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Screening FUS-binding RNA with HEK293 cells overexpressing FUS

ABSTRACT: Screening FUS-binding RNA with HEK293 cells overexpressing FUS

PROVIDER: PRJNA778799 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16872966_1.fastq.gz	Fastqsanger.gz
	SRR16872966_2.fastq.gz	Fastqsanger.gz
	SRR16872967_1.fastq.gz	Fastqsanger.gz
	SRR16872967_2.fastq.gz	Fastqsanger.gz
	SRR16872968_1.fastq.gz	Fastqsanger.gz

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Screening FUS-binding RNA with HEK293 cells overexpressing FUS

Project description:The flag-tagged human FUS was overexpressed in HEK293 cells. Extract RNA from the cell lysate, some of which are enriched with flag antibody. The high-throughput sequencing method was used to detect the difference between the total RNA and flag-enriched RNA profiles.

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RNA-seq analysis of HEK293 and synphilin-1 overexpressing HEK293 cell line

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Identification of in vivo, conserved, FUS RNA binding sites and the impact of FUS on the neuronal transcriptome

Project description:FUS, an RNA binding protein was recently implicated in Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal neurodegenerative disease. We report the identification of the conserved neuronal RNA targets of FUS and the assessment of the impact of FUS depletion on the neuronal transcriptome. We identified that FUS regulates splicing of conserved intron containing transcripts. FUS retains or excludes the conserved intron by binding to them. Identification of FUS neuronal targets using normal human brain samples and mouse neurons

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Identification of FUS RNA targets in HeLa cells

Project description:We identified a landscape of FUS-binding RNA targets in HeLa cells. The majority of the FUS binding sites are in introns of pre-mRNAs and less are in exons and untranslated regions. Significant FUS binding in introns flanking cassette exons, long intron (>100kb) containing transcripts and noncoding RNAs were detected in our study. We specifically determined the function of FUS in regulating the alternative splicing of cassette exons. The top FUS-associated cassette exon is exon 7 of the pre-mRNA of FUS itself. We demonstrated that FUS is a repressor of its own exon 7 splicing. FUS autoregulates its own protein levels by exon 7 alternative splicing and nonsense mediated decay. Moreover, Amyotrophic Lateral Sclerosis (ALS) linked FUS mutants are deficient in FUS autoregulation. CLIP-seq of FUS in HeLa cells

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HITS-CLIP analysis of FUS in lineage-committed cells.

Project description:In the present study, we performed HITS-CLIP analysis for FUS using mouse brain to extensively characterize tits RNA-binding sites and functional roles in RNA metabolisms. We identified preferential binding of FUS to stem-and-loop structures but without any discernible consensus motifs. FUS was preferentially bound to introns and 3' untranslated regions, but the exon/intron boundaries were mostly devoid of FUS-tags. Analysis of position-dependence of FUS-binding sites in regulating inclusion and skipping of exons disclosed that FUS is bound broadly around the alternatively spliced exons. Among them, however, noticeable CLIP-tags were observed in the downstream introns. We also noticed that FUS occasionally binds to the antisense strands in the promoter regions. Global analysis of CLIP-tags and expression profiles revealed that binding of FUS to the promoter antisense regions downgregulates transcription of the sense strand. HITS-CLIP (High Throughput Sequencing after Crosslinking and Immunoprecipitation) experiments targeting FUS in mouse cerebrums derived from 12-week-old C57BL/6 mice

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