosomal replication is a complicated process with many origins firing at different efficiencies and times during S phase. Prereplication complexes are assembled on all origins in G1 phase, and yet only a subset of complexes is activated during S phase by DDK (for Dbf4-dependent kinase) (Cdc7-Dbf4). The yeast mcm5-bob1 (P83L) mutation bypasses DDK but results in reduced intrinsic firing efficiency at 11 endogenous origins and at origins located on minichromosomes. Origin efficiency may result from Mcm5 protein assuming an altered conformation, as predicted from the atomic structure of an archaeal MCM (for minichromosome maintenance) homologue. Similarly, an intragenic mutation in a residue predicted to interact with P83L suppresses the mcm5-bob1 bypass phenotype. We propose DDK phosphorylation of the MCM complex normally results in a single, highly active conformation of Mcm5, whereas the mcm5-bob1 mutation produces a number of conformations, only one of which is permissive for origin activation. Random adoption of these alternate states by the mcm5-bob1 protein can explain both how origin firing occurs independently of DDK and why origin efficiency is reduced. Because similar mutations in mcm2 and mcm4 cannot bypass DDK, Mcm5 protein may be a unique Mcm protein that is the final target of DDK regulation.

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