Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila
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ABSTRACT:
PROVIDER: PRJNA384219 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5480960_1.fastq.gz | Fastqsanger.gz | |||
| SRR5480960_2.fastq.gz | Fastqsanger.gz | |||
| SRR5480970.fastq.gz | Fastqsanger.gz | |||
| SRR5480961_1.fastq.gz | Fastqsanger.gz | |||
| SRR5480961_2.fastq.gz | Fastqsanger.gz |
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Project description:In Drosophila female development is governed by a single RNA-binding protein, Sex lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Functional Sxl protein is only synthesized in female flies. Its expression is established in the pre-cellular, female embryo by an X-chromosome counting mechanism and maintained by a positive feedback loop with Sxl controlling alternative splicing of its own transcript. In male flies this feedback loop is not activated, keeping Sxl expression in the ‘off’ state. But what protects males against accidental triggering of the self-sustaining feedback loop and Sxl protein production snowballing out of control? Here we identify Sister of sex lethal (Ssx) as a protein that antagonizes Sxl in autoregulatory splicing by competition for the same RNA elements. Male flies mutant for ssx exhibit a low level of productive Sxl mRNA splicing and in cultured Drosophila cells, Sxl-induced changes in alternative splicing can be reverted by the expression of Ssx. In sum, this demonstrates that Ssx helps to establish a stable, male-specific gene expression pattern by protecting male flies against triggering Sxl expression.
2019-01-15 | GSE98188 | GEO
Project description:In Drosophila female development is governed by a single RNA-binding protein, Sex lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Functional Sxl protein is only synthesized in female flies. Its expression is established in the pre-cellular, female embryo by an X-chromosome counting mechanism and maintained by a positive feedback loop with Sxl controlling alternative splicing of its own transcript. In male flies this feedback loop is not activated, keeping Sxl expression in the ‘off’ state. But what protects males against accidental triggering of the self-sustaining feedback loop and Sxl protein production snowballing out of control? Here we identify Sister of sex lethal (Ssx) as a protein that antagonizes Sxl in autoregulatory splicing by competition for the same RNA elements. Male flies mutant for ssx exhibit a low level of productive Sxl mRNA splicing and in cultured Drosophila cells, Sxl-induced changes in alternative splicing can be reverted by the expression of Ssx. In sum, this demonstrates that Ssx helps to establish a stable, male-specific gene expression pattern by protecting male flies against triggering Sxl expression.
2019-01-15 | GSE98187 | GEO
Project description:Conversely to canonical splicing, back-splicing covalently ligates the upstream 3' splice site (SS) with downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely-identified in eukaryotes and have regulatory functions in gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA-seq of various sex-specific Drosophila samples including head, body and gonads from both genders, and identified more than ten thousand of circular RNAs, in which hundreds are sex-differentially expressed and back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene which only functionally spliced in females, promotes back-splicing of many female-differentially expressed circRNAs in the male S2 cells, while expression of a SXL mutant did not. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through a PAR-CLIP approach and revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing of those circRNAs, whereas SXL-binding on the circRNA exons inhibits the back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specifc circRNAs, as well as in the initiation of Drosophila sex-determination cascade through canoncial forward-splicing.
2023-04-23 | GSE221102 | GEO
Project description:The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls axon projection, locomotion, and memory. Here we define an unexpectedly specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and link the most prominent of these, female retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl), to a role in m6A-dependent mRNA splicing. Genetic evidence indicates that aberrant Sxl splicing underlies multiple phenotypes in Nab2 mutant females. At a molecular level, Nab2 associates with Sxl pre-mRNA and ensures proper female-specific splicing by preventing m6A hypermethylation by Mettl3 methyltransferase. Consistent with these results, reducing Mettl3 expression rescues developmental, behavioral and neuroanatomical phenotypes in Nab2 mutants. Overall these data identify Nab2 as a required regulator of m6A-regulated Sxl splicing and imply a broader link between Nab2 and Mettl3-regulated brain RNAs.
2020-12-02 | GSE162531 | GEO
Project description:Sex-lethal (Sxl), a feminizing switch gene in Drosophila, also generates male-specific proteins and non-sex-specific mRNAs, despite the fact that deleting the gene from males causes no obvious phenotypic abnormalities. We specifically investigate how Sxl may affect gene expression in the male head, where SXL isoforms have been detected. The information may help us understand how Sxl acquired its functional roles in sex determination during evolution in Drosophila Keywords: Comparative expression, genetic modification
2008-12-30 | GSE9571 | GEO
Project description:Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila (iCLIP)
| PRJNA384220 | ENA
Project description:Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila (RIP-Seq)
| PRJNA384221 | ENA
Project description:The Drosophila sex determination hierarchy consists of a splicing cascade with sex-specific transcription directing somatic sexual dimorphism. Our understanding of this pathway, and many others, is incomplete. Here we pioneer an approach to expand our knowledge of gene regulatory networks (GRNs) by leveraging natural genetic variation. This approach is generalizable to any natural population, including humans. Two studies from Drosophila female head tissue were used – the DSPR collection (alleles from 15 natural variants) and F1-hybrid collection (alleles from heterozygotes of 75 isogenic lines crossed to w1118) – in a structural equation model (SEM) analysis. We expanded the sex hierarchy GRN by adding novel links among genes in the pathway and by adding novel genes to the pathway. A link from fruitless (fru) to Sex-lethal (Sxl) was found in both populations, which is supported by the presence of fru binding sites in the Sxl locus. The splicing factors male-specific lethal 2 and Rm62 were correctly identified as downstream targets of Sxl. There were 754 additional candidate genes for an expanded sex hierarchy GRN. These candidates were enriched for genes with sex-biased splicing and many components of the spliceosome were placed in the GRN. As with other population-genetic analyses, the number of alleles limits the number of observable interactions. Network expansion was only clear in the F1-hybrid population, which has an average of twice as many alleles as the DSPR population. Independent studies of doublesex and transformer mutants support many novel connections, including evidence for a link between the sex hierarchy and metabolism, with the inclusion of Insulin-like receptor in the sex hierarchy GRN.
2015-09-01 | GSE67400 | GEO
Project description:N6-methyladenosine (m6A) has recently emerged as a widespread and conserved RNA modification that modulates messenger RNA (mRNA) processing and activity. As most m6A studies have been conducted in cultured cells, we established Drosophila as a model system that combines molecular and genomic analyses of m6A with investigations of organismal biology. We first apply miCLIP sequencing to map m6A modifications at single-nucleotide resolution during Drosophila embryogenesis. We next characterize Drosophila components of the m6A "writer" methyltransferase complex [MTC factors, METTL3/IME4, METTL14, FL(2)D and Nito], and characterize m6A-binding properties of the YTH domain-containing proteins, YT521-B and CG6422. We complement this by generating a collection of mutants in m6A writer and reader components. While Drosophila orthologs of mammalian MTC factors that have additional roles in splicing are lethal, our mutants in METTL and YTH factors are viable but present specific developmental and behavioral defects. We note that several mammalian m6A factors were originally identified as Drosophila regulators of Sxl splicing, which generates the master determinant of female identity. While our mutants in dedicated writer and reader machinery are not required to accumulate Sxl protein in the ovary, maternal loss of m6A writers and readers collaborates with reduction of Sxl to induce female lethality. Our data indicate Sxl is directly regulated by the m6A pathway, since miCLIP data show Sxl is a substantial target of intronic m6A in early embryos, in addition to bearing exonic m6A. Consistent with this, female-specific Sxl splicing is defective in m6A pathway mutants. YT521-B appears to be the major effector of m6A for Sxl regulation, as it shows much stronger genetic interactions with Sxl than CG6422 and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit for studying the m6A pathway in Drosophila reveals a major biological utilization in establishing sex-specific splicing.
2017-04-22 | GSE97004 | GEO
Project description:The Drosophila sex determination hierarchy consists of a splicing cascade with sex-specific transcription directing somatic sexual dimorphism. Our understanding of this pathway, and many others, is incomplete. Here we pioneer an approach to expand our knowledge of gene regulatory networks (GRNs) by leveraging natural genetic variation. This approach is generalizable to any natural population, including humans. Two studies from Drosophila female head tissue were used – the DSPR collection (alleles from 15 natural variants) and F1-hybrid collection (alleles from heterozygotes of 75 isogenic lines crossed to w1118) – in a structural equation model (SEM) analysis. We expanded the sex hierarchy GRN by adding novel links among genes in the pathway and by adding novel genes to the pathway. A link from fruitless (fru) to Sex-lethal (Sxl) was found in both populations, which is supported by the presence of fru binding sites in the Sxl locus. The splicing factors male-specific lethal 2 and Rm62 were correctly identified as downstream targets of Sxl. There were 754 additional candidate genes for an expanded sex hierarchy GRN. These candidates were enriched for genes with sex-biased splicing and many components of the spliceosome were placed in the GRN. As with other population-genetic analyses, the number of alleles limits the number of observable interactions. Network expansion was only clear in the F1-hybrid population, which has an average of twice as many alleles as the DSPR population. Independent studies of doublesex and transformer mutants support many novel connections, including evidence for a link between the sex hierarchy and metabolism, with the inclusion of Insulin-like receptor in the sex hierarchy GRN. RNA sequencing was performed on mRNA derived from adult male or female heads, for a total of 9 samples. These samples included females that produce the male isoform of dsx [w/+;DsxD/dsxm+r15 (XX)], and two dsx mutants: females [w/+; dsxm+r15/dsxd+r3 (XX)] and males [w;dsxm+r15/dsxd+r3 (XY)]. Two wild type genotypes (Berlin and Canton-S) were sequenced at the same time, but have previously been published as part of GSE50515. There were at least 3 replicates from biological samples.
2015-09-01 | E-GEOD-67400 | biostudies-arrayexpress