splicing

Insights into RNA Maturation and Genetic Regulation

Karine Choquet from the University of Sherbrooke in Canada presented at the Nanopore Community Meeting in Boston. The session’s title is “Genetic regulation of nascent RNA maturation revealed by direct RNA sequencing.” Newly synthesized RNAs are exported to the cytoplasm for translation. The research team was interested in learning more about RNA processing and poly(A) […]
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Alternative Splicing and Neurologic Disorders: Long-read CaptureSeq Findings

Sofia Kudasheva from Earlham Institute in the UK spoke at London Calling 2024 about “Long-read CaptureSeq identifies novel RNA isoforms of psychiatric risk genes.” They noted that alternative splicing is “a key regulator of neuronal differentiation,” occurring in 95% of human genes and involved in disorders. The team wanted to better understand the role of […]
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Splicing Detection with Long Reads

Kuan-Ting Li from Cold Spring Harbor Laboratory presented at London Calling 2019 on “PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.” PSI-Sigma is a splicing detection tool that measures percent spliced in. With nanopore long-read RNA-seq data, PSI sigma presents a newer splicing detection approach. PSI-sigma was benchmarked on synthetic RNAs and […]
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nano-COP to Investigate Nascent RNA Splicing Dynamics

Heather Drexler from Harvard Medical School presented at London Calling 2019 on “Direct sequencing of nascent RNA exposes splicing kinetics and order.” For example, Drexler explained that RNA splicing is complex, with distant exons being joined. Drexler emphasized that transcription rates affect alternative splicing and that transcription and splicing are physically and mechanistically coupled. The […]
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GoT-Splice as Mutations Accumulate

Mariela Cortes Lopez from the Weil Cornell Medicine and New York Genome Center presented at the Nanopore Community Meeting in Houston about “GoT-Splice: unraveling cell-type-specific impact of splicing factor mutations.” Cortes Lopez is investigating mutations in splicing factors. They started by explaining that cells accumulate mutations with age and, therefore, the genomes of cells are […]
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Long-read Sequencing Can Identify RNA Isoforms and NMD Modulators

Evangelos Karousis is a Senior Researcher at the University of Bern, Switzerland and presented at the Nanopore Community Meeting 2021 on “Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells.” They began by describing what nonsense-mediated mRNA decay (NMD) can do how how they can be dangerous. Endogenous mRNAs can be targeted by NMD. In […]
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Nanopore Sequencing to Investigate Splicing Order and Deadenylation Trends

Karine Choquet from Harvard Medical School spoke at the Nanopore Community Meeting 2022 about “Direct RNA sequencing reveals multi-intron splicing order and poly(A) tail lengths across subcellular compartments.” This five-minute session began by explaining RNA processing and removal of introns in eukaryotic gene expression. Choquet explained that “RNA processing is essential for eukaryotic gene expression” […]
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