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Series GSE87792 Query DataSets for GSE87792
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.
Overall design UV crosslinking and affinity purification (uvCLAP) for MLE wildtype and 4 MLE mutants in Drosophila melanogaster.
Contributor(s) Ibrahim I, Daniel M
Citation(s) 29066499
Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name Asifa Akhtar
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)
GSM2340378 K1 control replicateA
GSM2340379 K1 control replicateB
GSM2340380 K1 dmMLE-GET replicateA
BioProject PRJNA347623
SRA SRP091364

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Supplementary file Size Download File type/resource
GSE87792_K1_control_combined_dm3.bed.gz 674.6 Kb (ftp)(http) BED 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 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 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 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 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 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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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