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Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity

ABSTRACT: Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity

PROVIDER: PRJEB48601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7229432_1.fastq.gz	Fastqsanger.gz
	ERR7229432_2.fastq.gz	Fastqsanger.gz
	ERR7229433_1.fastq.gz	Fastqsanger.gz
	ERR7229433_2.fastq.gz	Fastqsanger.gz
	ERR7229434_1.fastq.gz	Fastqsanger.gz

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Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity

Project description:We analyzed function of DHX38 helicase in RNA splicing. We downregulated DHX38 in HEK293 cells by RNAi and compared the transcriptome of DHX38 knockdown cells with cells treated with negative control siRNA.

2022-03-11 | E-MTAB-11127 | biostudies-arrayexpress

Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.

Project description:Retinitis pigmentosa (RP) is a hereditary disease affecting tens of thousands of people world-wide. Here we analyzed the effect of an amino acid substitution in the RNA helicase DHX38 (Prp16) causing RP. DHX38 has been proposed as the helicase important for the 2nd step of splicing. We showed that DHX38 associates with key splicing factors involved in both splicing steps but did not find any evidence that the RP mutations changes DHX38 interaction profile with the spliceosome. We further downregulated DHX38 and monitored changes in splicing. We observed only minor perturbations of general splicing but detected modulation of ~70 alternative splicing events. Next, we probed DHX38 function in splicing of retina specific genes and found that FSCN2 splicing is dependent on DHX38. In addition, RHO splicing was inhibited specifically by expression of DHX38 RP variant. Finally, we showed that overexpression of DHX38 promotes usage of canonical as well as cryptic 5' splice sites in HBB splicing reporter. Together, our data show that DHX38 is a splicing factor that promotes splicing of cryptic splice sites and regulate alternative splicing. We further provide evidence that the RP-linked substitution G332D modulates DHX38 splicing activity.

| S-EPMC8985939 | biostudies-literature

Mutations in the Drosophila splicing regulator Prp31 as a model for Retinitis pigmentosa 11

Project description:A Drosophila mutant for the splicing factor Prp31 was generated and characterized as a model for Retinitis pigmentosa 11. The transcriptome of the mutant was compared to the genetic control white.

2019-01-01 | GSE99665 | GEO

Correction: Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.

Project description:[This corrects the article DOI: 10.1371/journal.pone.0265742.].

| S-EPMC9858684 | biostudies-literature

Inhibition of JNK ameliorates rod photoreceptor degeneration in a mouse model of retinitis pigmentosa

Project description:Retinitis pigmentosa (RP) is an inherited eye disease that causes progressive vision loss.To investigate the biological processes and molecular changes that occur in different cell types in the retinas in rd1 mice, a mouse model of retinitis pigmentosa, we performed single-cell RNA-seq to examine the transcriptomes of various retinal cells.

2024-06-23 | GSE261060 | GEO

Search for recessive retinitis pigmentosa genes using RNA expression analysis in lymphoblasts

Project description:Recessive retinitis pigmentosa (RP) is often caused by nonsense mutations that lead to low mRNA levels as a result of nonsense-mediated decay. Some RP genes are expressed at detectable levels in leukocytes as well as in the retina. We designed a microarray-based method to find recessive RP genes based on low lymphoblast mRNA expression levels Keywords: Recessive mutations; mRNA expression; nonsense mediated-decay; retinitis pigmentosa; lymphocyte; Affymetrix genechip Human Genome U133Plus2.0.

2008-07-14 | GSE12086 | GEO

Autosomal dominant retinitis pigmentosa rhodopsin mutation Q344X drives specific alterations in gene transcription

Project description:The goal of the study was to identify transcriptional modifications in retinal tissues from mouse model of rhodopsin mutation-associated retinitis pigmentosa (RP), Q344X compared to wild-type (WT). We implemented RNA-sequencing (RNA-seq) at poly(A) selected RNA for transcriptomic profiling. Differentially expressed genes were determined by DESeq2 using the Benjamini & Hochberg p-value adjustment and an absolute log2 fold change cutoff. The results indicate that there is specificity in transcriptional patterns in the retina from Q344x mice relative to WT, including differential expression in the potassium channel gene, Kcnv2, and differential expression in histone genes including the H1 family histone member, H1foo, the H3 histone family 3B, H3f3b, and the histone deacetylase 9, Hdac9.

2018-02-21 | GSE102247 | GEO

MicroRNA profiling of mouse wild type (C57) retina and a retina from a mouse model of retinitis pigmentosa (Pro347Ser)

Project description:Experiment to examine the miRNA profiles in the retina compared to the brain and other body regions. A comparison of a wild type C57 mouse retina versus a retina from a mouse model of retinitis pigmentosa (Pro347Ser) was under taken.

2007-11-22 | E-TABM-332 | biostudies-arrayexpress

A mutation in a splicing factor that causes retinitis pigmentosa (RP) has a transcriptome-wide effect on mRNA splicing

Project description:Background: Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci -- sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays. Results: Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting between 10\% and 25\% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT-rich, located towards the 5' end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition. Conclusions: Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. Eight samples consisting of four sibling pairs were analysed. One individual in each pair harboured an RP-causing mutation on the PRPF8 gene (cases). Unaffected siblings were used as controls.

2012-12-25 | E-GEOD-43134 | biostudies-arrayexpress

Inhibition of epigenetic modifiers LSD1 and HDAC1 blocks rod photoreceptor death in mouse models of Retinitis Pigmentosa.

Project description:In retinitis pigmentosa mouse models inhibitors of histone modification enzymes LSD1and HDAC1 blocked rod degeneration, preserved vision and affected the expression of multiple genes including maintenance of rod-specific transcripts and downregulation those involved in inflammation, gliosis and cell death.

2021-08-11 | GSE169527 | GEO

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