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Series GSE262518 Query DataSets for GSE262518
Status Public on Apr 17, 2024
Title Acute multi-level response to defective de novo chromatin assembly in S-phase
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary 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 replication speed and renders nascent DNA hyper-accessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. As a result, histone variants usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.
 
Overall design RPE1 degron cell line was treated for 2h with or DMSO (ctrl) or 1µM dTAG-V1 to induce CHAF1A degradation and disrupt de novo nucleosme assembly. Treated cells where then subjected to Repli-ATAC-seq, VASA-seq and scEdU-seq experiments to assess chromatin accessibility, transcriptome and DNA replication dynamics.
 
Contributor(s) Ricci G, Bhardwaj V, van den Berg J, Mattiroli F
Citation(s) 38585916
Submission date Mar 26, 2024
Last update date Apr 18, 2024
Contact name Francesca Mattiroli
E-mail(s) f.mattiroli@hubrecht.eu
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (72)
GSM8170823 repli-ATAC replicate 1 Nascent chromatin DMSO
GSM8170824 repli-ATAC replicate 1 Nascent chromatin dTAG
GSM8170825 repli-ATAC replicate 1 Mature 2h chromatin DMSO
Relations
BioProject PRJNA1092098

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE262518_RAW.tar 1.1 Gb (http)(custom) TAR (of BED, BW, TSV)
GSE262518_VASA_CAF1_rep1.tar.gz 79.4 Mb (ftp)(http) TAR
GSE262518_VASA_CAF1_rep2.tar.gz 77.1 Mb (ftp)(http) TAR
GSE262518_VASA_WT.tar.gz 43.7 Mb (ftp)(http) TAR
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