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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Alternative RNA Splicing02:18

Alternative RNA Splicing

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.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

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.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Pre-mRNA Processing02:01

Pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
RNA Splicing01:32

RNA Splicing

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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Updated: May 23, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Identification of allele-specific alternative mRNA processing via transcriptome sequencing.

Gang Li1, Jae Hoon Bahn, Jae-Hyung Lee

  • 1Department of Integrative Biology and Physiology, David Geffen School of Medicine and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.

Nucleic Acids Research
|April 3, 2012
PubMed
Summary

This study introduces a new method, allele-specific alternative mRNA processing (ASARP), to identify how genetic variants influence gene expression. ASARP reveals that many genes show allele-specific expression, impacting disease and diversity.

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Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding genetic variant function is crucial in the post-genomic era.
  • Identifying mechanisms of gene regulation influenced by genetic variation is a key challenge.

Purpose of the Study:

  • To develop and apply a novel method, allele-specific alternative mRNA processing (ASARP), for identifying genetically influenced mRNA processing events.
  • To investigate allele-specific expression (ASE) and its regulatory mechanisms using transcriptome sequencing (RNA-Seq) data.

Main Methods:

  • ASARP method analyzes RNA-Seq data at single-nucleotide and whole-gene/isoform levels.
  • Identifies allele-specific expression (ASE) and allele-specific regulation of mRNA processing.
  • Applies method to glioblastoma cell line (U87MG) and breast cancer tissues.

Main Results:

  • 26-45% of genes with sufficient coverage showed ASE, with overlap between cell types.
  • Identified mechanisms including alternative splicing, polyadenylation, and transcriptional initiation.
  • Reporter studies confirmed causal single nucleotide variants (SNVs) for allele-specific alternative splicing.

Conclusions:

  • ASARP effectively identifies genetically influenced mRNA processing events.
  • Allele-specific alternative splicing and polyadenylation are significant contributors to ASE.
  • Findings link genetic variants to gene regulation, disease, and phenotypic diversity.