Dataset Information

Histone modifications during acute S-phase defects

ABSTRACT: Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these functional defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly during DNA replication and analyse effects n histone modifications by mass spectrometry. Immediately upon CAF-1 depletion from human TERT-RPE-1 cells, we observe an acute cellular response affecting histone repertoire, global chromatin composition and transcriptional fidelity resulting in a p53-dependent cell cycle arrest. Our work reveals the immediate local and global consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.

INSTRUMENT(S): Orbitrap Exploris 240

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Moritz Voelker-Albert

LAB HEAD: Francesca Mattiroli

PROVIDER: PXD050618 | Pride | 2024-11-14

REPOSITORIES: Pride

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			Action	DRS
	Hubrecht_Institute_20231120_SdS_DDA_Mattiroli_G1_rep1.raw	Raw
	Hubrecht_Institute_20231120_SdS_DDA_Mattiroli_G1_rep2.raw	Raw
	Hubrecht_Institute_20231120_SdS_DDA_Mattiroli_G1_rep3.raw	Raw
	Hubrecht_Institute_20231120_SdS_DDA_Mattiroli_S_G2_Dmso_rep1.raw	Raw
	Hubrecht_Institute_20231120_SdS_DDA_Mattiroli_S_G2_Dmso_rep2.raw	Raw

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Publications

Acute multi-level response to defective de novo chromatin assembly in S-phase.

Dreyer Jan J Ricci Giulia G van den Berg Jeroen J Bhardwaj Vivek V Funk Janina J Armstrong Claire C van Batenburg Vincent V Sine Chance C VanInsberghe Michael A MA Marsman Richard R Mandemaker Imke K IK di Sanzo Simone S Costantini Juliette J Manzo Stefano G SG Biran Alva A Burny Claire C Völker-Albert Moritz M Groth Anja A Spencer Sabrina L SL van Oudenaarden Alexander A Mattiroli Francesca F

bioRxiv : the preprint server for biology 20240327

Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replica ...[more]

PMID: 38585916

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Project description:The meiotic cell division reduces the chromosome number from diploid to haploid to form gametes for sexual reproduction. Although much progress has been made in understanding meiotic recombination and the two meiotic divisions, the processes leading up to recombination, including the prolonged pre-meiotic S phase (meiS) and the assembly of meiotic chromosome axes, remain poorly defined. We have used genome-wide approaches in Saccharomyces cerevisiae to measure the kinetics of pre-meiotic DNA replication, and to investigate the interdependencies between replication and axis formation. We found that replication initiation was delayed for a large number of origins in meiS compared to mitosis, and that meiotic cells were far more sensitive to replication inhibition, most likely due to the starvation conditions required for meiotic induction. Moreover, replication initiation was delayed even in the absence of chromosome axes, indicating replication timing is independent of the process of axis assembly. Finally, we found that cells were able to install axis components and initiate recombination on unreplicated DNA. Thus, although pre-meiotic DNA replication and meiotic chromosome axis formation occur concurrently, they are not directly coupled. The functional separation of these processes reveals a modular method of building meiotic chromosomes, and predicts that any crosstalk between these modules must occur through superimposed regulatory mechanisms. Multiple studies of meiotic chromosomes were undertaken. To study DNA replication, the locations of replicative helicase (Mcm2-7) were mapped in pre-meiotic and pre-mitotic cells, and DNA replication profiles were created for pre-meiotic S (meiS) and pre-mitotic S (mitS) phases. Early origins were mapped in hydroxyurea for wild-type cells in mitS + 200mM HU, and meiS +20mM HU for wild-type, sml1, rec8 and spo11 deletion cells. Rec8, Hop1 and Red1 binding to meiotic chromosomes was evaluated using ChIP-chip in wild-type cells with and without 20 mM HU, and in cdc6-mn and clb5 clb6 delete cells. Finally, meiotic DNA double-strand breaks (DSBs) were mapped in cdc6-mn dmc1 delete cells by measuring the ssDNA that accumulates at DSB hotspots. This SuperSeries is composed of the following subset Series: GSE35658: Chromatin IP for Mcm2-7, Rec8, Hop1 and Red1 GSE35662: S phase and HU profiles in wild-type and mutant cells GSE35666: DSB formation in replication compromised cells

Dataset Information

Histone modifications during acute S-phase defects

Dataset's files

Publications

Acute multi-level response to defective <i>de novo</i> chromatin assembly in S-phase.

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