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| Status |
Public on Sep 28, 2020 |
| Title |
Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans. |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation and fertility. Here we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in altered replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.
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| Overall design |
Characterization of replication timing and replication origins in C. elegans. Analysis of differences between wild type and H3.3 null mutants. ChEC-seq, Repli-Seq, EdU-seq data done in C. elegans with different replicates. Free MNase and gDNA for control
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| |
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| Contributor(s) |
Steiner FA, Strobino M |
| Citation(s) |
33172964 |
| |
| Submission date |
Nov 21, 2019 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Florian Steiner |
| E-mail(s) |
florian.steiner@unige.ch
|
| Phone |
+41 22 379 36 85
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| Organization name |
University of Geneva
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
Steiner
|
| Street address |
30, Quai Ernest-Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
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| Platforms (1) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
|
| Samples (63)
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| Relations |
| BioProject |
PRJNA591001 |
| SRA |
SRP231167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140804_CDT1_20C_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_20C_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_20C_0min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_20C_30min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_20C_60min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_25C_0min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_25C_30min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_EdU_WT_Fork_25C_60min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_Free_MNase_final.bed.gz |
696.5 Kb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_20C_0min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_20C_30min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_20C_60min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_25C_0min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_25C_30min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_GSE140804_EdU_Fork_25C_60min_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_MNase.bed.gz |
6.3 Mb |
(ftp)(http) |
BED |
| GSE140804_H3_TRES1_25C_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_N2_MNase.bed.gz |
7.7 Mb |
(ftp)(http) |
BED |
| GSE140804_Origins_Clustered.bed.gz |
23.0 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_Domains.bed.gz |
2.3 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_GSE140804_H3_Early_final.bed.gz |
144.2 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_GSE140804_H3_Late_final.bed.gz |
144.1 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_GSE140804_H3_mid_final.bed.gz |
144.7 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_WT_Early_final.bed.gz |
144.3 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_WT_Late_final.bed.gz |
144.0 Kb |
(ftp)(http) |
BED |
| GSE140804_Repliseq_WT_mid_final.bed.gz |
144.6 Kb |
(ftp)(http) |
BED |
| GSE140804_TRES1_20C_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_TRES1_25C_WT_final.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE140804_gDNA_HU_final.bed.gz |
666.2 Kb |
(ftp)(http) |
BED |
| GSE140804_gDNA_final.bed.gz |
71.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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