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| Status |
Public on Feb 09, 2017 |
| Title |
Genome-wide maps of CREB/CRTC binding in Drosophila mushroom body. |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: Exploring the alteration in CREB/CRTC binding related to long-term memory
Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using Miseq, and aligned to dm3 using CLCbio. The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 1.5 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 2, and a density of reads at 0.12 for CREB and 0.2 for CRTC. The CREB and the CRTC binding sites were determined as the peak-called region in at least 2 samples out of the three replicates. The CREB and the CRTC binding sites located 200 bp vicinity to each other were defined as the CREB/CRTC binding sites. In parallel, the read counts were obtained in the 1 kb window covering entire genome and analyzed by DESeq2, to determine the region enriched with CREB/CRTC in a specific group of samples. The region with increased or decreased CREB/CRTC binding were determined if the region were defined by the CREB/CRTC binding sites in the above criteria.
Results: Using an optimized data analysis workflow, the filtered reads amounted to 8-11million reads for CREB in each of 3 replicates, 8-17 million reads for CRTC in each of 3 replicates, and 4.4 million reads for input. Using anti-CREB antibody, we found 239 significant increases in CREB binding out of 4995 CREB/CRTC binding sites 1 day after training. Using anti-CRTC antibody, we found 4989 significant increases in CRTC binding out of 4995 CREB/CRTC binding sites 1 day after spaced training.
Conclusions: Our study shows that, although CREB binding is mostly unchanged, CRTC binding is significantly increased after long-term memory formation in Drosophila mushroom bodies.
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| Overall design |
Examination of 2 different transcription factors (CREB and CRTC)
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| Contributor(s) |
Hirano Y, Ihara K |
| Citation(s) |
27841260 |
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| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kunio Ihara |
| E-mail(s) |
ihara@gene.nagoya-u.ac.jp
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| Phone |
81527894532
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| Organization name |
Nagoya University
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| Department |
Center for Gene Research
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| Street address |
Furo-cho 1, Chikusa-ku
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| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
4648602 |
| Country |
Japan |
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| Platforms (1) |
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA321666 |
| SRA |
SRP075199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81456_CREB_CRTC_binding_analyzed_by_DESeq2.txt.gz |
144.5 Kb |
(ftp)(http) |
TXT |
| GSE81456_CREB_sites.txt.gz |
101.3 Kb |
(ftp)(http) |
TXT |
| GSE81456_CRTC_sites.txt.gz |
87.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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