The Mcm2-Ctf4-Pola axis facilitates parental histone transfer to lagging strands
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ABSTRACT:
PROVIDER: PRJNA486148 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7696330_1.fastq.gz | Fastqsanger.gz | |||
| SRR7696330_2.fastq.gz | Fastqsanger.gz | |||
| SRR7696340_1.fastq.gz | Fastqsanger.gz | |||
| SRR7696340_2.fastq.gz | Fastqsanger.gz | |||
| SRR7696350_1.fastq.gz | Fastqsanger.gz |
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Project description:Although essential for epigenetic inheritance, the transfer of parental histone (H3-H4)2 tetramers that contain epigenetic modifications to replicating DNA strands is poorly understood. Here, we show that the Mcm2-Ctf4-Pol axis facilitates the transfer of parental (H3-H4)2 tetramers to lagging strands of DNA replication forks. Mutating the H3-H4 binding domain of Mcm2, a subunit of the CMG (Cdc45-MCM-GINS) replicative helicase that translocates along leading strands, impairs the transfer of parental (H3-H4)2 to lagging strands. Similar effects are observed in Ctf4 and Pol-primase mutants that disrupt the connection of the CMG helicase via Ctf4-Pol to lagging strands. Our results support a model whereby parental (H3-H4)2 displaced from nucleosomes through leading-strand DNA replication are transferred to lagging strands for nucleosome assembly via the CMG-Ctf4-Pol complex.
2018-09-24 | GSE118580 | GEO
Project description:Chromatin replication is intricately intertwined with DNA replication, and the recycling of parental histones is essential for epigenetic inheritance. The transfer of parental histones to both the DNA replication leading and lagging strands involves two distinct pathways: the leading strand utilizes DNA polymerase ε subunits Dpb3/Dpb4, while the lagging strand is facilitated by the MCM helicase subunit Mcm2. However, the process by which Mcm2, moving along the leading strand, facilitates the transfer of parental histones to the lagging strand remains unclear. Our study reveals that the deletion of Pol32, a non-essential subunit of major lagging-strand DNA polymerase δ, results in a predominant transfer of parental histone H3-H4 to the replication leading strand. Biochemical analyses further demonstrate that Pol32 can bind histone H3-H4 both in vivo and in vitro. The interaction of Pol32 with parental histone H3-H4 is disrupted by the mutation of Mcm2's histone H3-H4 binding domain. In conclusion, our findings identify the DNA polymerase delta subunit Pol32 as a novel key histone chaperone downstream of Mcm2, mediating the transfer of parental histones to the lagging strand during DNA replication.
2024-04-24 | GSE252049 | GEO
Project description:How parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications, are transferred to leading and lagging strands of DNA replication forks following DNA replication is an important question that remains not well understood. Here we show that DNA polymerase clamp PCNA and its partner involved in lagging strand DNA synthesis, Pol d, regulate parental histone transfer to lagging strands. Mutations at PCNA as well as at subunits of Pol d that impair the PCNA-Pol d interaction affect parental histone transfer to lagging strands, and this defect unlikely arises from their impacts on DNA synthesis. Moreover, Pol d interacts with H3-H4 in vitro. We suggest that the PCNA-Pol d complex, best known for its role in lagging strand DNA synthesis and DNA repair, couples lagging strand DNA synthesis to the transfer of the parental histones H3-H4 for the inheritance of chromatin structures following DNA replication and possibly DNA repair.
2024-05-31 | GSE203465 | GEO
Project description:Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion (dpb3[DELTA]) or Mcm2 mutation (mcm2-3A), which each disrupt one parental histone transfer pathway, leads to the other[prime]s predominance. However, the impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3[DELTA]/mcm2-3A double mutant did not exhibit the single dpb3[DELTA] and mcm2-3A mutants[prime] asymmetric parental histone patterns, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3[DELTA], mcm2-3A, and dpb3[DELTA]/mcm2-3A mutants relative to the wild-type strain, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones to the leading and lagging strands during DNA replication is essential for maintaining chromatin structure and that high levels of free histones due to parental histone transfer defects are detrimental to cells.
2024-04-24 | GSE240331 | GEO
Project description:Although essential for epigenetic inheritance, the transfer of parental histone (H3-H4)2 tetramers that contain epigenetic modifications to replicating DNA strands is poorly understood. Here, we show that the Mcm2-Ctf4-Pol? axis facilitates the transfer of parental (H3-H4)2 tetramers to lagging-strand DNA at replication forks. Mutating the conserved histone-binding domain of the Mcm2 subunit of the CMG (Cdc45-MCM-GINS) DNA helicase, which translocates along the leading-strand template, results in a marked enrichment of parental (H3-H4)2 on leading strand, due to the impairment of the transfer of parental (H3-H4)2 to lagging strands. Similar effects are observed in Ctf4 and Pol? primase mutants that disrupt the connection of the CMG helicase to Pol? that resides on lagging-strand template. Our results support a model whereby parental (H3-H4)2 complexes displaced from nucleosomes by DNA unwinding at replication forks are transferred by the CMG-Ctf4-Pol? complex to lagging-strand DNA for nucleosome assembly at the original location.
| S-EPMC6193272 | biostudies-literature
Project description:During DNA replication parental, nucleosomic histones are segregated almost symmetrically to the two daughter DNA strands enabling mitotic inheritance of histones and their PTMs. In MCM2 histone-binding mutant ESCs (MCM2-2A), histones are recycled asymmetrically to the leading strand. To evaluate if loss of parental histones contributes to the asymmetry, we tracked new and old histones quantitatively by pulse-Triple-SILAC-MS. The quantification showed no change in dilution and incorporation dynamics in MCM2-2A cells, demonstrating that parental histones are not lost at replication forks but re-routed from the lagging to the leading strand.
2023-08-30 | PXD030364 | Pride
Project description:How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we develop the eSPAN method (enrichment and sequencing of protein associated nascent DNA) in mouse embryonic stem (ES) cells, which detects the distribution of histones with distinct modifications on leading and lagging strands in a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes primers used for synthesis of both leading and lagging strands, binds histone H3-H4 preferentially. The Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strand in both yeast and mouse ES cells. Finally, dysregulation of both coding genes and non-coding endogenous retroviruses (ERVs) is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication coupled processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.
2020-09-02 | GSE142996 | GEO
Project description:Chromatin-based epigenetic memory relies on the accurate distribution of parental histone tetramers to newly replicated DNA strands, serving as templates for chromatin structure duplication. Mcm2, a subunit of the replicative helicase, and the Dpb3/4, subunits of polymerase epsilon, govern parental histone deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here we show in fission yeast that a Mcm2 histone chaperone mutation severely disrupts heterochromatin inheritance, while Dpb3/4 mutations cause only moderate defects. Surprisingly, simultaneous Mcm2 and Dpb3/4 mutations stabilizes heterochromatin inheritance. eSPAN analyses confirm the conservation of Mcm2 and Dpb3/4 functions in parental histone segregation, with their collective absence reducing segregation bias. Furthermore, the FACT histone chaperone also regulates parental histone transfer independently of strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone density, ensuring faithful heterochromatin inheritance. These results underscore the importance of precise parental histone segregation to the lagging strand for epigenetic inheritance and unveil unique properties of parental histone chaperones during DNA replication.
2024-04-17 | GSE237770 | GEO
Project description:Parental histone recycling is essential for the restoration of chromatin-based epigenetic information during chromatin replication; however, the specific mechanisms underlying the local recycling of parental histones remain poorly understood. Here, we reveal an unexpected role of the Spt16-N domain in histone chaperone FACT during parental histone recycling and transfer in budding yeast. We found that depletion of Spt16 or mutations in the Spt16 middle domain leads to defects in both parental histone recycling and new histone deposition, affecting both the leading and lagging strands of DNA replication forks, highlighting the essential role of the FACT complex in both parental histone recycling and new histone deposition. Surprisingly, Spt16-N deletion results in an apparent defect in parental histone recycling, with a more pronounced defect on the lagging strand than the corresponding leading strand. Mechanistically, the Spt16-N domain acts as a protective barrier, shielding FACT-bound histone H3-H4 and facilitating its interaction with Mcm2, which ensures efficient local parental histone recycling. Collectively, the Spt16-N domain provides a protein–protein interaction module allowing FACT to act as a shuttle chaperone, cooperate with multiple replisome components, which act as co-chaperones, to form a complex involving the shuttle chaperone, histones, and co-chaperones, during parental histone recycling and transfer.
2024-01-26 | PXD043392 | Pride
Project description:In eukaryotic cells, inheritable changes in gene expression in response to environmental and developmental stimuli is associated with changes in histone modifications and relies on the passage of these changes into daughter cells during cell division, a process that remains elusive. Here, we show that parental histone (H3-H4)2 tetramers, the primary carrier of epigenetic modifications, are assembled into nucleosomes onto both replicating leading and lagging strands, with a preference for lagging strands of DNA replication forks. This asymmetric distribution of parental (H3-H4)2 is exacerbated in cells lacking Dpb3 and Dpb4, two subunits of DNA polymerase Pol ε. Dpb3-Dpb4 binds (H3-H4)2 and participates in the transfer of parental (H3-H4)2 tetramers onto leading strands of DNA replication forks. Cells lacking Dpb3 and Dpb4 exhibits defects in epigenetic inheritance. These results reveal a previously undocumented mechanism of histone segregation and a direct role for Pol ε in this poorly understood process.
2018-08-28 | GSE112522 | GEO