|
| Status |
Public on Feb 27, 2020 |
| Title |
Dissecting the transcriptional regulation during the transition from proliferation to terminal differentiation during fly spermatogenesis |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To investigate how the cell-type-specific gene expression program for spermatocyte differentiation turns on in male flies, we used RNA-seq to map transcript levels, CAGE to map transcription start sites (TSS), and ATAC-seq to map chromatin accessibility as proliferating spermatogonia transition to differentiating spermatocytes. Combining these data, we showed that the promoters that turn on when germ cells become spermatocytes lack most of the canonical core promoter motifs. Instead these promoters require tMAC function to become open and accessible, and are enriched for the tMAC ChIP motif and putative Achi/Vis binding motif. Within the local open region that tMAC creates, a good match to the Inr at +1 and ACA and CNAAATT motifs at specific positions downstream correlates with efficiency of individual TSS usage. Our results reveal a robust cell-type-specific and gene-selective developmental transcription program orchestrated by promoter-proximal elements and protein complexes that interact with them.
|
| |
|
| Overall design |
Each sequencing assay included spermagonia-enriched and spermatocyte-enriched samples, with 2 or 3 replicates for each condition
|
| |
|
| Contributor(s) |
Lu D, Sin H, Fuller MT |
| Citation(s) |
32217666 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM061986 |
Regulation of Cell-Type Specific Transcription in Spermatocytes |
STANFORD UNIVERSITY |
MARGARET T FULLER |
| F32 HD086986 |
Chromatin dynamics, transcriptional activators and repressors in transition from proliferating progenitors to terminal differentiation during adult stem cell differentiation |
STANFORD UNIVERSITY |
Dan Lu |
| S10 OD018220 |
High Throughput DNA Sequencer Upgrade |
STANFORD UNIVERSITY |
John Coller |
|
| |
| Submission date |
Feb 26, 2020 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Margaret Fuller |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Fuller
|
| Street address |
279 Campus Drive, Beckman Center B301
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
|
| Samples (32)
|
|
| Relations |
| BioProject |
PRJNA608910 |
| SRA |
SRP250825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE145975_ATAC_nucleosome_48hrPHS.bed.gz |
3.6 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_48hrPHS.bw |
275.5 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_nucleosome_72hrPHS.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_72hrPHS.bw |
243.0 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_nucleosome_aly_mutant.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_aly_mutant.bw |
206.9 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_nucleosome_bam_mutant.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_bam_mutant.bw |
229.4 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_nucleosome_ctrl_48hrPHS.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_ctrl_48hrPHS.bw |
221.2 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_nucleosome_topi_mutant.bed.gz |
3.8 Mb |
(ftp)(http) |
BED |
| GSE145975_ATAC_nucleosome_topi_mutant.bw |
284.0 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_48hrPHS.bw |
193.7 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_72hrPHS.bw |
162.3 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_aly_mutant.bw |
93.9 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_bam_mutant.bw |
98.8 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_ctrl_48hrPHS.bw |
148.8 Mb |
(ftp)(http) |
BW |
| GSE145975_ATAC_seq_topi_mutant.bw |
176.0 Mb |
(ftp)(http) |
BW |
| GSE145975_MACS2_ATAC_48hrPHS_peaks.narrowPeak.gz |
891.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_MACS2_ATAC_aly_peaks.narrowPeak.gz |
713.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_MACS2_ATAC_bam_peaks.narrowPeak.gz |
716.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_MACS2_ATAC_ctrl_48hrPHS_peaks.narrowPeak.gz |
755.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_MACS2_ATAC_hs72hrPHS_peaks.narrowPeak.gz |
863.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_MACS2_ATAC_topi_peaks.narrowPeak.gz |
904.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE145975_RAW.tar |
129.8 Mb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
Less...
More...