Origin Firing Regulations to Control Genome Replication Timing

Complete genome duplication is essential for genetic homeostasis over successive cell generations. Higher eukaryotes possess a complex genome replication program that involves replicating the genome in units of individual chromatin domains with a reproducible order or timing. Two types of replication origin firing regulations ensure complete and well-timed domain-wise genome replication: (1) the timing of origin firing within a domain must be determined and (2) enough origins must fire with appropriate positioning in a short time window to avoid inter-origin gaps too large to be fully copied. Fundamental principles of eukaryotic origin firing are known. We here discuss advances in understanding the regulation of origin firing to control firing time. Work with yeasts suggests that eukaryotes utilise distinct molecular pathways to determine firing time of distinct sets of origins, depending on the specific requirements of the genomic regions to be replicated. Although the exact nature of the timing control processes varies between eukaryotes, conserved aspects exist: (1) the first step of origin firing, pre-initiation complex (pre-IC formation), is the regulated step, (2) many regulation pathways control the firing kinase Dbf4-dependent kinase, (3) Rif1 is a conserved mediator of late origin firing and (4) competition between origins for limiting firing factors contributes to firing timing. Characterization of the molecular timing control pathways will enable us to manipulate them to address the biological role of replication timing, for example, in cell differentiation and genome instability.

Download Full-text

231 A SHORT TIME WINDOW TO PROFIT FROM IL-4 PLUS IL-10 ADDITION TO PROTECT CARTILAGE FROM BLOOD-INDUCED DAMAGE IN VITRO

Osteoarthritis and Cartilage ◽

10.1016/s1063-4584(11)60258-6 ◽

2011 ◽

Vol 19 ◽

pp. S113

Author(s):

M.E. van Meegeren ◽

N.W. Jansen ◽

G. Roosendaal ◽

S.C. Mastbergen ◽

F.P. Lafeber

Keyword(s):

Time Window ◽

Short Time Window ◽

Short Time

Download Full-text

The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.24.11.4769-4780.2004 ◽

2004 ◽

Vol 24 (11) ◽

pp. 4769-4780 ◽

Cited By ~ 108

Author(s):

Jennifer G. Aparicio ◽

Christopher J. Viggiani ◽

Daniel G. Gibson ◽

Oscar M. Aparicio

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Deacetylase ◽

Transcriptional Repression ◽

Replication Timing ◽

Histone Deacetylation ◽

Origin Firing ◽

Replication Checkpoint ◽

Genome Transcription ◽

Late Origin

ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.

Download Full-text

Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms

10.1101/2020.07.04.187286 ◽

2020 ◽

Cited By ~ 3

Author(s):

Y. Hu ◽

A. Tareen ◽

Y-J. Sheu ◽

W. T. Ireland ◽

C. Speck ◽

...

Keyword(s):

Dna Replication ◽

Gene Silencing ◽

Origin Recognition Complex ◽

Replication Initiation ◽

Separate Analysis ◽

Genome Replication ◽

Sequence Specificity ◽

Sequence Motifs ◽

Origin Firing ◽

Α Helix

AbstractDNA replication in eukaryotic cells initiates from chromosomal locations, called replication origins, that bind the Origin Recognition Complex (ORC) prior to S phase. Origin establishment is guided by well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. At present, the mechanistic and evolutionary reasons for this difference are unclear. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed, among other things, that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove1. We show that this Orc4 α-helix mediates the sequence-specificity of origins in S. cerevisiae. Specifically, mutations were identified within this α-helix that alter the sequence-dependent activity of individual origins as well as change global genomic origin firing patterns. This was accomplished using a massively parallel origin selection assay analyzed using a custom mutual-information-based modeling approach and a separate analysis of whole-genome replication profiling and statistics. Interestingly, the sequence specificity of DNA replication initiation, as mediated by the Orc4 α-helix, has evolved in close conjunction with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference.

Download Full-text

383. Feasibility of Specimen Self-collection in Young Children Undergoing SARS-CoV-2 Surveillance for In-person Learning

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.584 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S293-S293

Author(s):

Jonathan Altamirano ◽

Grace Tam ◽

Marcela Lopez ◽

India Robinson ◽

Leanne Chun ◽

...

Keyword(s):

Young Children ◽

Time Window ◽

School Administrators ◽

Error Rates ◽

Independent Observer ◽

Specimen Collection ◽

Timing Data ◽

Short Time Window ◽

Short Time ◽

Over Time

Abstract Background While pediatric cases of COVID-19 are at low risk for adverse events, schoolchildren should be considered for surveillance as they can become infected at school and serve as sources of household or community transmission. Our team assessed the feasibility of young children self-collecting SARS-CoV-2 samples for surveillance testing in an educational setting. Methods Students at a K-8 school were tested weekly for SARS-CoV-2 from September 2020 - June 2021. Error rates were collected from September 2020 - January 2021. Clinical staff provided all students with instructions for anterior nares specimen self-collection and then observed them to ensure proper technique. Instructions included holding the sterile swab while making sure not to touch the tip, inserting the swab into their nostril until they start to feel resistance, and rubbing the swab in four circles before repeating the process in their other nostril. An independent observer timed random sample self-collections from April - June 2021. Results 2,590 samples were collected from 209 students during the study period when data on error rates were collected. Errors occurred in 3.3% of all student encounters (n=87). Error rates over time are shown in Figure 1, with the highest rate occurring on the first day of testing (n=20/197, 10.2%) and the lowest in January 2021 (n=1/202, 0.5%). 2,574 visits for sample self-collection occurred during the study period when independent timing data was collected (April - June 2021). Of those visits, 7.5% (n=193) were timed. The average duration of each visit was 70 seconds. Figure 1. Swab Error Rates Over Time Conclusion Pediatric self-collected lower nasal swabs are a viable and easily tolerated specimen collection method for SARS-CoV-2 surveillance in school settings, as evidenced by the low error rate and short time window of sample self-collection during testing. School administrators should expect errors to drop quickly after implementing testing. Disclosures All Authors: No reported disclosures

Download Full-text

Harvest strategies for the elimination of low prevalence wildlife diseases

Royal Society Open Science ◽

10.1098/rsos.210124 ◽

2021 ◽

Vol 8 (3) ◽

Author(s):

Atle Mysterud ◽

Hildegunn Viljugrein ◽

Christer M. Rolandsen ◽

Aniruddha V. Belsare

Keyword(s):

Disease Surveillance ◽

Rangifer Tarandus ◽

Time Window ◽

Disease Prevalence ◽

Management Approach ◽

Wildlife Diseases ◽

Demographic Groups ◽

Short Time Window ◽

Transmission Period ◽

Low Prevalence

The intensive harvesting of hosts is often the only practicable strategy for controlling emerging wildlife diseases. Several harvesting approaches have been explored theoretically with the objective of lowering transmission rates, decreasing the transmission period or specifically targeting spatial disease clusters or high-risk demographic groups. Here, we present a novel model-based approach to evaluate alternative harvest regimes, in terms of demographic composition and rates, intended to increase the probability to remove all infected individuals in the population during the early phase of an outbreak. We tested the utility of the method for the elimination of chronic wasting disease based on empirical data for reindeer ( Rangifer tarandus ) in Norway, in populations with (Nordfjella) and without (Hardangervidda) knowledge about exact disease prevalence and population abundance. Low and medium harvest intensities were unsuccessful in eliminating the disease, even at low prevalence. High-intensity harvesting had a high likelihood of eliminating the disease, but probability was strongly influenced by the disease prevalence. We suggest that the uncertainty about disease prevalence can be mitigated by using an adaptive management approach: forecast from models after each harvest season with updated data, derive prevalence estimates and forecast further harvesting. We identified the problems arising from disease surveillance with large fluctuations in harvesting pressure and hence sample sizes. The elimination method may be suitable for pathogens that cause long-lasting infections and with slow epidemic growth, but the method should only be attempted if there is a low risk of reinfection, either by a new disease introduction event (e.g. dispersing hosts) or due to environmental reservoirs. Our simulations highlighted the short time window when such a strategy is likely to be successful before approaching near complete eradication of the population.

Download Full-text

Dual origin of the floor plate in the avian embryo

Development ◽

10.1242/dev.129.20.4785 ◽

2002 ◽

Vol 129 (20) ◽

pp. 4785-4796 ◽

Cited By ~ 6

Author(s):

Jean-Baptiste Charrier ◽

Françoise Lapointe ◽

Nicole M. Le Douarin ◽

Marie-Aimée Teillet

Keyword(s):

Time Window ◽

Gene Expression Pattern ◽

Floor Plate ◽

Avian Embryo ◽

Plate Formation ◽

Unknown Factor ◽

Short Time Window ◽

Neural Ectoderm ◽

Dual Origin ◽

Short Time

Molecular analysis carried out on quail-chick chimeras, in which quail Hensen’s node was substituted for its chick counterpart at the five- to six-somite stage (ss), showed that the floor plate of the avian neural tube is composed of distinct areas: (1) a median one (medial floor plate or MFP) derived from Hensen’s node and characterised by the same gene expression pattern as the node cells (i.e. expression of HNF3β and Shh to the exclusion of genes early expressed in the neural ectoderm such as CSox1); and (2) lateral regions that are differentiated from the neuralised ectoderm (CSox1 positive) and form the lateral floor plate (LFP). LFP cells are induced by the MFP to express HNF3β transiently, Shh continuously and other floor-plate characteristic genes such as Netrin. In contrast to MFP cells, LFP cells also express neural markers such as Nkx2.2 and Sim1. This pattern of avian floor-plate development presents some similarities to floor-plate formation in zebrafish embryos. We also demonstrate that, although MFP and LFP have different embryonic origins in normal development, one can experimentally obtain a complete floor plate in the neural epithelium by the inductive action of either a notochord or a MFP. The competence of the neuroepithelium to respond to notochord or MFP signals is restricted to a short time window, as only the posterior-most region of the neural plate of embryos younger than 15 ss is able to differentiate a complete floor plate comprising MFP and LFP. Moreover, MFP differentiation requires between 4 and 5 days of exposure to the inducing tissues. Under the same conditions LFP and SHH-producing cells only induce LFP-type cells. These results show that the capacity to induce a complete floor plate is restricted to node-derived tissues and probably involves a still unknown factor that is not SHH, the latter being able to induce only LFP characteristics in neuralised epithelium.

Download Full-text

Distribution of interspike intervals estimated from multiple spike trains observed in a short time window

Physical Review E ◽

10.1103/physreve.83.011910 ◽

2011 ◽

Vol 83 (1) ◽

Cited By ~ 4

Author(s):

Zbyněk Pawlas ◽

Petr Lansky

Keyword(s):

Time Window ◽

Spike Trains ◽

Interspike Intervals ◽

Short Time Window ◽

Short Time

Download Full-text

A New Method for Automated Clearcut Disturbance Detection in Mediterranean Coppice Forests Using Landsat Time Series

Remote Sensing ◽

10.3390/rs12223720 ◽

2020 ◽

Vol 12 (22) ◽

pp. 3720 ◽

Cited By ~ 1

Author(s):

Francesca Giannetti ◽

Raffaello Pegna ◽

Saverio Francini ◽

Ronald E. McRoberts ◽

Davide Travaglini ◽

...

Keyword(s):

Time Series ◽

Sustainable Forest Management ◽

Time Window ◽

Detection Algorithm ◽

Forest Disturbances ◽

Forest Change ◽

Short Time Window ◽

Short Time ◽

Automated Procedures ◽

Disturbance Detection

A Landsat time series has been recognized as a viable source of information for monitoring and assessing forest disturbances and for continuous reporting on forest dynamics. This study focused on developing automated procedures for detecting disturbances in Mediterranean coppice forests which are characterized by rapid regrowth after a cut. Specifically, new methods specific to Mediterranean coppice forests are needed for mapping clearcut disturbances over time and for estimating related indicators in the context of Sustainable Forest Management and Biodiversity International monitoring frameworks. The aim of this work was to develop a new change detection algorithm for mapping clearcut disturbances in Mediterranean coppice forests with Landsat time series (LTS) using a short time window. Accuracy for the new algorithm, characterized as the Two Thresholds Method (TTM), was evaluated using an independent clearcut reference dataset over a temporal period of the 13 years between 2001 and 2013. TTM was also evaluated against two benchmark approaches: (i) LandTrendr, and (ii) the forest loss category of the Global Forest Change Map. Overall Accuracy for LandTrendr and TTM were greater than 0.94. Meanwhile, smaller accuracies were always obtained for the GFC. In particular, Producer’s Accuracy ranged between 0.45 and 0.84 for TTM and between 0.49 and 0.83 for LT, while for the GFC, PA ranged between 0 and 0.38. User’s Accuracy ranged between 0.86 and 0.96 for TTM and between 0.73 and 0.91 for LT, while for the GFC UA ranged between 0.19 and 1.00. Moreover, to illustrate the utility of TTM for mapping clearcut disturbances in Mediterranean coppice forests, we applied TTM to a Landsat scene that covered almost the entirety of the Tuscany region in Italy.

Download Full-text

Parameters of Spike Trains Observed in a Short Time Window

Neural Computation ◽

10.1162/neco.2007.01-07-442 ◽

2008 ◽

Vol 20 (5) ◽

pp. 1325-1343 ◽

Cited By ~ 13

Author(s):

Zbyněk Pawlas ◽

Lev B. Klebanov ◽

Martin Prokop ◽

Petr Lansky

Keyword(s):

Coefficient Of Variation ◽

Point Processes ◽

Interspike Interval ◽

Time Window ◽

Time Windows ◽

Time Interval ◽

Short Time Interval ◽

Target Neuron ◽

Short Time Window ◽

Short Time

We study the estimation of statistical moments of interspike intervals based on observation of spike counts in many independent short time windows. This scenario corresponds to the situation in which a target neuron occurs. It receives information from many neurons and has to respond within a short time interval. The precision of the estimation procedures is examined. As the model for neuronal activity, two examples of stationary point processes are considered: renewal process and doubly stochastic Poisson process. Both moment and maximum likelihood estimators are investigated. Not only the mean but also the coefficient of variation is estimated. In accordance with our expectations, numerical studies confirm that the estimation of mean interspike interval is more reliable than the estimation of coefficient of variation. The error of estimation increases with increasing mean interspike interval, which is equivalent to decreasing the size of window (less events are observed in a window) and with decreasing the number of neurons (lower number of windows).

Download Full-text