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Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome (CRISPR)

ABSTRACT: Exon-intron circRNA (EIciRNA) is a subclass of backsplicing-generated circRNAs featured with intron retention, among which some play roles in transcriptional regulation. We aim to characterize EIciRNAs by developing pipeline and investigate the factors involved in regulating EIciRNA biogenesis using CRISPR-Cas9 screen, as well as the physiology functions of EIciRNAs during neuronal differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE241682 | GEO | 2024/03/04

REPOSITORIES: GEO

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Systematic identification and characterization of Exon-intron circRNAs

Project description:Exon-intron circRNA (EIciRNA) is a subclass of backsplicing-generated circRNAs featured with intron retention, among which some play roles in transcriptional regulation. We aim to characterize EIciRNAs by developing pipeline and investigate the factors involved in regulating EIciRNA biogenesis using CRISPR-Cas9 screen, as well as the physiology functions of EIciRNAs during neuronal differentiation.

2024-03-04 | GSE253233 | GEO

Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq)

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The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis

Project description:Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.

2020-09-09 | GSE157622 | GEO

Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq)

Project description:Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq)

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Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome

Project description:Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome

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Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome (CRISPR)

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Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-03-04 | GSE241685 | GEO

Intron retention analysis using isogrowth profiling

Project description:We present an analysis of intron retention under stress from two different drugs and their combinations in yeast Saccharomyces cerevisiae. We previously established isogrowth profiling, a method to abstract the non-specific effects of growth rate inhibition from the specific effect of perturbation by a small molecule: two drugs are used at varied ratios, but at fixed overall growth inhibition. Here, cycloheximide and LiCl were used at seven different ratios along the 50% growth inhibition isobole and the total ribodepleted RNA was sequenced. This allowed us to gauge the changes in intron retention due to the used drugs, while ensuring that the effects are not caused by growth inhibition. We found a prominent increase in intron retention under LiCl treatment that preferentially affects introns contained in the transcripts of ribosomal proteins.

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