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Related Concept Videos

RNA Splicing01:32

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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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. 
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Annotation-free quantification of RNA splicing using LeafCutter.

Yang I Li1,2, David A Knowles3,4,5, Jack Humphrey6,7

  • 1Department of Genetics, Stanford University, Stanford, CA, USA. yangili1@uchicago.edu.

Nature Genetics
|December 13, 2017
PubMed
Summary
This summary is machine-generated.

LeafCutter analyzes intron splicing variation from RNA sequencing data without needing transcript annotations. This method efficiently identifies splicing quantitative trait loci (sQTLs) and links them to complex traits and diseases.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Intron excision is crucial for messenger RNA (mRNA) processing.
  • Studying variations in intron splicing is essential for understanding gene regulation and disease mechanisms.

Purpose of the Study:

  • To develop LeafCutter, a novel tool for analyzing sample and population variation in intron splicing.
  • To identify complex splicing events and map splicing quantitative trait loci (sQTLs) efficiently.

Main Methods:

  • LeafCutter processes short-read RNA sequencing (RNA-seq) data to identify variable splicing events.
  • The approach does not require transcript annotations, overcoming challenges with complex splicing.
  • It enables detection of differential splicing and mapping of sQTLs.

Main Results:

  • LeafCutter identified 1.4-2.1 times more sQTLs than contemporary methods.
  • Many identified sQTLs helped link molecular effects to disease-associated variants.
  • Transcriptome-wide associations using LeafCutter increased associated disease genes by an average of 2.1-fold compared to gene expression alone.

Conclusions:

  • LeafCutter is a fast, scalable, and user-friendly tool for intron splicing analysis.
  • The method enhances the discovery of disease-associated genes and variants through sQTL mapping.
  • LeafCutter provides a powerful approach for studying splicing variation in complex traits.