Related papers: Optimal Placement of Origins for DNA Replication
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Genome replication, a key process for a cell, relies on stochastic initiation by replication origins, causing a variability of replication timing from cell to cell. While stochastic models of eukaryotic replication are widely available, the…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
DNA synthesis in \textit{Xenopus} frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes…
Background: In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory…
DNA replication in Xenopus laevis is extremely reliable, failing to complete before cell division no more than once in 10,000 times; yet replication origins sites are located and initiated stochastically. Using a model based on 1d theories…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
Isogenic Escherichia coli growing exponentially in a constant environment display large variation in growth-rates, division-sizes and generation-times. It is unclear how these seemingly random cell cycles can be reconciled with the precise…
Many biological processes, from cell division to viral lysis, are triggered when an internal stochastic variable reaches a threshold. Here we introduce Branching under First-Passage Resetting, a general framework in which replication events…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
DNA replication is a process which is common to all domains of life yet different replication mechanisms are seen among different organisms. The mechanism of replication on such a structure is not yet understood. With this bigger picture in…
A self-replicating system where the elements belonging to a solution category can replicate themselves by copying their own informations, is considered. The information carried by each element is defined by an element of all the n multiple…