Similar Datasets
Project description:Small nucleolar RNAs (snoRNAs) are prevailing components of the chromatin-associated transcriptome. We have studied a specific chromatin-associated snoRNA, snoRNA:U3:9B, that binds to a large number of protein coding genes in the genome of Drosophila melanogaster, including immune response genes. We have used CRISPR/Cas9 to delete snoRNA:U3:9B. SnoRNA:U3:9B-deficient larvae were viable in control conditions but failed to develop into pupae when challenged by expression of a Sindbis virus replicon, which suggests that snoRNA:U3:9B is required for the activation of an effective antiviral response. Consistent with this hypothesis, the chromatin decompaction and gene activation typically observed at immune response genes in response to Sindbis replicon expression were abolished in snoRNA:U3:9B-deficient larvae. Moreover, snoRNA:U3:9B was required for the recruitment of the ATP-dependent helicase brm to a set of target immune genes. The association of snoRNA:U3:9B with immune response genes in vivo shown by ChIRP-qPCR suggests that the chromatin and gene expression defects observed in the snoRNA:U3:9B knock-out strains are due to direct regulatory events. In summary, our findings reveal an immune defence mechanism that relies on a snoRNA for the recruitment of chromatin remodelling factors to immune genes, thereby modulating local chromatin accessibility to facilitate immune gene activation.
2025-07-29 | GSE281409 | GEO
Project description:Small nucleolar RNAs (snoRNAs) are prevailing components of the chromatin-associated transcriptome. We have studied a specific chromatin-associated snoRNA, snoRNA:U3:9B, that binds to a large number of protein coding genes in the genome of Drosophila melanogaster, including immune response genes. We have used CRISPR/Cas9 to delete snoRNA:U3:9B. SnoRNA:U3:9B-deficient larvae were viable in control conditions but failed to develop into pupae when challenged by expression of a Sindbis virus replicon, which suggests that snoRNA:U3:9B is required for the activation of an effective antiviral response. Consistent with this hypothesis, the chromatin decompaction and gene activation typically observed at immune response genes in response to Sindbis replicon expression were abolished in snoRNA:U3:9B-deficient larvae. Moreover, snoRNA:U3:9B was required for the recruitment of the ATP-dependent helicase brm to a set of target immune genes. The association of snoRNA:U3:9B with immune response genes in vivo shown by ChIRP-qPCR suggests that the chromatin and gene expression defects observed in the snoRNA:U3:9B knock-out strains are due to direct regulatory events. In summary, our findings reveal an immune defence mechanism that relies on a snoRNA for the recruitment of chromatin remodelling factors to immune genes, thereby modulating local chromatin accessibility to facilitate immune gene activation.
2025-07-29 | GSE281900 | GEO
Project description:SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster
| PRJNA1186163 | ENA
Project description:SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster [RNA-Seq]
| PRJNA1183813 | ENA
Project description:SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster [ATAC-Seq]
| PRJNA1186160 | ENA
Project description:A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.
| S-EPMC5932544 | biostudies-literature
Project description:In eukaryotes, ribosomes are made from precursor rRNA (pre-rRNA) and ribosomal proteins in a maturation process that requires a large number of snoRNPs and processing factors. A fundamental problem is how the coordinated and productive folding of the pre-rRNA and assembly of successive pre-rRNA-protein complexes is achieved cotranscriptionally. The conserved protein Mrd1p, which contains five RNA binding domains (RBDs), is essential for processing events leading to small ribosomal subunit synthesis. We show that full function of Mrd1p requires all five RBDs and that the RBDs are functionally distinct and needed during different steps in processing. Mrd1p mutations trap U3 snoRNA in pre-rRNP complexes both in base-paired and non-base-paired interactions. A single essential RBD, RBD5, is involved in both types of interactions, but its conserved RNP1 motif is not needed for releasing the base-paired interactions. RBD5 is also required for the late pre-rRNP compaction preceding A(2) cleavage. Our results suggest that Mrd1p modulates successive conformational rearrangements within the pre-rRNP that influence snoRNA-pre-rRNA contacts and couple U3 snoRNA-pre-rRNA remodeling and late steps in pre-rRNP compaction that are essential for cleavage at A(0) to A(2). Mrd1p therefore coordinates key events in biosynthesis of small ribosome subunits.
| S-EPMC2772733 | biostudies-literature
Project description:BackgroundU3 snoRNA is a box C/D small nucleolar RNA (snoRNA) involved in the processing events that liberate 18S rRNA from the ribosomal RNA precursor (pre-rRNA). Although U3 snoRNA is present in all eukaryotic organisms, most investigations of it have focused on fungi (particularly yeasts), animals and plants. Relatively little is known about U3 snoRNA and its gene(s) in the phylogenetically broad assemblage of protists (mostly unicellular eukaryotes). In the euglenozoon Euglena gracilis, a distant relative of the kinetoplastid protozoa, Southern analysis had previously revealed at least 13 bands hybridizing with U3 snoRNA, suggesting the existence of multiple copies of U3 snoRNA genes.ResultsThrough screening of a lambda genomic library and PCR amplification, we recovered 14 U3 snoRNA gene variants, defined by sequence heterogeneities that are mostly located in the U3 3'-stem-loop domain. We identified three different genomic arrangements of Euglena U3 snoRNA genes: i) stand-alone, ii) linked to tRNAArg genes, and iii) linked to a U5 snRNA gene. In arrangement ii), the U3 snoRNA gene is positioned upstream of two identical tRNAArg genes that are convergently transcribed relative to the U3 gene. This scenario is reminiscent of a U3 snoRNA-tRNA gene linkage previously described in trypanosomatids. We document here twelve different U3 snoRNA-U5 snRNA gene arrangements in Euglena; in each case, the U3 gene is linked to a downstream and convergently oriented U5 gene, with the intergenic region differing in length and sequence among the variants.ConclusionThe multiple U3 snoRNA-U5 snRNA gene linkages, which cluster into distinct families based on sequence similarities within the intergenic spacer, presumably arose by genome, chromosome, and/or locus duplications. We discuss possible reasons for the existence of the unusually large number of U3 snoRNA genes in the Euglena genome. Variability in the signal intensities of the multiple Southern hybridization bands raises the possibility that Euglena contains a naturally aneuploid chromosome complement.
| S-EPMC2784804 | biostudies-literature
Project description:The U3 snoRNA coding sequences from the genomic DNAs of Kluyveromyces delphensis and four variants of the Kluyveromyces marxianus species were cloned by PCR amplification. Nucleotide sequence analysis of the amplification products revealed a unique U3 snoRNA gene sequence in all the strains studied, except for K. marxianus var. fragilis. The K. marxianus U3 genes were intronless, whereas an intron similar to those of the Saccharomyces cerevisiae U3 genes was found in K. delphensis. Hence, U3 genes with and without intron are found in yeasts of the Saccharomycetoideae subfamily. The secondary structure of the K. delphensis pre-U3 snoRNA and of the K. marxianus mature snoRNAs were studied experimentally. They revealed a strong conservation in yeasts of (1) the architecture of U3 snoRNA introns, (2) the 5'-terminal domain of the mature snoRNA, and (3) the protein-anchoring regions of the U3 snoRNA 3' domain. In contrast, stem-loop structures 2, 3, and 4 of the 3' domain showed great variations in size, sequence, and structure. Using a genetic test, we show that, in spite of these variations, the Kluyveromyces U3 snoRNAs are functional in S. cerevisiae. We also show that S. cerevisiae U3A snoRNAs lacking the stem-loop structure 2 or 4 are functional. Hence, U3 snoRNA function can accommodate great variations of the RNA 3'-terminal domain.
| S-EPMC1369618 | biostudies-other
Project description:U3 small nucleolar RNA (snoRNA) is a member of the Box C/D family of snoRNAs which functions in ribosomal RNA processing. U3-55k is a protein that has been found to interact with U3 but not other members of the Box C/D snoRNA family. We have found that interaction of the U3-55k protein with U3 RNA in vivo is mediated by the conserved Box B/C motif which is unique to U3 snoRNA. Mutation of Box B and Box C, but not of other conserved sequence elements, disrupted interaction of U3-55k with U3 RNA. Furthermore, a fragment of U3 containing only these two conserved elements was bound by U3-55k in vivo. RNA binding assays performed in vitro indicate that Box C may be the primary determinant of the interaction. We have cloned the cDNA encoding the Xenopus laevis U3-55k protein and find strong homology to the human sequence, including six WD repeats. Deletion of WD repeats or sequences near the C-terminus of U3-55k resulted in loss of association with U3 RNA and also loss of localization of U3-55k to the nucleolus, suggesting that protein-protein interactions contribute to the localization and RNA binding of U3-55k in vivo.
| S-EPMC110750 | biostudies-literature