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| Status |
Public on Aug 21, 2015 |
| Title |
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
A central question in biology is how enhancers are made accessible. The Drosophila embryo is a good model system to study this question as the gene regulatory networks regulating early developmental events have been well characterized. Zelda (Zld) is a uniformly distributed transcription factor (TF) integral to these networks, acting prior to and in collaboration with the patterning TFs to regulate target enhancers. Here we test the hypothesis that Zld directs TF binding, examplified by Dorsal (Dl) which patterns the dorsoventral axis, across the genome by displacing nucleosomes at enhancers. By performing ChIP-seq and MNase-seq experiments on early embryos with or without Zld, we demonstrated that early enhancers are characterized by an intrinsically high nucleosome barrier, which is overcome by Zld, and that without Zld, Dl binding decreases at enhancers and redistributes to open regions devoid of enhancer activity. We propose that enhancers are initially specified across the genome by the binding of Zld, which locally decreases nucleosome occupancy, thereby assisting TFs in accessing their binding motifs and promoting transcriptional activity.
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| Overall design |
Zld, Dl, Pol II ChIP-seq and MNase-seq profiles comparing 2-3h wild-type (wt) and zld- embryos, and MNase-seq profiles comparing 2-4h wt and gd7 embryos, all in 2 replicates
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| Contributor(s) |
Sun Y, Nien C, Chen K, Liu H, Johnston J, Koenecke N, Zeitlinger J, Rushlow C |
| Citation(s) |
26335633 |
| Submission date |
Jan 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christine Rushlow |
| E-mail(s) |
car2@nyu.edu
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| Organization name |
NYU
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| Department |
Biology
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| Lab |
Rushlow
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| Street address |
100 Washington Sq. E. Room 1001
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platforms (3) |
| GPL11203 |
Illumina Genome Analyzer IIx (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA273997 |
| SRA |
SRP052975 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65441_Dl_DESeq.txt.gz |
147.4 Kb |
(ftp)(http) |
TXT |
| GSE65441_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of BW) |
| GSE65441_Zld_DESeq.txt.gz |
425.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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