Single-cell analysis of PA14-treated control and roX2 depleted ISCs (PA14 treated)
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE190886 | GEO | 2026/06/08
REPOSITORIES: GEO
Similar Datasets
Project description:Maintenance of the genome and epigenome stability is vital for animal longevity. Long noncoding RNAs (LncRNAs), roX1 and roX2, are only known to be important in the male X chromosome dosage complex to double the expression levels of the genes on the X chromosome in Drosophila males. However, their functions in Drosophila females have never been explored. This study demonstrates the surprising role of roX1 and roX2 in acquiring heterochromatin in intestinal stem cells (ISCs) and progenitor enteroblasts (EBs) of Drosophila females under pathogen infection or aging. Increased heterochromatin formation in ISCs/EBs is associated with decreased active epigenetic modifications and global gene repression.
2026-06-09 | GSE334809 | GEO
Project description:Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress. Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.
2020-03-11 | GSE120217 | 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: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.
2017-10-01 | GSE87792 | GEO
Project description:RNA-seq data in WT, roX1, roX2, roX1roX2 mutants in D. melanogaster
| PRJNA475992 | ENA
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:We perfomed RNA-sequencing for searching upstream regulators regulated by NDRG3 gene. RNA profiles of each cell line were used to figure out Differentially Expressed Genes (DEG) by NDRG3 depletion, we found NDRG3-related upstream regulators by applicating DEG to Ingenuity Pathway Analysis (IPA).
2022-08-31 | GSE189171 | GEO
Project description:Long non-coding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed CHART, a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly-crosslinked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from fly and human. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage-compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the MSL-complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to ChIP for proteins. Examination of the binding sites of roX2 ncRNA from S2 cells using two different elution strategies compared with a sense control or input control. Processed data file 'roX2.2.peaks.bed' (for roX2 CHART RNase eluted, combined replicates) linked below as supplementary file.
2011-12-07 | E-GEOD-28180 | biostudies-arrayexpress