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Biomedical subjects

David M Gilbert

Publications and source records attributed to David M Gilbert.

At least 19 recordsLinked to original sources
PubMed2019

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control.

DNA replication occurs in a defined temporal order known as the replication timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs) by combining them into more complex circuitries of composite and bipartite networks. Results identified novel trans interactions linking transcription factors that are core to the regulatory circuitry of each cell type to RT changes occurring in those cell types. These core transcription factors were found to bind cooperatively to sites in the affected replication domains, providing provocative evidence that they constitute biologically significant directional interactions. Our findings suggest a regulatory link between the establishment of cell-type-specific TRNs and RT control during lineage specification.

Cell Differentiation↗
PubMed2006

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

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.

Animals↗
PubMed2006

The Chinese hamster dihydrofolate reductase replication origin decision point follows activation of transcription and suppresses initiation of replication within transcription units.

Chinese hamster ovary (CHO) cells select specific replication origin sites within the dihydrofolate reductase (DHFR) locus at a discrete point during G1 phase, the origin decision point (ODP). Origin selection is sensitive to transcription but not protein synthesis inhibitors, implicating a pretranslational role for transcription in origin specification. We have constructed a DNA array covering 121 kb surrounding the DHFR locus, to comprehensively investigate replication initiation and transcription in this region. When nuclei isolated within the first 3 h of G1 phase were stimulated to initiate replication in Xenopus egg extracts, replication initiated without any detectable preference for specific sites. At the ODP, initiation became suppressed from within the Msh3, DHFR, and 2BE2121 transcription units. Active transcription was mostly confined to these transcription units, and inhibition of transcription by alpha-amanitin resulted in the initiation of replication within transcription units, indicating that transcription is necessary to limit initiation events to the intergenic region. However, the resumption of DHFR transcription after mitosis took place prior to the ODP and so is not on its own sufficient to suppress initiation of replication. Together, these results demonstrate a remarkable flexibility in sequence selection for initiating replication and implicate transcription as one important component of origin specification at the ODP.

Animals↗
PubMed2005

Origins go plastic.

Replication origins should no longer be thought of as housekeeping elements that function similarly in all cell types. provide the most authoritative evidence to date that mammalian replication origins can be dynamically regulated during differentiation.

Animals↗
PubMed2005

Overexpression of ORC subunits and increased ORC-chromatin association in transformed mammalian cells.

The origin recognition complex (ORC) is a conserved heterohexamer required for the formation of pre-replication (pre-RC) complexes at origins of DNA replication. Many studies of ORC subunits have been carried out in transformed human cell lines but the properties of ORC in primary cells have not been addressed. Here, we compare the expression levels and chromatin-association of ORC subunits in HeLa cells to the primary human cell line, WI38, and a virally transformed derivative of WI38, VA13. ORC subunits 2 and 4 were highly overexpressed in both HeLa and VA13, whereas ORC1 levels were elevated in VA13 but considerably higher in HeLa cells. Cellular extraction revealed that the proportion of ORC2 and ORC4 subunits bound to chromatin was similar in all three cell lines throughout the cell-cycle. In contrast, very little ORC1 was associated with chromatin after extraction of primary WI38 cells, whereas the majority of overexpressed ORC1 in both HeLa and VA13 co-fractionated with chromatin throughout the cell-cycle. Although none of the cell lines displayed significant changes in the levels or chromatin-association of ORC during the cell-cycle, the chromatin-associated fraction of ORC1 displayed an increase in apparent molecular weight during S-phase. Similar experiments comparing immortalized CHO cells to an isogenic virally transformed derivative revealed no changes in levels of ORC subunits but an increase in the proportion of all three ORC subunits associated with chromatin. These results demonstrate a complex influence of cellular immortalization and transformation properties on the expression and regulation of ORC subunits. These results extend the potential link between cancer and deregulation of pre-RC proteins, and underscore the importance of considering the transformation status of cell lines when working with these proteins.

Animals↗
PubMed2005

Sequential electrolytic oxidation and reduction of aqueous phase energetic compounds.

Contamination of soils and groundwater with energetic compounds has been documented at many former ammunition manufacturing plants and ranges. Recent research at Colorado State University (CSU) has demonstrated the potential utility of electrolytic degradation of organic compounds using an electrolytic permeable reactive barrier (e-barrier). In principle, an electrolytic approach to degrade aqueous energetic compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or 2,4,6-trinitrotoluene (TNT) can overcome limitations of management strategies that involve solely oxidation or reduction, through sequential oxidation-reduction or reduction-oxidation. The objective of this proof-of-concept research was to evaluate transformation of aqueous phase RDX and TNT in flow-through electrolytic reactors. Laboratory experiments were conducted using six identical column reactors containing porous media and expanded titanium-mixed-metal-oxide electrodes. Three columns tested TNT transformation and three tested RDXtransformation. Electrode sequence was varied between columns and one column for each contaminant acted as a no-voltage control. Over 97% of TNT and 93% of RDX was transformed in the reactors under sequential oxidation-reduction. Significant accumulation of known degradation intermediates was not observed under sequential oxidation-reduction. Removal of approximately 90% of TNT and 40% of RDX was observed under sequential reduction-oxidation. Power requirements on the order of 3 W/m2 were measured during the experiment. This suggests that an in-situ electrolytic approach may be cost-practical for managing groundwater contaminated with explosive compounds.

Electrodes↗
PubMed2005

Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle.

In yeast, the Origin Recognition Complex (ORC) is bound to replication origins throughout the cell-cycle, but in animal cells, there are conflicting data as to whether and when ORC is removed from chromatin. We find ORC1, 2 and ORC4 to be metabolically stable proteins that co-fractionate with chromatin throughout the cell-cycle in Chinese hamster fibroblasts. Since cellular extraction methods cannot directly examine the chromatin binding properties of proteins in vivo, we examined ORC:chromatin interactions in living cells. Fluorescence loss in photobleaching (FLIP) studies revealed ORC1 and ORC4 to be highly dynamic proteins during the cell-cycle with exchange kinetics similar to other regulatory chromatin proteins. In vivo interaction with chromatin was not significantly altered throughout the cell-cycle, including S-phase. These data support a model in which ORC subunits dynamically interact with chromatin throughout the cell-cycle.

Animals↗
PubMed2005

Electrolytic transformation of ordinance related compounds (ORCs) in groundwater: laboratory mass balance studies.

Electrolytic reactive barriers (e(-) barriers) consist of closely spaced permeable electrodes installed across a groundwater contaminant plume in a permeable reactive barrier format. Application of sufficient potential to the electrodes results in sequential oxidation and reduction of the target contaminant. The objective of this study was to quantify the mass distribution of compounds produced during sequential electrolytic oxidation and reduction of ordinance related compounds (ORCs) in a laboratory analog to an e(-) barrier. In this study, a series of column tests were conducted using RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) and TNT (2,4,6-trinitrotoluene) as representative ORCs. The experimental setup consisted of a plexiglass column packed with quartz-feldspar sand to simulate aquifer conditions. A single set of porous electrodes consisting of expanded titanium-mixed metal oxide mesh was placed at the midpoint of the sand column as a one-dimensional analog to an e(-) barrier. Constant current of 20mA (variable voltage) was applied to the electrode set. Initial studies involved quantification of reaction products using unlabeled RDX and TNT. Approximately 70% of the influent concentration was transformed, in one pass, through sequential oxidation-reduction for both contaminants. Following the unlabeled studies, (14)C labeled RDX and TNT were introduced to determine the mass balance. An activity balance of up to 96% was achieved for both (14)C-RDX and (14)C-TNT. For both contaminants, approximately 21% of the influent activity was mineralized to (14)CO(2). The proportion of the initial activity in the dissolved fraction was different for the two test contaminants. Approximately 30% of the initial (14)C-RDX was recovered as unreacted in the dissolved phase. The balance of the (14)C-RDX was recovered as non-volatile, non-nitroso transformation products. None of the (14)C-RDX was sorbed to the column sand packing. For (14)C-TNT approximately 51% of the initial activity was recovered in the dissolved phase, the majority was unreacted TNT. The balance of the (14)C-TNT was either sorbed to the sand packing (approximately 24%) or dissolved/mineralized as unidentified ring cleavage products ( approximately 4%).

Carbon Radioisotopes↗
PubMed2005

Spatio-temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells.

The extent to which chromosomal domains are reorganized within the nucleus during differentiation is central to our understanding of how cells become committed to specific developmental lineages. Spatio-temporal patterns of DNA replication are a reflection of this organization. Here, we demonstrate that the temporal order and relative duration of these replication patterns during S-phase are similar in murine pluripotent embryonic stem (ES) cells, primary adult myoblasts, and an immortalized fibroblast line. The observed patterns were independent of fixation and denaturation techniques. Importantly, the same patterns were detected when fluorescent nucleotides were introduced into living cells, demonstrating their physiological relevance. These data suggest that heritable gene silencing during commitment to specific cell lineages is not mediated by global changes in the sub-nuclear organization and replication timing of chromosome domains.

Animals↗
PubMed2005

Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states.

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.

Animals↗
PubMed2004

Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores.

The replication timing of some genes is developmentally regulated, but the significance of replication timing to cellular differentiation has been difficult to substantiate. Studies have largely been restricted to the comparison of a few genes in established cell lines derived from different tissues, and most of these genes do not change replication timing. Hence, it has not been possible to predict how many or what types of genes might be subject to such control. Here, we have evaluated the replication timing of 54 tissue-specific genes in mouse embryonic stem cells before and after differentiation to neural precursors. Strikingly, genes residing within isochores rich in GC and poor in long interspersed nuclear elements (LINEs) did not change their replication timing, whereas half of genes within isochores rich in AT and long interspersed nuclear elements displayed programmed changes in replication timing that accompanied changes in gene expression. Our results provide direct evidence that differentiation-induced autosomal replication-timing changes are a significant part of mammalian development, provide a means to predict genes subject to such regulation, and suggest that replication timing may be more related to the evolution of metazoan genomes than to gene function or expression pattern.

Animals↗
PubMed2004

Heterochromatin and tri-methylated lysine 20 of histone H4 in animals.

Tri-methylated lysine 20 on histone H4 (Me(3)K20H4) is a marker of constitutive heterochromatin in murine interphase and metaphase cells. Heterochromatin marked by Me(3)K20H4 replicates late during S phase of the cell cycle. Serum starvation increases the number of cells that exhibit high levels of Me(3)K20H4 at constitutive heterochromatin. Me(3)K20H4 is also present at the centromeric heterochromatin of most meiotic chromosomes during spermatogenesis and at the pseudoautosomal region, as well as at some telomeres. It is not present on the XY-body. During murine embryogenesis the maternal pronucleus contains Me(3)K20H4; Me(3)K20H4 is absent from the paternal pronucleus. On Drosophila polytene chromosomes Me(3)K20H4 is present in a 'punctate pattern' at many chromosomal bands, including the chromocenter. In coccids it is present on the facultatively heterochromatinised paternal chromosome set. We also present evidence that Me(3)K20H4 is dependent upon H3-specific Suv(3)9 histone methyltransferase activity, suggesting that there may be 'epigenetic cross-talk' between histones H3 and H4.

Animals↗
PubMed2004

The future of human embryonic stem cell research: addressing ethical conflict with responsible scientific research.

Embryonic stem (ES) cells have almost unlimited regenerative capacity and can potentially generate any body tissue. Hence they hold great promise for the cure of degenerative human diseases. But their derivation and the potential for misuse have raised a number of ethical issues. These ethical issues threaten to paralyze pubic funding for ES cell research, leaving experimentation in the hands of the private sector and precluding the public's ability to monitor practices, research alternatives, and effectively address the very ethical issues that are cause for concern in the first place. With new technology being inevitable, and the potential for abuse high, government must stay involved if the public is to play a role in shaping the direction of research. In this essay, I will define levels of ethical conflict that can be delineated by the anticipated advances in technology. From the urgent need to derive new ES cell lines with existing technology, to the most far-reaching goal of deriving genetically identical tissues from an adult patients cells, technology-specific ethical dilemmas can be defined and addressed. This staged approach provides a solid ethical framework for moving forward with ES cell research. Moreover, by anticipating the moral conflicts to come, one can predict the types of scientific advances that could overcome these conflicts, and appropriately direct federal funding toward these goals to offset potentially less responsible research directives that will inevitably go forward via private or foreign funding.

Bioethics↗
PubMed2004

Structure of a palindromic amplicon junction implicates microhomology-mediated end joining as a mechanism of sister chromatid fusion during gene amplification.

Amplification of the copy number of oncogenes is frequently associated with tumor progression. Often, the amplified DNA consists of large (tens to hundreds of kilobases) 'head-to-head' inverted repeat palindromes (amplicons). Several mechanisms have been proposed to explain palindrome formation but their relative contributions in nature have been difficult to assess without precise knowledge of the sequences involved at the junction of natural amplicons. Here, we have sequenced one such junction and compared this sequence to the un-rearranged structure, allowing us to pinpoint the site of sister chromatid fusion. Our results support a novel model, consistent with all described sister chromatid fusions, in which sister chromatid fusion is initiated by microhomology-mediated end joining of double strand breaks.

Animals↗
PubMed2004

In search of the holy replicator.

After 40 years of searching for the eukaryotic replicator sequence, it is time to abandon the concept of 'the' replicator as a single genetic entity. Here I propose a 'relaxed replicon model' in which a positive initiator-replicator interaction is facilitated by a combination of several complex features of chromatin. An important question for the future is whether the positions of replication origins are simply a passive result of local chromatin structure or are actively localized to coordinate replication with other chromosomal activities.

Animals↗
PubMed2004

RB reversibly inhibits DNA replication via two temporally distinct mechanisms.

The retinoblastoma (RB) tumor suppressor is a critical negative regulator of cellular proliferation. Repression of E2F-dependent transcription has been implicated as the mechanism through which RB inhibits cell cycle progression. However, recent data have suggested that the direct interaction of RB with replication factors or sites of DNA synthesis may contribute to its ability to inhibit S phase. Here we show that RB does not exert a cis-acting effect on DNA replication. Furthermore, the localization of RB was distinct from replication foci in proliferating cells. While RB activation strongly attenuated the RNA levels of multiple replication factors, their protein expression was not diminished coincident with cell cycle arrest. During the first 24 h of RB activation, components of the prereplication complex, initiation factors, and the clamp loader complex (replication factor C) remained tethered to chromatin. In contrast, the association of PCNA and downstream components of the processive replication machinery was specifically disrupted. This signaling from RB occurred in a manner dependent on E2F-mediated transcriptional repression. Following long-term activation of RB, we observed the attenuation of multiple replication factors, the complete cessation of DNA synthesis, and impaired replicative capacity in vitro. Therefore, functional distinctions exist between the "chronic" RB-mediated arrest state and the "acute" arrest state. Strikingly, attenuation of RB activity reversed both acute and chronic replication blocks. Thus, continued RB action is required for the maintenance of two kinetically and functionally distinct modes of replication inhibition.

Alleles↗