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| Status |
Public on Apr 23, 2015 |
| Title |
High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
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| Summary |
At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, which genetic and chromatin features define metazoan replication start sites remains largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and show their ability to transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence specificity, mark and predict replication origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship between DNA topology, chromatin, transcription and replication initiation across metazoa.
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| Overall design |
Our dataset consists of SNS-Seq profiles in Drosophila S2 and Bg3 cells. Small nascent leading strands (SNS) have been purified with an enhanced sensitivity SNS purification protocol. For standard SNS-Seq experiments (from pooled gradient fractions, denoted as "pool"), SNS were purified from two biological replicates. For single-fraction SNS-Seq experiments, two libraries were prepared for each fraction. The genomic coordinates of S2 and Bg3 replication origins are also provided.
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| Contributor(s) |
Comoglio F, Schlumpf T, Schmid V, Rohs R, Beisel C, Paro R |
| Citation(s) |
25921534 |
| Submission date |
Feb 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico Comoglio |
| E-mail(s) |
federico.comoglio@bsse.ethz.ch
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| Organization name |
ETH Zurich
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| Department |
Department of Biosystems Science and Engineering
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| Lab |
Epigenomics Lab
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| Street address |
Mattenstrasse, 26
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| City |
Basel |
| State/province |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (9)
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| GSM1603251 |
SNS-Seq (pool) from S2 cells, pooling replicates 1 and 2 |
| GSM1603252 |
SNS-Seq (pool) from S2 cells, replicate 1 |
| GSM1603253 |
SNS-Seq (pool) from S2 cells, replicate 2 |
| GSM1603254 |
SNS-Seq (pool) from Bg3 cells, pooling replicates 1 and 2 |
| GSM1603255 |
SNS-Seq (pool) from Bg3 cells, replicate 1 |
| GSM1603256 |
SNS-Seq (pool) from Bg3 cells, replicate 2 |
| GSM1603257 |
SNS-Seq (single fraction) from S2 cells, fraction 4 (short SNS fragments) |
| GSM1603258 |
SNS-Seq (single fraction) from S2 cells, fraction 5 (middle-sized SNS fragments) |
| GSM1603259 |
SNS-Seq (single fraction) from S2 cells, fraction 6 (long SNS fragments) |
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| Relations |
| BioProject |
PRJNA274733 |
| SRA |
SRP053286 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65692_Bg3origins.txt.gz |
137.1 Kb |
(ftp)(http) |
TXT |
| GSE65692_F4origins.txt.gz |
37.7 Kb |
(ftp)(http) |
TXT |
| GSE65692_F5origins.txt.gz |
52.8 Kb |
(ftp)(http) |
TXT |
| GSE65692_F6origins.txt.gz |
48.1 Kb |
(ftp)(http) |
TXT |
| GSE65692_S2origins.txt.gz |
120.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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