scholarly journals Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin

2006 ◽  
Vol 174 (2) ◽  
pp. 185-194 ◽  
Author(s):  
Rong Wu ◽  
Prim B. Singh ◽  
David M. Gilbert
Keyword(s):  
Replication Timing ◽  
Pericentric Heterochromatin ◽  
S Phase ◽  
Fine Tuning ◽  
G1 Phase ◽  
Late Replication ◽  
Free System ◽  
Replication Time ◽  
A Cell ◽  
Early Replication

Mouse chromocenters are clusters of late-replicating pericentric heterochromatin containing HP1 bound to trimethylated lysine 9 of histone H3 (Me3K9H3). Using a cell-free system to initiate replication within G1-phase nuclei, we demonstrate that chromocenters acquire the property of late replication coincident with their reorganization after mitosis and the establishment of a global replication timing program. HP1 dissociated during mitosis but rebound before the establishment of late replication, and removing HP1 from chromocenters by competition with Me3K9H3 peptides did not result in early replication, demonstrating that this interaction is neither necessary nor sufficient for late replication. However, in cells lacking the Suv39h1,2 methyltransferases responsible for K9H3 trimethylation and HP1 binding at chromocenters, replication of chromocenter DNA was advanced by 10–15% of the length of S phase. Reintroduction of Suv39h1 activity restored the later replication time. We conclude that Suv39 activity is required for the fine-tuning of pericentric heterochromatin replication relative to other late-replicating domains, whereas separate factors establish a global replication timing program during early G1 phase.

A Cell-Free Assay To Screen for Compounds That Modulate the Fanconi/BRCA Pathway.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4351-4351
Author(s):  
Stacie Stone ◽  
Alexandra Sobeck ◽  
Igor Landais ◽  
Alexis LaChapelle ◽  
Maureen E. Hoatlin
Keyword(s):  
Dna Damage ◽  
Cancer Susceptibility ◽  
Bone Marrow Failure ◽  
Current Model ◽  
S Phase ◽  
Mobility Shift ◽  
Western Blots ◽  
Free System ◽  
Egg Extracts ◽  
A Cell

Abstract Fanconi anemia is a multi-gene cancer susceptibility and bone marrow failure syndrome. In the current model, at least eight proteins (FANCA, -B-C,-E, -F, -G, -L, -M) are part of a nuclear complex that is required for the S phase and DNA-damage dependent monoubiquitination of FANCD2. This event is thought to functionally link the FA complex proteins to major breast cancer susceptibility proteins BRCA1, BRCA2 (FANCD1), and the BRCA1-associated helicase Brip1(FANCJ). An understanding of the function of the FA protein network is incomplete not only because some FA proteins are still unidentified, but also because the functions of individual proteins may be interdependent and are difficult to assess out of context with the entire FA network. We recently developed a cell-free system to evaluate the function of the Fanconi/BRCA pathway proteins in an S phase context in Xenopus egg extracts (Sobeck, et al. 2006). Egg extracts are naturally cell-cycle synchronized and mimic the complex interplay of proteins that support cellular DNA replication and regulated DNA damage checkpoint activation. Intricate protein interactions can be assayed in egg extracts, even without knowing each of the components if there is a measurable endpoint. We tested the hypothesis that the mobility shift of FANCD2 could be used as an endpoint in cell-free assays to determine FA pathway function. We found that an antibody specific for the Xenopus FANCD2 protein detected a single band of the expected size in western blots of proteins separated by SDS-PAGE from unstimulated egg extracts. Addition of DNA substrates to extracts resulted in the appearance of a slower mobility form of FANCD2, consistent with the monoubiquitinated FANCD2-L isoform observed in human cells following DNA damage. We measured inhibition or stimulation of xFANCD2-L in the presence of a series of candidate compounds. We found compounds that inhibit FANCD2-L, including curcumin, which was also identified in a cell-based assay as an inhibitor of FANCD2-L (Chirnomas, et al., 2006). Thus, this cell-free assay successfully mirrors the outcome obtained with a small molecule inhibitor of the FA/BRCA pathway in cell-based assays. This new approach is an improvement relative to cell-based screens because the extracts are fully synchronized, which maximizes the sensitivity of detection of S-phase events. Moreover, cell-free screens are rapid, inexpensive and well suited for semi- or high-throughput methods to identify small molecules that modulate the FA/BRCA DNA-damage response pathway.

scholarly journals Replication timing maintains the global epigenetic state in human cells

2019 ◽  
Author(s):  
Kyle N. Klein ◽  
Peiyao A. Zhao ◽  
Xiaowen Lyu ◽  
Daniel A. Bartlett ◽  
Amar Singh ◽  
...  
Keyword(s):  
Embryonic Stem ◽  
Cancer Cell Line ◽  
Replication Timing ◽  
Cell Types ◽  
Control Factor ◽  
Epigenetic State ◽  
Genome Wide ◽  
A Genome ◽  
A Cell ◽  
Early Replication

AbstractDNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B chromatin compartments, respectively. Early replication is also associated with active histone modifications and transcriptional permissiveness. However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that RT is central to epigenome maintenance and compartmentalization in both human embryonic stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches as previously suspected, lead to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone modification changes coincided with global reorganization of genome compartments, transcription changes and a genome wide strengthening of TAD structures. Inducible degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-regulation, supporting previously speculative models in which the timing of chromatin assembly at the replication fork plays a key role in maintaining the global epigenetic state, which in turn drives genome architecture.

scholarly journals The Protecting Role of Dormant Origins in Response to Replicative Stress

2018 ◽  
Author(s):  
Lilas Courtot ◽  
Jean-Sébastien Hoffmann ◽  
Valérie Bergoglio
Keyword(s):  
Single Cell ◽  
Replication Fork ◽  
Replication Timing ◽  
G1 Phase ◽  
Human Chromosomes ◽  
Entire Genome ◽  
Replicative Stress ◽  
Origin Activation ◽  
A Cell

Maintenance of the human chromosomes stability requires a tight regulation of DNA replication to duplicate once and only once the entire genome of a single cell. In mammalians cells, origin activation is controlled in space and time by a cell specific and robust program called replication timing. About 100 000 of potential origins are loaded onto the chromatin at the G1 phase but only 20-30% are selected and active during the replication of a given cell. When the replication fork is slowed down by exogenous or endogenous sources, the cell need to activate more origins to complete the replication on time. Thus, the large choice of origins that can be activated may be a key player in the protection of the genome. The aim of this review is to discuss about the role of these dormant origins as housekeepers of the human genome in response to replicative stress.

scholarly journals Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

2019 ◽  
Author(s):  
Nina Kirstein ◽  
Alexander Buschle ◽  
Xia Wu ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
Dna Replication ◽  
Temporal Order ◽  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
G1 Phase ◽  
Environmental Cues ◽  
Transcriptional Program ◽  
Active Transcription ◽  
Transcription And Replication

AbstractEukaryotic replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with replication initiation events obtained by Okazaki fragment sequencing. We demonstrate that MCM is displaced from early replicating, actively transcribed gene bodies, while ORC is mainly enriched at active TSS. Late replicating, H4K20me3 containing initiation zones display enhanced ORC and MCM levels. Furthermore, we find early RTDs being primarily enriched in ORC, compared to MCM, indicating that ORC levels are involved in organizing the temporal order of DNA replication. The organizational connection between active transcription and replication competence directly links changes in the transcriptional program to flexible replication patterns, which ensures the cell’s flexibility to respond to environmental cues.

scholarly journals Differential Subnuclear Localization and Replication Timing of Histone H3 Lysine 9 Methylation States

2005 ◽  
Vol 16 (6) ◽  
pp. 2872-2881 ◽  
Author(s):  
Rong Wu ◽  
Anna V. Terry ◽  
Prim B. Singh ◽  
David M. Gilbert
Keyword(s):  
Mammalian Cells ◽  
Histone H3 ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Pericentric Heterochromatin ◽  
S Phase ◽  
Subnuclear Localization ◽  
Chromosome Domains ◽  
Mouse Cells ◽  
Additional Level

Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

Macrophages kill capillary cells in G1 phase of the cell cycle during programmed vascular regression

Development ◽  
1999 ◽  
Vol 126 (10) ◽  
pp. 2141-2147 ◽  
Author(s):  
G. Diez-Roux ◽  
M. Argilla ◽  
H. Makarenkova ◽  
K. Ko ◽  
R.A. Lang
Keyword(s):  
Cell Cycle ◽  
Cell Death ◽  
Cell Cycle Progression ◽  
S Phase ◽  
G1 Phase ◽  
Target Cells ◽  
Dependent Manner ◽  
Restriction Point ◽  
A Cell ◽  
Tight Correlation

Programmed capillary regression occurs during normal development of the eye and serves as a useful model for assessing the forces that drive vascular involution. Using a combination of S-phase labeling and liposome-mediated macrophage elimination, we show that during regression, macrophages induce apoptosis of both pericytes and endothelial cells in a cell cycle stage-dependent manner. Target cells are signaled to die by macrophages approximately 15 hours after S-phase labeling and this corresponds to a point in mid-G1 phase of the cell cycle. The tight correlation between the restriction point of the cell cycle and the point where the macrophage death signal is received suggests that the mitogen, matrix and cytoskeletal signals essential for cell-cycle progression may be inhibited by macrophages as a means of inducing cell death. Furthermore, these experiments show that cells from two distinct lineages are induced to die as a consequence of macrophage action, and this provides evidence that macrophage-induced cell death may be a general phenomenon during development and homeostasis.

scholarly journals Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping

2017 ◽  
Author(s):  
Kyle Klein ◽  
Weitao Wang ◽  
Tyler Borrman ◽  
Saki Chan ◽  
Denghong Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
Replication Origins ◽  
Origin Firing ◽  
Efficient Replication ◽  
Mapping Technology ◽  
Low Efficiency ◽  
Early Replication

AbstractThe timing of DNA replication is largely regulated by the location and timing of replication origin firing. Therefore, much effort has been invested in identifying and analyzing human replication origins. However, the heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual origins in metazoans has made mapping the location and timing of replication initiation in human cells difficult. We have mapped early-firing origins in HeLa cells using Optical Replication Mapping, a high-throughput single-molecule approach based on Bionano Genomics genomic mapping technology. The single-molecule nature and 290-fold coverage of our dataset allowed us to identify origins that fire with as little as 1% efficiency. We find sites of human replication initiation in early S phase are not confined to well-defined efficient replication origins, but are instead distributed across broad initiation zones consisting of many inefficient origins. These early-firing initiation zones co-localize with initiation zones inferred from Okazaki-fragment-mapping analysis and are enriched in ORC1 binding sites. Although most early-firing origins fire in early-replication regions of the genome, a significant number fire in late-replicating regions, suggesting that the major difference between origins in early and late replicating regions is their probability of firing in early S-phase, as opposed to qualitative differences in their firing-time distributions. This observation is consistent with stochastic models of origin timing regulation, which explain the regulation of replication timing in yeast.

scholarly journals The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase

2001 ◽  
Vol 154 (2) ◽  
pp. 283-292 ◽  
Author(s):  
Feng Li ◽  
Jianhua Chen ◽  
Masako Izumi ◽  
Mark C. Butler ◽  
Susan M. Keezer ◽  
...  
Keyword(s):  
Chinese Hamster Ovary Cells ◽  
Globin Gene ◽  
Nuclear Periphery ◽  
Chinese Hamster ◽  
Replication Timing ◽  
S Phase ◽  
G1 Phase ◽  
Ovary Cells ◽  
Peripheral Heterochromatin

We have examined the dynamics of nuclear repositioning and the establishment of a replication timing program for the actively transcribed dihydrofolate reductase (DHFR) locus and the silent β-globin gene locus in Chinese hamster ovary cells. The DHFR locus was internally localized and replicated early, whereas the β-globin locus was localized adjacent to the nuclear periphery and replicated during the middle of S phase, coincident with replication of peripheral heterochromatin. Nuclei were prepared from cells synchronized at various times during early G1 phase and stimulated to enter S phase by introduction into Xenopus egg extracts, and the timing of DHFR and β-globin replication was evaluated in vitro. With nuclei isolated 1 h after mitosis, neither locus was preferentially replicated before the other. However, with nuclei isolated 2 or 3 h after mitosis, there was a strong preference for replication of DHFR before β-globin. Measurements of the distance of DHFR and β-globin to the nuclear periphery revealed that the repositioning of the β-globin locus adjacent to peripheral heterochromatin also took place between 1 and 2 h after mitosis. These results suggest that the CHO β-globin locus acquires the replication timing program of peripheral heterochromatin upon association with the peripheral subnuclear compartment during early G1 phase.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

scholarly journals Effect of detergents on sterol synthesis in a cell-free system of yeast

1982 ◽  
Vol 23 (6) ◽  
pp. 803-810
Author(s):  
S Hata ◽  
T Nishino ◽  
N Ariga ◽  
H Katsuki
Keyword(s):  
Sterol Synthesis ◽  
Free System ◽  
Cell Free System ◽  
A Cell
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