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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Nonsense-mediated mRNA Decay02:27

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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Related Experiment Video

Updated: Jan 7, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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CRYPTID-exon: streamlined detection of cryptic exons from RNA-seq data.

Eraj S Khokhar1, Kaitlyn Brokaw1, Zachary J Kartje1

  • 1RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA.

Biorxiv : the Preprint Server for Biology
|December 25, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed CRYPTID-exon, a computational tool to identify cryptic exons in gene expression. This method aids in understanding cryptic exon functions and their potential therapeutic applications in diseases.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Cryptic splicing is a common yet poorly understood aspect of gene expression in mammals.
  • Identifying functional cryptic exons is challenging due to difficulties in pinpointing exact mRNA sequences.

Purpose of the Study:

  • To introduce CRYPTID-exon, a novel computational method for accurate cryptic exon boundary prediction.
  • To characterize cryptic exons in human cells and assess their role in gene expression regulation.
  • To explore the therapeutic potential of targeting cryptic exons in disease-relevant genes.

Main Methods:

  • Development of CRYPTID-exon, a computational approach modeling RNA-seq read coverage around splice sites.
  • Application of CRYPTID-exon to identify and characterize thousands of cryptic exons in human RNA.
  • Validation of CRYPTID-exon's ability to detect exons sensitive to translation-mediated degradation.

Main Results:

  • Thousands of previously unannotated cryptic exons were identified and characterized in human cells.
  • CRYPTID-exon successfully identified exons affected by translation-mediated degradation.
  • Targeting identified cryptic exons with antisense oligonucleotides (ASOs) demonstrated modulation of gene expression and splicing.

Conclusions:

  • CRYPTID-exon provides a robust framework for systematic identification and characterization of cryptic exons.
  • This approach facilitates understanding the impact of cryptic exons on mRNA stability and translation.
  • Targeting cryptic exons offers a potential strategy for modulating gene expression in disease contexts.