Conservation of replication timing reveals global and local regulation of replication origin activity

DNA replication occurs throughout the S phase of the cell cycle, initiating from replication origin loci that fire at different times. Debate remains about whether origins are a fixed set of loci used across all cells or a loose agglomeration of potential origins used stochastically in individual cells, and about how consistent their firing time during S phase is across cells. Here, we develop an approach for profiling DNA replication in single human cells and apply it to 2,305 replicating cells spanning the entire S phase. The resolution and scale of the data enabled us to specifically analyze initiation sites and show that these sites have confined locations that are consistently used among individual cells. Further, we find that initiation sites are activated in a similar, albeit not fixed, order across cells. Taken together, our results suggest that replication timing variability is constrained both spatially and temporally, and that the degree of variation is consistent across human cell lines.

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Global and Local Regulation of Clathrin-Coated Pit Dynamics Detected on Patterned Substrates

Biophysical Journal ◽

10.1016/j.bpj.2009.06.003 ◽

2009 ◽

Vol 97 (4) ◽

pp. 1038-1047 ◽

Cited By ~ 40

Author(s):

Allen P. Liu ◽

Dinah Loerke ◽

Sandra L. Schmid ◽

Gaudenz Danuser

Keyword(s):

Patterned Substrates ◽

Local Regulation ◽

Global And Local

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Identification of a putative DNA replication origin in the λ-aminobutyric acid receptor subunit β3 and α5 gene cluster on human chromosome 15q11-q13, a region associated with parental imprinting and allele-specific replication timing

Gene ◽

10.1016/0378-1119(96)00106-0 ◽

1996 ◽

Vol 173 (2) ◽

pp. 171-177 ◽

Cited By ~ 11

Author(s):

D. Sinnett ◽

E. Woolf ◽

W. Xie ◽

K. Glatt ◽

E.F. Kirkness ◽

...

Keyword(s):

Dna Replication ◽

Human Chromosome ◽

Gene Cluster ◽

Replication Origin ◽

Replication Timing ◽

Aminobutyric Acid ◽

Receptor Subunit ◽

Dna Replication Origin ◽

Parental Imprinting ◽

Allele Specific

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DNA Replication Timing Data CorroborateIn SilicoHuman Replication Origin Predictions

Physical Review Letters ◽

10.1103/physrevlett.99.248102 ◽

2007 ◽

Vol 99 (24) ◽

Cited By ~ 31

Author(s):

B. Audit ◽

S. Nicolay ◽

M. Huvet ◽

M. Touchon ◽

Y. d’Aubenton-Carafa ◽

...

Keyword(s):

Dna Replication ◽

Replication Origin ◽

Replication Timing ◽

Timing Data ◽

Dna Replication Timing

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Dynamics of replication origin over-activation

10.1101/2020.01.27.922211 ◽

2020 ◽

Author(s):

Haiqing Fu ◽

Christophe E. Redon ◽

Koichi Utani ◽

Bhushan L. Thakur ◽

Sangmin Jang ◽

...

Keyword(s):

Cancer Cells ◽

Molecular Interactions ◽

Replication Origin ◽

Replication Timing ◽

Replication Stress ◽

Single Fiber ◽

Replication Origins ◽

Initiation Frequency

AbstractWe determined replication patterns in cancer cells in which the controls that normally prevent excess replication were disrupted (“re-replicating cells”). Single-fiber analyses suggested that replication origins were activated at a higher frequency in re-replicating cells. However, nascent strand sequencing demonstrated that re-replicating cells utilized the same pool of potential replication origins as normally replicating cells. Surprisingly, re-replicating cells exhibited a skewed initiation frequency correlating with replication timing. These patterns differed from the replication profiles observed in non-re-replicating cells exposed to replication stress, which activated a novel group of dormant origins not typically activated during normal mitotic growth. Hence, disruption of the molecular interactions that regulates origin initiation can activate two distinct pools of potential replication origins: re-replicating cells over-activate flexible origins while replication stress in normal mitotic growth activates dormant origins.

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Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci

Molecular and Cellular Biology ◽

10.1128/mcb.13.5.2971-2981.1993 ◽

1993 ◽

Vol 13 (5) ◽

pp. 2971-2981

Author(s):

S M Carroll ◽

M L DeRose ◽

J L Kolman ◽

G H Nonet ◽

R E Kelly ◽

...

Keyword(s):

Dna Replication ◽

Adenosine Deaminase ◽

Gene Amplification ◽

Replication Origin ◽

Replication Timing ◽

Single Copy ◽

S Phase ◽

Chromosomal Locus ◽

Template Strand ◽

Dna Replication Origin

Gene amplification is frequently mediated by the initial production of acentric, autonomously replicating extrachromosomal elements. The 4,000 extrachromosomal copies of the mouse adenosine deaminase (ADA) amplicon in B-1/50 cells initiate their replication remarkably synchronously in early S phase and at approximately the same time as the single-copy chromosomal locus from which they were derived. The abundance of ADA sequences and favorable replication timing characteristics in this system led us to determine whether DNA replication initiates in ADA episomes within a preferred region and whether this region is the same as that used at the corresponding chromosomal locus prior to amplification. This study reports the detection and localization of a discrete set of DNA fragments in the ADA amplicon which label soon after release of synchronized B-1/50 cells into S phase. A switch in template strand complementarity of Okazaki fragments, indicative of the initiation of bidirectional DNA replication, was found to lie within the same region. This putative replication origin is located approximately 28.5 kbp upstream of the 5' end of the ADA gene. The same region initiated DNA replication in the single-copy ADA locus of the parental cells. These analyses provide the first evidence that the replication of episomal intermediates involved in gene amplification initiates within a preferred region and that the same region is used to initiate DNA synthesis within the native locus.

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Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci.

Molecular and Cellular Biology ◽

10.1128/mcb.13.5.2971 ◽

1993 ◽

Vol 13 (5) ◽

pp. 2971-2981 ◽

Cited By ~ 27

Author(s):

S M Carroll ◽

M L DeRose ◽

J L Kolman ◽

G H Nonet ◽

R E Kelly ◽

...

Keyword(s):

Dna Replication ◽

Adenosine Deaminase ◽

Gene Amplification ◽

Replication Origin ◽

Replication Timing ◽

Single Copy ◽

S Phase ◽

Chromosomal Locus ◽

Template Strand ◽

Dna Replication Origin

Gene amplification is frequently mediated by the initial production of acentric, autonomously replicating extrachromosomal elements. The 4,000 extrachromosomal copies of the mouse adenosine deaminase (ADA) amplicon in B-1/50 cells initiate their replication remarkably synchronously in early S phase and at approximately the same time as the single-copy chromosomal locus from which they were derived. The abundance of ADA sequences and favorable replication timing characteristics in this system led us to determine whether DNA replication initiates in ADA episomes within a preferred region and whether this region is the same as that used at the corresponding chromosomal locus prior to amplification. This study reports the detection and localization of a discrete set of DNA fragments in the ADA amplicon which label soon after release of synchronized B-1/50 cells into S phase. A switch in template strand complementarity of Okazaki fragments, indicative of the initiation of bidirectional DNA replication, was found to lie within the same region. This putative replication origin is located approximately 28.5 kbp upstream of the 5' end of the ADA gene. The same region initiated DNA replication in the single-copy ADA locus of the parental cells. These analyses provide the first evidence that the replication of episomal intermediates involved in gene amplification initiates within a preferred region and that the same region is used to initiate DNA synthesis within the native locus.

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An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles

eLife ◽

10.7554/elife.63542 ◽

2021 ◽

Vol 10 ◽

Author(s):

Rossana Droghetti ◽

Nicolas Agier ◽

Gilles Fischer ◽

Marco Gherardi ◽

Marco Cosentino Lagomarsino

Keyword(s):

Replication Origin ◽

Yeast Species ◽

Evolutionary Model ◽

Replication Timing ◽

Death Process ◽

Genome Replication ◽

Replication Forks ◽

Evolutionary Models ◽

Replication Origins ◽

Evolutionary Studies

Recent results comparing the temporal program of genome replication of yeast species belonging to the Lachancea clade support the scenario that the evolution of replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins, and use it to identify the evolutionary biases that shape the replication timing profiles. Comparing different evolutionary models with data, we find that replication origin birth and death events are mainly driven by two evolutionary pressures, the first imposes that events leading to higher double-stall probability of replication forks are penalized, while the second makes less efficient origins more prone to evolutionary loss. This analysis provides an empirically grounded predictive framework for quantitative evolutionary studies of the replication timing program.

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