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Intron retention analysis using isogrowth profiling

ABSTRACT: Intron retention analysis using isogrowth profiling

PROVIDER: PRJNA648363 | ENA |

REPOSITORIES: ENA

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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.

2022-02-15 | GSE155060 | GEO

Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention

Project description:Exposure to certain stresses leads to readthrough transcription downstream of gene ends. Here we found that this phenomenon impacts the expression of genes located downstream to readthrough genes, whereby readthrough transcription proceeds into downstream genes, termed read-in genes. Using polyA-selected RNA-seq data from mouse fibroblasts, we identified widespread read-in in heat shock, oxidative and osmotic stress conditions. Read-in genes share distinctive genomic characteristics; they are extremely short, mainly due to less, shorter, introns, and they are highly GC rich. Furthermore, using ribosome footprint profiling we found that the translation of genes with high degrees of read-in is significantly reduced. Strikingly, read-in genes show extremely high levels of intron retention during stress, mostly in their first intron. While read-in genes share features that are generally associated with increased likelihood of intron retention, such as short introns and high GC content, intron retention in read-in genes during stress exceeds greatly beyond what is expected given their genomic properties. Finally, we found that first introns in read-in genes have weaker 5’ and 3’ splice sites. Our data portray a relationship between read-in and intron retention, suggesting it may have co-evolved to facilitate reduced translation of read-in genes during stress.

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Gene expression and intron retention analysis of ZCRB1-knockdown human cells

Project description:ZCRB1 is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down ZCRB1 in HCT116 cells to analysis the function of ZCRB1 in gene expression and intron retention.

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Gene expression and intron retention analysis of 15.5K-knockdown human cells

Project description:15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in gene expression and intron retention.

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Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

Project description:We report that retention of intron 2 which affects expression of CD19 in CART-19 relapsed leukemia occurs in the context of full length CD19 transcript using Oxford Nanopore sequencing technology. By performing Direct RNA sequencing on Reh leukemia cell lines, we showed that intron 2 retention is functionally equivalent to nonsense mutations.

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Targeted intron retention and excision for rapid gene regulation in response to neuronal activity

Project description:A substantial population of intron retentions are stably maintained in poly-adenylated transcripts and a subset of them are excised upon neuronal stimulation. These regulated intron retention events in fully transcribed RNAs represent a mechanism to rapidly mobilize a pool of mRNAs in response to neuronal activity.

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Orchestrated intron retention regulates normal granulocyte differentiation [RNA-Seq]

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Project description:Reactive astrocytes in ALS models display dysregulated intron retention

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