|
| Status |
Public on May 18, 2021 |
| Title |
Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans |
| Organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae; Homo sapiens; Mus musculus x Mus spretus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S-phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed identical individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution. Nonetheless, most fluctuations in replication timing in all four organisms could be accounted for by differences in chromosomal MCM distribution. We conclude that, although certain genomic regions, most notably the inactive X-chromosome, are subject to post-licensing regulation, most differences in replication timing along the chromosome reflect uneven chromosomal distribution of stochastically firing pre-replication complexes.
|
| |
|
| Overall design |
MCM helicase genes are tagged with micrococcal nuclease (MNase), arrested in G1, MNase is activated with calcium, DNA is subjected to high throughput sequencing (all 4 organisms); sonicated DNA is isolated from flow-sorted cells from S phase and G1 and subjected to high throughput sequencing (mouse only).
We used the MCM2-Mnase fusion proteins to identify the sites of binding of the MCM replicative helicase in budding yeast, fission, mouse and humans.
|
| |
|
| Contributor(s) |
Foss EJ, Sripathy S, Gatbonton-Schwager T, Kwak H, Thiesen AH, Lao U, Bedalov A |
| Citation(s) |
34473702 |
| |
| Submission date |
May 18, 2020 |
| Last update date |
Sep 23, 2021 |
| Contact name |
Eric Jan Foss |
| E-mail(s) |
efoss@fredhutch.org
|
| Phone |
206 667 5832
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Clinical Research Division
|
| Lab |
Antonio Bedalov
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17225 |
Illumina HiSeq 2500 (Schizosaccharomyces pombe) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
| GPL29362 |
Illumina HiSeq 2500 (Mus musculus x Mus spretus) |
|
| Samples (22)
|
|
| Relations |
| BioProject |
PRJNA633612 |
| SRA |
SRP262200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150800_cerevisiae_MCM2ChEC_MCM4ChEC_MCM6ChEC_read_depths_3_size_ranges_081121_1.txt.gz |
42.5 Mb |
(ftp)(http) |
TXT |
| GSE150800_mm10_musculusSNPStospretusSNPs.fasta.gz |
775.5 Mb |
(ftp)(http) |
FASTA |
| GSE150800_musculus_G1_sonicated_081121_1.bedgraph.gz |
145.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_musculus_S_sonicated_081121_1.bedgraph.gz |
144.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_pombe_MCM2ChEC_HU_G1_read_depths_3_size_ranges_081121_1.txt.gz |
59.7 Mb |
(ftp)(http) |
TXT |
| GSE150800_processed_cerevisiae_free_MNase_rep1_081221_1.txt.gz |
42.4 Mb |
(ftp)(http) |
TXT |
| GSE150800_processed_human_MCM2ChEC_mergereps1and2_bin100.bedgraph.gz |
198.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_processed_mouse_MCM2ChEC_mergereps1to3_musculus_reads_bin1000_080621_1.bedgraph.gz |
17.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_processed_mouse_MCM2ChEC_mergereps1to3_spretus_reads_bin1000_080621_1.bedgraph.gz |
17.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_processed_pombe_MCM2ChEC_HU_rep2_080621_1.txt.gz |
41.4 Mb |
(ftp)(http) |
TXT |
| GSE150800_processed_pombe_free_MNase_rep1_081221_1.txt.gz |
36.4 Mb |
(ftp)(http) |
TXT |
| GSE150800_spretus_G1_sonicated_081121_1.bedgraph.gz |
142.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE150800_spretus_S_sonicated_081121_1.bedgraph.gz |
141.3 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
Less...
More...