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| Status |
Public on Apr 07, 2016 |
| Title |
Transcriptional regulators compete with nucleosomes post-replication |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, we have developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. We find that the characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII and remodelers minutes after replication fork passage.
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| Overall design |
Using MINCE-seq, we mapped the newly replicated and maturing chromatin landscape at promoters and enhancers. There are 24 samples, 12 input-pulldown pairs. Three of these pairs are biological replicates.
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| Contributor(s) |
Ramachandran S, Henikoff S |
| Citation(s) |
27062929 |
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| Submission date |
Dec 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (1) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (24)
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| GSM1974511 |
BG3_rep2_pd_(2015-01-13.4) |
| GSM1974512 |
dsCaf1_input_(2015-05-13.6,2015-05-21.6) |
| GSM1974513 |
dsCaf1_pd_(2015-05-13.10,2015-05-21.10) |
| GSM1974514 |
dsGFP_input_(2015-05-13.5,2015-05-21.5) |
| GSM1974515 |
dsGFP_pd_(2015-05-13.9,2015-05-21.9) |
| GSM1974516 |
EdU_labeling_rep_1_input_(2013-12-20.10,2014-01-07.10) |
| GSM1974517 |
EdU_labeling_rep_1_pd_(2013-12-20.12,2014-01-07.12) |
| GSM1974518 |
EdU_labeling_rep_2_input_(2013-12-20.11,2014-01-07.11) |
| GSM1974519 |
EdU_labeling_rep_2_pd_(2013-12-20.13,2014-01-07.13) |
| GSM1974520 |
Long_term_labeling_input_(2015-11-19.6) |
| GSM1974521 |
Long_term_labeling_pd_(2015-11-18.7) |
| GSM1974522 |
MNase_0.5X_input_(2015-11-18.8) |
| GSM1974523 |
MNase_0.5X_pd_(2015-11-18.9) |
| GSM1974524 |
MNase_1X_input_(2015-11-18.10) |
| GSM1974525 |
MNase_1X_pd_(2015-11-18.11) |
| GSM1974526 |
MNase_4X_input_(2015-11-18.12) |
| GSM1974527 |
MNase_4X_pd_(2015-11-18.19) |
| GSM1974528 |
Thymidine_Chase_rep_1_input_(2013-12-20.14,2014-01-07.14) |
| GSM1974529 |
Thymidine_Chase_rep_1_pd_(2013-12-20.1,2014-01-07.1) |
| GSM1974530 |
Thymidine_Chase_rep_2_input_(2013-12-20.15,2014-01-07.15) |
| GSM1974531 |
Thymidine_Chase_rep_2_pd_(2013-12-20.2,2014-01-07.2) |
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| Relations |
| BioProject |
PRJNA306358 |
| SRA |
SRP067519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76120_RAW.tar |
3.1 Gb |
(http)(custom) |
TAR (of BED, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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