|
| Status |
Public on Oct 01, 2017 |
| Title |
A mutually exclusive stem loop arrangement in roX2 RNA is essential for X chromosome regulation in Drosophila |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX lncRNAs harbor several redundant domains to interact with the ubiquitin ligase MSL2 and the RNA helicase MLE for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By employing the uvCLAP methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild type and various MLE mutant derivatives including a catalytic inactive MLE derivative MLEGET we show that the minimal roX RNA contains two mutually exclusive stem-loops which exist in a peculiar structural arrangement: when one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.
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| |
|
| Overall design |
UV crosslinking and affinity purification (uvCLAP) for MLE wildtype and 4 MLE mutants in Drosophila melanogaster.
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| |
|
| Contributor(s) |
Ibrahim I, Daniel M |
| Citation(s) |
29066499 |
| |
| Submission date |
Oct 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platforms (1) |
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA347623 |
| SRA |
SRP091364 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE87792_K1_control_combined_dm3.bed.gz |
674.6 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_control_combined_dm3.bw |
389.9 Kb |
(ftp)(http) |
BW |
| GSE87792_K1_control_combined_gaps_dm3.bed.gz |
11.1 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_control_combined_gaps_dm3.bigWig |
42.2 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_K1_dmMLE-GET_combined_dm3.bed.gz |
3.6 Mb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE-GET_combined_dm3.bw |
2.5 Mb |
(ftp)(http) |
BW |
| GSE87792_K1_dmMLE-GET_jamm_dm3.narrowPeak.gz |
525.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE87792_K1_dmMLE-GET_peakachu_dm3.gff.gz |
3.6 Kb |
(ftp)(http) |
GFF |
| GSE87792_K1_dmMLE-HR_combined_dm3.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE-HR_combined_dm3.bw |
1.2 Mb |
(ftp)(http) |
BW |
| GSE87792_K1_dmMLE-HR_jamm_dm3.narrowPeak.gz |
188.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE87792_K1_dmMLE-HR_peakachu_dm3.gff.gz |
474 b |
(ftp)(http) |
GFF |
| GSE87792_K1_dmMLE-KHR_combined_dm3.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE-KHR_combined_dm3.bw |
822.1 Kb |
(ftp)(http) |
BW |
| GSE87792_K1_dmMLE-KHR_jamm_dm3.narrowPeak.gz |
87.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE87792_K1_dmMLE-KHR_peakachu_dm3.gff.gz |
347 b |
(ftp)(http) |
GFF |
| GSE87792_K1_dmMLE-K_combined_dm3.bed.gz |
3.6 Mb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE-K_combined_dm3.bw |
1.7 Mb |
(ftp)(http) |
BW |
| GSE87792_K1_dmMLE-K_jamm_dm3.narrowPeak.gz |
386.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE87792_K1_dmMLE-K_peakachu_dm3.gff.gz |
1.4 Kb |
(ftp)(http) |
GFF |
| GSE87792_K1_dmMLE-wt_combined_dm3.bed.gz |
4.8 Mb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE-wt_combined_dm3.bw |
2.8 Mb |
(ftp)(http) |
BW |
| GSE87792_K1_dmMLE-wt_jamm_dm3.narrowPeak.gz |
678.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE87792_K1_dmMLE-wt_peakachu_dm3.gff.gz |
4.1 Kb |
(ftp)(http) |
GFF |
| GSE87792_K1_dmMLE_GET_combined_gaps_dm3.bed.gz |
87.8 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE_GET_combined_gaps_dm3.bigWig |
105.8 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_K1_dmMLE_HR_combined_gaps_dm3.bed.gz |
41.0 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE_HR_combined_gaps_dm3.bigWig |
59.2 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_K1_dmMLE_KHR_combined_gaps_dm3.bed.gz |
27.8 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE_KHR_combined_gaps_dm3.bigWig |
53.2 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_K1_dmMLE_K_combined_gaps_dm3.bed.gz |
105.5 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE_K_combined_gaps_dm3.bigWig |
106.7 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_K1_dmMLE_wt_combined_gaps_dm3.bed.gz |
119.0 Kb |
(ftp)(http) |
BED |
| GSE87792_K1_dmMLE_wt_combined_gaps_dm3.bigWig |
123.0 Kb |
(ftp)(http) |
BIGWIG |
| GSE87792_RAW.tar |
16.2 Mb |
(http)(custom) |
TAR (of BED) |
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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