Widespread Generation of Alternative UTRs Contributes to Sex-specific RNA Binding by UNR
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE33178 | GEO | 2011/10/25
SECONDARY ACCESSION(S): PRJNA149193
REPOSITORIES: GEO
Similar Datasets
Project description:Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the non-coding RNA roX plays key roles in the control of X-chromosome dosage compensation in both sexes. In order to investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of non-coding RNAs in a sex-specific fashion. Two replicates of UNR IP were performed in D.melanogaster adult males and females, and enrichment in either sex was compared with IgG IP as control. To correlate sex-specific UNR binding with sex-specific transcription and splicing we performed RNA-Seq experiments in males and females.
2011-10-25 | E-GEOD-33178 | biostudies-arrayexpress
Project description:Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to various RNAs plays key roles in the control of X chromosome dosage compensation in both sexes. In order to investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of non-coding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.
2011-10-31 | GSE30963 | GEO
Project description:Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to various RNAs plays key roles in the control of X chromosome dosage compensation in both sexes. In order to investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of non-coding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner. Of the total 6 chips, three are independent immunoprecipitations, while the other three microarrays are their dye-swaps (same IPs).
2011-10-31 | E-GEOD-30963 | 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: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 | GSE129796 | GEO
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 | GSE129795 | GEO
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
Project description:The male-specific lethal dosage compensation complex (MSL complex or DCC), which consists of five proteins and two non-coding roX RNAs, is necessary for the transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila XY males, compared with XX females. MSL2 is a single protein component of the DCC that is expressed only in males and is essential for the specific recruitment of the DCC to the high-affinity “entry” sites (HASs) on the X chromosome. MSL2, together with MSL1, forms the heterotetrameric DCC core. Here, we demonstrated that the N-terminal unstructured region of MSL1 interacts with many different DNA-binding proteins that contain clusters of the C2H2 zinc-finger domains. Amino acid deletions in the N-terminal region of MSL1 strongly affect the binding of the DCC to the HASs on the male X chromosome. However, the binding of MSL2 to autosomal promoters was unaffected by amino acid deletions in MSL1. Males expressing mutant variants of MSL1 died during the larvae stage, demonstrating the critical role played by the N-terminal region in DCC activity. Our results suggest that MSL1 interacts with a variety of DNA-binding proteins to increase the specificity of DCC recruitment to the male X chromosome.
2022-08-30 | GSE161128 | GEO
Project description:The Drosophila male-specific lethal (MSL) complex binds to the male X chromosome to activate transcription, and consists of five proteins, MSL1, MSL2, MSL3, MOF, MLE, and two roX RNAs. The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. MSL2 is expressed only in males and interacts with the N-terminal zinc-finger of the transcription factor CLAMP that is important for specific recruitment of the MSL complex on the male X chromosome. Here we found that the unstructured C-terminal region of MLE interacts with 6-7 zinc-finger domains of CLAMP. In vitro 4-5 zinc fingers are critical for specific DNA-binding of CLAMP with GA-repeats, which constitute the core motif at the high affinity binding sites for MSL proteins. Deletion of the Clamp Binding Domain (CBD) in MLE results in decreasing of MSL proteins association with male X chromosome and increasing of male lethality. These results suggest that interactions of unstructured regions in MSL2 and MLE with CLAMP zinc finger domains are important for the specific recruitment of the MSL complex on the male X chromosome.
2024-03-20 | GSE239354 | GEO
Project description:Widespread Generation of Alternative UTRs Contributes to Sex-specific RNA Binding by UNR
| PRJNA146223 | ENA