Chromatin structure restricts origin utilization when quiescent cells re-enter the cell cycle
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ABSTRACT:
PROVIDER: PRJNA655722 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12403409.fastq.gz | Fastqsanger.gz | |||
| SRR12403410.fastq.gz | Fastqsanger.gz | |||
| SRR12403411.fastq.gz | Fastqsanger.gz | |||
| SRR12403412.fastq.gz | Fastqsanger.gz | |||
| SRR12403413.fastq.gz | Fastqsanger.gz |
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Project description:Quiescent cells reside in G0 phase, which is characterized by the absence of cell growth and proliferation. These cells remain viable and re-enter the cell cycle when prompted by appropriate signals. Using a budding yeast model of cellular quiescence, we investigated the program that initiated DNA replication when these G0 cells resumed growth. We performed BrdU IP-Seq to examine the DNA replication profile genome-wide. These data revealed that the initiation of replication was delayed and fewer origins were active when G0 cells entered the cell cycle compared to the entry of G1 cells into S phase. We found that both the transcript and protein levels of these replication factors were significantly diminished during the development of proliferating cells into quiescence. The levels of these factors, including MCM2-7 helicase, increased as G0 cells re-entered the cell cycle, suggesting that the replication program is re-established de novo. Consistent with these results, Mcm4 ChIP-seq analysis showed fewer and reduced binding at a number of origins during the re-entry of G0 cells into the cell cycle. In support of this evidence, the chromatin context surrounding inactive origins of G0 cells exhibits greater increased nucleosome occupancy and reduced periodicity of nucleosome positioning. Altogether, these observations provide insights into the important role of chromatin context that determines the ability of replication origin to accrue limiting replication factors during the the re-entry of quiescent cells into the cell cycle.
2020-08-07 | GSE155831 | GEO
Project description:Quiescent cells reside in G0 phase, which is characterized by the absence of cell growth and proliferation. These cells remain viable and re-enter the cell cycle when prompted by appropriate signals. Using a budding yeast model of cellular quiescence, we investigated the program that initiated DNA replication when these G0 cells resumed growth. Quiescent cells contained very low levels of replication initiation factors, and their entry into S phase was delayed until these factors were re-synthesized. A longer S phase in these cells correlated with the activation of fewer origins of replication compared to G1 cells. The chromatin structure around inactive origins in G0 cells showed increased H3 occupancy and decreased nucleosome positioning compared to the same origins in G1 cells, inhibiting the origin binding of the Mcm4 subunit of the MCM licensing factor. Thus, quiescent yeast cells are under-licensed during their re-entry into S phase.
| S-EPMC7826286 | biostudies-literature
Project description:We report gene expression patterns and chromatin architecture changes as yeast re-enter the cell cycle from quiescence
2021-02-16 | GSE166789 | GEO
Project description:phytoplankton exudate utilization by bacteria
| PRJEB44710 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE8542: BY4742 Quiescent and Non-quiescent replicates GSE8558: Proteinase K treatment of Q and NQ cells GSE8559: S288c Quiescent and Non-quiescent replicates GSE8560: Mutant1 GSE8561: Mutant2 Refer to individual Series
2010-05-29 | E-GEOD-8624 | biostudies-arrayexpress
Project description:Gene expression after mammosphere culture, quiescent single cells
| EGAD00010001964 | EGA
Project description:Adenoviruses force quiescent cells to re-enter the cell cycle to replicate their DNA, and for the most part, this is accomplished after they express the E1A protein immediately after infection. In this context, E1A is believed to inactivate cellular proteins (e.g., p130) that are known to be involved in the silencing of E2F-dependent genes that are required for cell cycle entry. However, the potential perturbation of these types of genes by E1A relative to their functions in regulatory networks and canonical pathways remains poorly understood. We have used DNA microarrays analyzed with Bayesian ANOVA for microarray (BAM) to assess changes in gene expression after E1A alone was introduced into quiescent cells from a regulated promoter. Approximately 2,401 genes were significantly modulated by E1A, and of these, 385 and 1033 met the criteria for generating networks and functional and canonical pathway analysis respectively, as determined by using Ingenuity Pathway Analysis software. After focusing on the highest-ranking cellular processes and regulatory networks that were responsive to E1A in quiescent cells, we observed that many of the up-regulated genes were associated with DNA replication, the cell cycle and cellular compromise. We also identified a cadre of up regulated genes with no previous connection to E1A; including genes that encode components of global DNA repair systems and DNA damage checkpoints. Among the down-regulated genes, we found that many were involved in cell signalling, cell movement, and cellular proliferation. Remarkably, a subset of these was also associated with p53-independent apoptosis, and the putative suppression of this pathway may be necessary in the viral life cycle until sufficient progeny have been produced. These studies have identified for the first time a large number of genes that are relevant to E1A’s activities in promoting quiescent cells to re-enter the cell cycle in order to create an optimum environment for adenoviral replication. Six independent cell cultures (n = 6) were randomly assigned to two treatment groups with three independent biological replicates per group. The control group, denoted ‘Q’, are quiescent cells without Doxycycline, i.e. no E1A expression (untreated for 8 hr, total RNA harvested 1 hour after). The stimulated group, denoted ‘S’, are stimulated cells with Doxycycline, i.e. with E1A expression (treated with Doxycycline for 8 hr, total RNA harvested 1 hour after treatment).
2011-05-01 | E-GEOD-28420 | biostudies-arrayexpress
Project description:Adenoviruses force quiescent cells to re-enter the cell cycle to replicate their DNA, and for the most part, this is accomplished after they express the E1A protein immediately after infection. In this context, E1A is believed to inactivate cellular proteins (e.g., p130) that are known to be involved in the silencing of E2F-dependent genes that are required for cell cycle entry. However, the potential perturbation of these types of genes by E1A relative to their functions in regulatory networks and canonical pathways remains poorly understood. We have used DNA microarrays analyzed with Bayesian ANOVA for microarray (BAM) to assess changes in gene expression after E1A alone was introduced into quiescent cells from a regulated promoter. Approximately 2,401 genes were significantly modulated by E1A, and of these, 385 and 1033 met the criteria for generating networks and functional and canonical pathway analysis respectively, as determined by using Ingenuity Pathway Analysis software. After focusing on the highest-ranking cellular processes and regulatory networks that were responsive to E1A in quiescent cells, we observed that many of the up-regulated genes were associated with DNA replication, the cell cycle and cellular compromise. We also identified a cadre of up regulated genes with no previous connection to E1A; including genes that encode components of global DNA repair systems and DNA damage checkpoints. Among the down-regulated genes, we found that many were involved in cell signalling, cell movement, and cellular proliferation. Remarkably, a subset of these was also associated with p53-independent apoptosis, and the putative suppression of this pathway may be necessary in the viral life cycle until sufficient progeny have been produced. These studies have identified for the first time a large number of genes that are relevant to E1A’s activities in promoting quiescent cells to re-enter the cell cycle in order to create an optimum environment for adenoviral replication.
2011-05-01 | GSE28420 | GEO
Project description:We have applied cryo-tomography and proteomics analyses to centrosomes isolated from young lamb thymus– a convenient source of quiescent and differentiated cells. Those analyses have allow us to better depict the protein organization joining the two centrioles in such a cellular system, in the form of a disperse network of fibers and an amorphous density, both parts linked together. Protein composition of the centrosome have been compared with published data on centrosome extracted from cell culture , and presence of various protein reported implicated in the disengagement and dissociation processes questioned. C-NAP1, cohesin smc1 and furthermore condensin smc4 and ncapd2 have been localized on the amorphous density, however DNA hasn't. Subtomogram averaging processing have been applied to the centriolar wall, both on the proximal microtubule triplets and distal doublets; results have been compared to the already published structures of centriolar wall triplet from distant species basal bodies.
2019-11-08 | PXD003928 | Pride
Project description:BackgroundQuiescent CD4+ T lymphocytes are highly refractory to HIV-1 infection due to a block at reverse transcription.ResultsExamination of SAMHD1 expression in peripheral blood lymphocytes shows that SAMHD1 is expressed in both CD4+ and CD8+ T cells at levels comparable to those found in myeloid cells. Treatment of CD4+ T cells with Virus-Like Particles (VLP) containing Vpx results in the loss of SAMHD1 expression that correlates with an increased permissiveness to HIV-1 infection and accumulation of reverse transcribed viral DNA without promoting transcription from the viral LTR. Importantly, CD4+ T-cells from patients with Aicardi-Goutières Syndrome harboring mutation in the SAMHD1 gene display an increased susceptibility to HIV-1 infection that is not further enhanced by VLP-Vpx-treatment.ConclusionHere, we identified SAMHD1 as the restriction factor preventing efficient viral DNA synthesis in non-cycling resting CD4+ T-cells. These results highlight the crucial role of SAMHD1 in mediating restriction of HIV-1 infection in quiescent CD4+ T-cells and could impact our understanding of HIV-1 mediated CD4+ T-cell depletion and establishment of the viral reservoir, two of the HIV/AIDS hallmarks.
| S-EPMC3494655 | biostudies-literature