Replication Timing Of Genes Research Articles

Three classes of recurrent DNA break clusters in brain progenitors identified by 3D proximity-based break joining assay

We recently discovered 27 recurrent DNA double-strand break (DSB) clusters (RDCs) in mouse neural stem/progenitor cells (NSPCs). Most RDCs occurred across long, late-replicating RDC genes and were found only after mild inhibition of DNA replication. RDC genes share intriguing characteristics, including encoding surface proteins that organize brain architecture and neuronal junctions, and are genetically implicated in neuropsychiatric disorders and/or cancers. RDC identification relies on high-throughput genome-wide translocation sequencing (HTGTS), which maps recurrent DSBs based on their translocation to "bait" DSBs in specific chromosomal locations. Cellular heterogeneity in 3D genome organization allowed unequivocal identification of RDCs on 14 different chromosomes using HTGTS baits on three mouse chromosomes. Additional candidate RDCs were also implicated, however, suggesting that some RDCs were missed. To more completely identify RDCs, we exploited our finding that joining of two DSBs occurs more frequently if they lie on the same cis chromosome. Thus, we used CRISPR/Cas9 to introduce specific DSBs into each mouse chromosome in NSPCs that were used as bait for HTGTS libraries. This analysis confirmed all 27 previously identified RDCs and identified many new ones. NSPC RDCs fall into three groups based on length, organization, transcription level, and replication timing of genes within them. While mostly less robust, the largest group of newly defined RDCs share many intriguing characteristics with the original 27. Our findings also revealed RDCs in NSPCs in the absence of induced replication stress, and support the idea that the latter treatment augments an already active endogenous process.

Robustness of synthetic oscillators in growing and dividing cells

Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator. More recently, Stricker etal. [Nature(London) 456, 516 (2008)NATUAS0028-083610.1038/nature07389] presented another synthetic oscillator, called the dual-feedback oscillator, which is more stable. Detailed studies have been carried out to determine how the stability of these oscillators is affected by the intrinsic noise of the interactions between the components and the stochastic expression of their genes. However, as all biological oscillators reside in growing and dividing cells, an important question is how these oscillators are perturbed by the cell cycle. In previous work we showed that the periodic doubling of the gene copy numbers due to DNA replication can couple not only natural, circadian oscillators to the cell cycle [Paijmans et al., Proc. Natl. Acad. Sci. (USA) 113, 4063 (2016)PNASA60027-842410.1073/pnas.1507291113], but also these synthetic oscillators. Here we expand this study. We find that the strength of the locking between oscillators depends not only on the positions of the genes on the chromosome, but also on the noise in the timing of gene replication: noise tends to weaken the coupling. Yet, even in the limit of high levels of noise in the replication times of the genes, both synthetic oscillators show clear signatures of locking to the cell cycle. This work enhances our understanding of the design of robust biological oscillators inside growing and diving cells.

GATA-1 DNA Binding Activity Is Down-regulated in Late S Phase in Erythroid Cells

We have set out to test a model for tissue-specific gene expression that relies on the early replication of expressed genes to sequester limiting activating transcription factors. Using an erythroid cell line, we have tested the changes in the DNA binding activity of the lineage-restricted transcription factor GATA-1 through the cell cycle. We find that GATA-1 activity is low in G1, peaks in mid-S phase, and then decreases in G2/M. In contrast, the binding activities of two ubiquitous transcription factors, Oct1 and Sp1, remain high in G2/M. GATA-1 protein and mRNA vary in a similar manner through the cell cycle, suggesting that the expression of the gene or the stability of its message is regulated. Although a number of transcription factors involved in the control of the cell cycle or DNA replication have been shown to peak in S phase, this is the first example of a lineage-restricted transcription factor displaying S phase-specific DNA binding activity. One interpretation of these data leads to a model in which the peak in GATA-1 DNA binding amplifies the effect of early replication on the activation of erythroid-specific genes at the same time as preventing activation of non-erythroid genes containing GATA-responsive elements. These results may also relate to recent data implicating GATA-1 function in apoptosis and cell cycle progression.

Timing of replication of differentially transcribed genes in Syrian hamster embryo fibroblasts.

Syrian hamster embryo cell lines have been used as models of neoplastic progression in vitro. Changes in phenotype and biological properties have been observed in these cell lines in association with modulation of gene transcription. We explored this natural evolution of cells in culture to investigate the reported relationship between transcriptional activity and replication in early S phase. In this study we used two nontumorigenic cell lines that had either retained (supB+) or lost (supB-) the ability to suppress tumorigenicity of malignantly transformed hamster fibroblasts (BP6T). In association with the loss of suppressor gene function, supB- cells have downregulated the expression of the H19 and tropomyosin-I (TM-I) genes, which are actively transcribed in supB+ cells. Synchronous populations of supB+ and supB- cells were pulse-labeled with [3H]thymidine and bromodeoxyuridine at 1-h intervals during S phase; the replicating DNA was isolated by centrifugation in cesium chloride gradients and hybridized to 32P-labeled gene probes. No correlation was found between the timing of gene replication and the status of expression of these two genes. TM-I replicated during the first hour and H19 replicated between the second and third hours of the S phase in the expressing and nonexpressing cell lines. Immunoglobulin gene sequences, known to be late-replicating in fibroblasts, replicated at the end of the S phase. These results suggest that downregulation of transcription is not always accompanied by a concomitant change in time of gene replication from early to late S phase.

Replication timing of genes and middle repetitive sequences.

DNA replication in mammals is temporally bimodal. "Housekeeping" genes, which are active in all cells, replicate during the first half of the S phase of cell growth. Tissue-specific genes replicate early in those cells in which they are potentially expressed, and they usually replicate late in tissues in which they are not expressed. Replication during the first half of the S phase is, therefore, a necessary but not sufficient condition for gene transcription. A change in the replication timing of a tissue-specific gene appears to reflect the commitment of that gene to transcriptional competence or to quiescence during ontogeny. Most families of middle repetitive sequences replicate either early or late. These data are consistent with a model in which two functionally distinct genomes coexist in the nucleus.

Changes in gene position are accompanied by a change in time of replication

The globin and immunoglobulin multigene families have been used to study the effect of chromosomal organization on the time of gene replication. Some of the genes are late-replicating, providing the first identification of late-replicating sequences that are not highly repetitive. One is a member of the mouse α-globin gene family, which consists of genes mapping to three different chromosomes. The other genes in this family replicate early during S. Our studies demonstrate that immunoglobulin gene rearrangements and rearrangements between these genes and the c- myc oncogene are accompanied by dramatic differences in their temporal order of replication. We conclude that a gene's position in the chromosome, rather than its sequence, determines the time of replication. We suggest that the differences in association with gene rearrangement result from changes in the proximity of the affected gene to sites that control the temporal order of replication during S.

Identifying sites of simultaneous DNA replication in eukaryotes by N-methyl-N′-nitro-N-nitrosoguanidine multiple mutagenesis

N-methyl-N'-nitro-N-nitrosoguanidine (NG) induces certain classes of multiple mutations in yeast at high frequency. By selecting for mutation at one locus (his4 or leu1) one frequently obtains double mutants where another mutation to temperature sensitivity has also been induced. This multiple mutagenesis exhibits a considerable specificity: for mutation at one particular locus there is a high chance that another mutation will be found in the same cell at one of a restricted number of other loci. For any given locus (e.g. his4) there is a spectrum of sites at which temperature-sensitivity mutations are co-induced. This spectrum differs for different loci, such that the spectrum of sites co-mutating with leu1 differs completely from that for sites co-mutating with his4. This NG'induced co-mutation is interpreted in terms of NG acting to enhance mutagenesis at sites of simultaneous DNA replication within the cell. The results so obtained indicate a very strict control over the order and timing of gene replication in Saccharomyces cerevisiae, and it is suggested that it is now possible to use NG double mutagenesis to try and locate origins of replication in yeast.