|
| Status |
Public on Feb 07, 2022 |
| Title |
The role of insulators and transcription in 3D chromatin organisation of flies |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
Expression profiling by high throughput sequencing
|
| Summary |
The DNA in humans and many animals is compartmentalised in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but we are still missing evidence that these proteins have a functional role in TAD maintenance. Here, we show that depletion of BEAF-32, Cp190 and Chro leads to changes in TAD organisation and chromatin loops. Their depletion affects mainly TAD borders in heterochromatin, while euchromatin TAD borders are resilient to these mutants. Furthermore, transcriptomic data identified thousands of genes displaying differential expression in these mutants and that majority of differentially expressed genes are in TADs that are reorganised. In contrast, we observed a lower effect on gene expression by the loss of chromatin loops. Our work identified for the first time a functional role for architectural proteins at TAD borders in Drosophila and a strong link between TAD reorganisation and changes in gene expression.
|
| |
|
| Overall design |
Comparison of Hi-C and RNA-seq data in WT and mutant (BEAF-32; Cp190 and Chro; BEAF-32 and Dref) Drosophila melanogaster cell lines BG3 (derived from larval central nervous system)
|
| |
|
| Contributor(s) |
Zabet NR, Chathoth KT, Mikheeva L |
| Citation(s) |
35354608 |
| |
| Submission date |
Mar 16, 2020 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Nicolae Radu Zabet |
| E-mail(s) |
nzabet@essex.ac.uk
|
| Phone |
+44(0)1206872630
|
| Organization name |
University of Essex
|
| Department |
School of Life Sciences
|
| Street address |
School of Life Sciences, University of Essex,
|
| City |
Colchester |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
| |
|
| Platforms (2) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA612860 |
| SRA |
SRP252990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE147059_Loops_BG3_BEAF_DREF_KD_HiC_hiccups.bedpe.gz |
47.1 Kb |
(ftp)(http) |
BEDPE |
| GSE147059_Loops_BG3_BEAF_KD_HiC_hiccups.bedpe.gz |
72.8 Kb |
(ftp)(http) |
BEDPE |
| GSE147059_Loops_BG3_Cp190_Chrom_KD_HiC_hiccups.bedpe.gz |
130.5 Kb |
(ftp)(http) |
BEDPE |
| GSE147059_RAW.tar |
820.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE147059_TADs_BG3_BEAF_DREF_KD_merged_dpnII.bed.gz |
29.6 Kb |
(ftp)(http) |
BED |
| GSE147059_TADs_BG3_BEAF_DREF_KD_merged_dpnII_strong.bed.gz |
9.3 Kb |
(ftp)(http) |
BED |
| GSE147059_TADs_BG3_BEAF_KD_merged_dpnII.bed.gz |
53.1 Kb |
(ftp)(http) |
BED |
| GSE147059_TADs_BG3_BEAF_KD_merged_dpnII_strong.bed.gz |
23.9 Kb |
(ftp)(http) |
BED |
| GSE147059_TADs_BG3_Cp190_Chrom_KD_merged_dpnII.bed.gz |
45.1 Kb |
(ftp)(http) |
BED |
| GSE147059_TADs_BG3_Cp190_Chrom_KD_merged_dpnII_strong.bed.gz |
18.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
Less...
More...