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Identification of gene expression and splicing changes upon eye-specific downregulation of tri-snRNP components in Drosophila

ABSTRACT: Identification of gene expression and splicing changes upon eye-specific downregulation of tri-snRNP components in Drosophila

PROVIDER: PRJNA474241 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7250800_1.fastq.gz	Fastqsanger.gz
	SRR7250800_2.fastq.gz	Fastqsanger.gz
	SRR7250801_1.fastq.gz	Fastqsanger.gz
	SRR7250801_2.fastq.gz	Fastqsanger.gz
	SRR7250802_1.fastq.gz	Fastqsanger.gz

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Identification of gene expression and splicing changes upon eye-specific downregulation of tri-snRNP components in Drosophila

Project description:The spliceosome is a dynamic RNA-protein complex that executes pre-mRNA splicing and is composed of five core small nuclear ribonucleoprotein particles (U1, U2, U4/5/6 snRNP) and >150 additional proteins specific for each snRNP. We report a circadian role for Pre-mRNA Processing factor 4 (PRP4), a conserved component of the spliceosomal U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex. We broadly hypothesized that downregulation of prp4 led to the aberrant splicing of one or many of the core clock transcripts. To identify these splicing events in an unbiased way, we performed RNA-Sequencing (RNA-Seq) analysis. We reasoned that we could have a more targeted approach if we could zoom in on the overlapping splicing changes that would be driven by the knockdown of at least two different tri-snRNP components. Because the pan-neuronal knockdown of all tri-snRNP components tested in our study led to lethality, we decided to utilize an alternative broad driver. For that purpose, we selected a strong eye-specific Glass Multiple Promoter driver (GMR-Gal4). Because most of the signal from head lysates comes directly from the eye tissue and because the core splicing factors are ubiquitously expressed, GMR-specific downregulation of prp4 and prp8 promised to be a viable alternative to the pan-neuronal knockdown. We examined changes in both the total transcript levels and splicing events upon prp4 knockdown in the eye. The overall gene expression seemed to be dramatically influenced by prp4 downregulation (433 DOWN, 310 UP at FDR < 0.05). Despite the fact that PRP4 is a component of the core spliceosome that is required for constitutive exon splicing, we did not detect dramatic effects on global splicing. Only 45 genes exhibited differential alternate splicing upon prp4 downregulation at FDR < 0.05).

2018-11-30 | GSE115163 | GEO

SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes

Project description:Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome––the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal subcomplexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and USH. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.

2021-05-25 | PXD023942 | Pride

EAPP is essential for tri-snRNP biogenesis and controls cell fate and tumor growth via the alternative splicing of MDM4

Project description:Precursor messenger RNA (pre-mRNA) splicing is catalyzed by the spliceosome, a highly dynamic machinery with sequentially assembled small nuclear ribonucleoproteins (snRNPs) and splicing factors. Aberrant spliceosome composition and function result in the dysregulation of pre-mRNA alternative splicing, which may cause cellular stresses and diseases such as cancer. Here, we identify a splicing factor, E2F-associated phosphoprotein (EAPP), that directly binds to the U4/U6. U5 tri-snRNP and PRPF19 complex. Notably, the C-terminal “bucket” domain in EAPP composed of several beta-sheets is required for its interaction with the tri-snRNP. EAPP is prominently located at Cajal bodies within the nucleus where it colocalizes with the spliceosome. Loss of EAPP impedes the assembly and homeostasis of the tri-snRNP complex in Cajal bodies and increases the frequency of splicing abnormalities, mostly exon skipping. Moreover, EAPP depletion promotes MDM4 exon 6 skipping, which suppresses cell growth and tumor progression via p53 overactivation. Our study demonstrates a previously uncharacterized function of EAPP in spliceosome regulation and reveals that EAPP-mediated alternative splicing of MDM4 is a critical determinant of cell fate and tumor growth.

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Genome-wide mapping of H3K27 tri-methylation in PRC2 components of Pyricularia oryzae

Project description:We report different roles of three PRC2 components, KMT6, P55 and SIN3 played in distribution of genome-wide H3K27 tri-methylation of Pyricularia oryzae. Polycomb repressive complex 2 (PRC2), which is composed of Ezh(Kmt6), Su(z)12, Esc(Eed) and accessory subunits RbAp48/Nurf55(P55), catalyzes the methylation of histone H3 at lysine 27. Loss of P55 caused severe global defects in the normal distribution of H3K27me3 and transcriptional reprogramming on the H3K27me3-occupied genes. Furthermore, we found that the Sin3 histone deacetylase complex was required to sustain H3K27me3 occupancy and stably maintain gene repression by directly interacting with P55.

2022-02-20 | GSE195863 | GEO

Sequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif

Project description:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in isolation, and in broader context with components of the U1 snRNP. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.

2022-02-22 | PXD027189 | Pride

Composition and processing activity of a semi-recombinant holo U7 snRNP

Project description:In animal cells, replication-dependent histone pre-mRNAs are cleaved at the 3’ end by U7 snRNP consisting of two core components: a ~60-nucleotide U7 snRNA and a ring of seven proteins, with Lsm10 and Lsm11 replacing the spliceosomal SmD1 and SmD2. Lsm11 interacts with FLASH and together they recruit the endonuclease CPSF73 and other polyadenylation factors, forming catalytically active holo U7 snRNP. Here, we assembled core U7 snRNP bound to FLASH from recombinant components and analyzed its appearance by electron microscopy and ability to support histone pre-mRNA processing in the presence of polyadenylation factors from nuclear extracts. We demonstrate that semi-recombinant holo U7 snRNP reconstituted in this manner has the same composition and functional properties as endogenous U7 snRNP, being capable of accurately cleaving histone pre-mRNAs in a reconstituted in vitro processing reaction. We also demonstrate that the U7-specific Sm ring assembles efficiently in vitro on a spliceosomal Sm site but the resultant semi-recombinant holo U7 snRNP fails to accurately cleave histone pre-mRNAs. This approach offers a unique opportunity to create engineered U7 snRNPs to study the role of various regions in the Sm proteins and U7 snRNA in the biogenesis of a functional holo U7 snRNP.

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