Mapping of MLE and MSL2 using iCLIP
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Asifa Akhtar
PROVIDER: E-MTAB-1669 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila.
Ilik Ibrahim Avsar IA Quinn Jeffrey J JJ Georgiev Plamen P Tavares-Cadete Filipe F Maticzka Daniel D Toscano Sarah S Wan Yue Y Spitale Robert C RC Luscombe Nicholas N Backofen Rolf R Chang Howard Y HY Akhtar Asifa A
Molecular cell 20130701 2
Dosage compensation in Drosophila is an epigenetic phenomenon utilizing proteins and long noncoding RNAs (lncRNAs) for transcriptional upregulation of the male X chromosome. Here, by using UV crosslinking followed by deep sequencing, we show that two enzymes in the Male-Specific Lethal complex, MLE RNA helicase and MSL2 ubiquitin ligase, bind evolutionarily conserved domains containing tandem stem-loops in roX1 and roX2 RNAs in vivo. These domains constitute the minimal RNA unit present in multi ...[more]
Similar Datasets
Project description:roX RNAs are involved in the chromosome-wide gene regulation that occurs during dosage compensation in Drosophila. Dosage compensation equalizes expression of X-linked and autosomal genes. Drosophila males increase transcription two-fold from their single X chromosome. This is mediated by the MSL complex, which is composed of the male-specific lethal (MSL) proteins and two noncoding roX RNAs, roX1 and roX2. Upon elimination of both roX transcripts, a global decrease of X-linked gene expression is observed in males. Expression of the genes on the entire 4th chromosome also decreased in the absence of both roX transcripts. roX1 RNA also presents in females in the early stages. To investigate the effect of loss of roX transcripts on gene expression in females, gene expression was analyzed by microarrays in roX1-roX2- female flies. To eliminate inconsistency caused by differences in genetic background, expression of roX1-roX2- females with females of virtually identical genetic background but carrying the [hsp83-roX1+] transgene were compared. Expression of any chromosome did not change in roX1-roX2- females. It was concluded that roX RNAs only effect in males . Experiment Overall Design: Total RNA was prepared from groups of 50 third instar larvae by TRIzol (Invitrogen) extraction and purified using the RNeasy kit (Qiagen). Three independent RNA preparations for each genotype served as templates for probe synthesis. These probes were hybridized to Affymetrix Drosophila Genome 2.0 chips (Santa Clara, CA). Genes were filtered for present/absent calls by a PM-MM (Perfect match-Mismatch) comparison. Affymetrix Gene expression data was background corrected, normalized and summarized into a one expression value per replicate sample and probeset using the RMA (robust multi-array average) algorithm. Changes in gene expression were determined by comparing the mean signal intensities of genes on arrays hybridized with roX1- roX2- (mutant) probes to those hybridized with roX1- roX2-; [hsp83-roX1+] (control) probes.
2009-08-08 | E-GEOD-12076 | biostudies-arrayexpress
Project description:During sexual dimorphism, the loss of one entire X chromosome in Drosophila males is achieved largely via a broad genome-wide aneuploid effect. Exploring how MSL proteins and two large non coding RNAs (roX1 and roX2) modulate trans-acting aneuploid effect for equality to females, we employ a system biology approach (microarray) to investigate the global aneuploid effect of maleless(mle) mutation by disrupting MSL binding. A large number of the genes (144) that encode a broad spectrum of cellular transport proteins and transcription factors are located in the autosomes of Drosophila melanogaster. We find these autosomal targets are sensitive to the aneuploid effect and are poorly conserved in primitive Drosophila species and Anopheles gambiae autosomes. It is expected that during evolutionary process, they shifted gradually from their X chromosomal position in primitive Drosophila to autosomes in melanogaster, suggesting that MSL favors inverse counteraction of these autosomal targets along with X-linked genes. These findings suggest a remarkable and previously unsuspected level of complexity among aneuploid-sensitive genes, that creates a functional shift of the aneuploid effect from X to autosomes during evolution, which is resolved by the binding of MSL complex on the X chromosome.. Drosophila larvae were selected based on genotypes particularly with Tb phenotypes. Total cellular RNA were extracted from each genotypes and hebridized with affymetrix Drosophila Microarray chip. Gene Expression profiling of fly base to understand the role of maleless mutation in aneuploid targets.
2016-03-31 | E-GEOD-78227 | biostudies-arrayexpress
Project description:roX RNAs are involved in the chromosome-wide gene regulation that occurs during dosage compensation in Drosophila. Dosage compensation equalizes expression of X-linked and autosomal genes. Drosophila males increase transcription two-fold from their single X chromosome. This is mediated by the MSL complex, which is composed of the male-specific lethal (MSL) proteins and two noncoding roX RNAs, roX1 and roX2. Upon elimination of both roX transcripts, a global decrease of X-linked gene expression is observed in males. Expression of the genes on the entire 4th chromosome also decreased in the absence of both roX transcripts. roX1 RNA also presents in females in the early stages. To investigate the effect of loss of roX transcripts on gene expression in females, gene expression was analyzed by microarrays in roX1-roX2- female flies. To eliminate inconsistency caused by differences in genetic background, expression of roX1-roX2- females with females of virtually identical genetic background but carrying the [hsp83-roX1+] transgene were compared. Expression of any chromosome did not change in roX1-roX2- females. It was concluded that roX RNAs only effect in males .
2009-08-03 | GSE12076 | GEO
Project description:We identified orthologs of the roX lncRNAs across diverse Drosophilid species, and then mapped the genomic binding sites of roX1 and roX2 in four Drosophila species (D. melanogaster, D. willistoni, D. virilis, and D. busckii) using ChIRP-seq (chromatin isolation by RNA Purification and sequencing), thus revealing the interplay of the evolution of roX1 and roX2 and their genomic binding sites.
2016-01-25 | GSE69208 | GEO
Project description:Unusually among fungi, Saccharomyces cerevisiae is able to grow in environments containing almost no oxygen. A major feature of its response to hypoxia is a transition in expression from aerobic to hypoxic genes, which often code for duplicated isoforms of the same protein. In aerobic conditions, expression of the hypoxic gene set is repressed by the HMG domain protein Rox1. Here, we examined the evolution of ROX1 and related genes in the subphylum Saccharomycotina and find that a substantial reorganization of hypoxic gene regulation occurred during yeast evolution. S. cerevisiae lost ROX2, an ancient paralog of ROX1, which is almost universally present in other yeast species. ROX2 is orthologous to Candida albicans RFG1, a regulator of filamentous growth. Many yeasts, such as Candida glabrata, lack ROX1 and contain only ROX2. Others such as Naumovozyma castellii retain both genes. Although the ancestral function of ROX2 is uncertain, we find that it is not a regulator of hypoxic genes except in C. glabrata where it has taken over this function from the absent ROX1. We also find that N. castellii has a greatly attenuated transcriptional response to hypoxia as compared to other species, but that the ergosterol pathway which is normally induced by hypoxia can be induced by cobalt chloride stress in N. castellii.
2018-07-31 | GSE75235 | GEO
Project description:Drosophila males double transcription of their single X chromosome to equalize X-linked gene expression with females, which carry two X chromosomes. Increased transcription requires the Male-Specific Lethal (MSL) complex. One of the primary functions of the MSL complex is thought to be enrichment of H4Ac16 on the male X chromosome, a modification linked to elevated transcription. The roX1 and roX2 RNAs are essential but redundant components of the MSL complex. Simultaneous removal of both roX RNAs reduces MSL X-localization and leads to ectopic binding of these proteins at autosomal sites and to the chromocenter. Some H4Ac16 accumulates at these ectopic sites in roX1- roX2- males, suggesting the possibility of increased expression. The global effect of roX mutations on gene expression was measured by microarray analysis. We found that expression of the X chromosome was decreased by 26% in roX1- roX2- male larvae, supporting the involvement of roX RNAs in the up-regulation of X-linked genes. This finding is broadly comparable to reports of reduced X chromosome expression following msl2 RNAi knockdown in S2 cells. In spite of strong MSL binding and H4Ac16 accumulation at autosomal sites in roX1- roX2- males, enhanced gene expression could not be detected at these sites by microarray analysis or reverse northern blotting. Thus, failure to compensate X-linked genes, rather than inappropriate up-regulation of autosomal genes at ectopic sites of MSL binding, appears to cause male lethality upon loss of roX RNAs. Keywords: effect of roX1-roX2- mutant on gene expression
2007-01-06 | GSE3990 | GEO
Project description:Drosophila males double transcription of their single X chromosome to equalize X-linked gene expression with females, which carry two X chromosomes. Increased transcription requires the Male-Specific Lethal (MSL) complex. One of the primary functions of the MSL complex is thought to be enrichment of H4Ac16 on the male X chromosome, a modification linked to elevated transcription. The roX1 and roX2 RNAs are essential but redundant components of the MSL complex. Simultaneous removal of both roX RNAs reduces MSL X-localization and leads to ectopic binding of these proteins at autosomal sites and to the chromocenter. Some H4Ac16 accumulates at these ectopic sites in roX1- roX2- males, suggesting the possibility of increased expression. The global effect of roX mutations on gene expression was measured by microarray analysis. We found that expression of the X chromosome was decreased by 26% in roX1- roX2- male larvae, supporting the involvement of roX RNAs in the up-regulation of X-linked genes. This finding is broadly comparable to reports of reduced X chromosome expression following msl2 RNAi knockdown in S2 cells. In spite of strong MSL binding and H4Ac16 accumulation at autosomal sites in roX1- roX2- males, enhanced gene expression could not be detected at these sites by microarray analysis or reverse northern blotting. Thus, failure to compensate X-linked genes, rather than inappropriate up-regulation of autosomal genes at ectopic sites of MSL binding, appears to cause male lethality upon loss of roX RNAs. Experiment Overall Design: Total RNA was prepared from groups of 50 third instar larvae by TRIzol (Invitrogen) extraction and purified using the RNeasy kit (Qiagen). Three independent RNA preparations for each genotype served as templates for probe synthesis. Affymetrix Drosophila Genome 2.0 chips were hybridized to these probes (Santa Clara, CA). The affymertrix Drosophila annotation of December 2004 was used to map genes to their cytological locations. Genes were filtered for present/absent calls by a PM-MM (Perfect match- Mismatch) comparison. Autosomal transcripts were normalized on a chip-by-chip basis to bring their median values to 100. The identical degree of adjustment was used to normalize X-linked transcripts. Changes in gene expression were determined by comparing the mean signal intensities of genes on arrays hybridized with roX1SMC17A roX2- probes to those hybridized with roX1+ roX2- probes.
2008-03-13 | E-GEOD-3990 | biostudies-arrayexpress
Project description:Confinement of the X chromosome into a territory for dosage compensation (DC) is a prime example of subnuclear compartmentalization for transcription regulation at the megabase scale. In D. melanogaster, two sex-specific non-coding (nc) RNAs roX1 and roX2 are transcribed from the X chromosome. They associate with the Male-specific lethal (MSL) complex, which by acetylating histone H4 lysine 16 (H4K16ac) confers approximately 2-fold upregulated expression of male X-linked genes. Current models explain X-over-autosome specificity based on the MSL2 subunit recognizing cis-regulatory DNA high-affinity sites (HAS). However, HAS motifs are also found on autosomes, indicating that additional factors have evolved to confer stable association of the MSL complex with the X. Here, we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX ncRNAs. roX-MSL2-CTD form a stably condensated state, and functional analyses in Drosophila and mammalian cells reveal the critical importance of their interplay for DC in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic DC in mammalian cells. Thus, the condensating nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X in Drosophila.
2020-08-07 | GSE129831 | GEO
Project description:iCLIP-seq experiment to asses the binding of mitochondrially targeted MRB8170 and MRB4160 involved in RNA editing on a genomic scale. Furthermore, to investigate what subsets of maxicircles transcripts (pan-edited, minimally-edited and never-edited) are bound to both the above proteins in vivo.
2016-08-14 | E-MTAB-4934 | biostudies-arrayexpress
Project description:Confinement of the X chromosome into a territory for dosage compensation (DC) is a prime example of subnuclear compartmentalization for transcription regulation at the megabase scale. In D. melanogaster, two sex-specific non-coding (nc) RNAs roX1 and roX2 are transcribed from the X chromosome. They associate with the Male-specific lethal (MSL) complex, which by acetylating histone H4 lysine 16 (H4K16ac) confers approximately 2-fold upregulated expression of male X-linked genes. Current models explain X-over-autosome specificity based on the MSL2 subunit recognizing cis-regulatory DNA high-affinity sites (HAS). However, HAS motifs are also found on autosomes, indicating that additional factors have evolved to confer stable association of the MSL complex with the X. Here, we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX ncRNAs. roX-MSL2-CTD form a stably condensated state, and functional analyses in Drosophila and mammalian cells reveal the critical importance of their interplay for DC in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic DC in mammalian cells. Thus, the condensating nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X in Drosophila. This SuperSeries is composed of the SubSeries listed below.
2020-08-07 | GSE129834 | GEO