 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 01, 2022 |
| Title |
Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bam∆86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
|
| |
|
| Overall design |
Amplified PCR fragments from DamID procedure were sequenced on Illumina HiSeq 2000, cDNA libraries were sequenced on Illumina Novaseq 6000
|
| |
|
| Contributor(s) |
Ilyin AA |
| Citation(s) |
35166842 |
| |
| Submission date |
Sep 06, 2020 |
| Last update date |
Apr 19, 2022 |
| Contact name |
Artem Ilin |
| E-mail(s) |
artem.ilin@su.se
|
| Organization name |
Stockholm University
|
| Department |
MBW
|
| Street address |
Svante Arrhenius väg 20C
|
| City |
Stockholm |
| ZIP/Postal code |
11418 |
| Country |
Sweden |
| |
|
| Platforms (2) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
|
| Samples (14)
|
| GSM4770606 |
Dam in spermatogonia, rep 2 |
| GSM4770607 |
Dam-Lam in spermatocytes, rep 1 |
| GSM4770608 |
Dam-Lam in spermatocytes, rep 2 |
| GSM4770609 |
Dam in spermatocytes, rep 1 |
| GSM4770610 |
Dam in spermatocytes, rep 2 |
| GSM4770611 |
total RNA from control testes, rep 1 |
| GSM4770612 |
total RNA from control testes, rep 2 |
| GSM4770613 |
total RNA from control testes, rep 3 |
| GSM4770614 |
total RNA from Lam Dm0 and Lam C KD testes, rep 1 |
| GSM4770615 |
total RNA from Lam Dm0 and Lam C KD testes, rep 2 |
| GSM4770616 |
total RNA from Lam Dm0 and Lam C KD testes, rep 3 |
|
| Relations |
| BioProject |
PRJNA661761 |
| SRA |
SRP280281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157565_LAM.SCL.300nt.domains.bed.gz |
54.4 Kb |
(ftp)(http) |
BED |
| GSE157565_LAM.SCL.wt.sum.norm.bedgraph.gz |
3.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157565_LAM.SG.300nt.domains.bed.gz |
75.6 Kb |
(ftp)(http) |
BED |
| GSE157565_LAM.SG.wt.sum.norm.bedgraph.gz |
4.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157565_RAW.tar |
20.6 Mb |
(http)(custom) |
TAR (of BEDGRAPH, 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...