Related Experiment Video
Updated: May 2, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
5.9K
Microarray meta-analysis of RNA-binding protein functions in alternative polyadenylation
Wenchao Hu1, Yuting Liu1, Jun Yan1
1CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Plos One
|March 14, 2014
Summary
Alternative polyadenylation (APA) generates mRNA diversity. This study identifies differential APA events in mouse tissues and biological processes, revealing RNA-binding proteins regulate APA, offering a valuable resource for researchers.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Alternative polyadenylation (APA) is a key post-transcriptional mechanism.
- APA generates mRNA transcript diversity with different 3'UTRs from a single gene.
Purpose of the Study:
- To systematically identify differentially expressed APA events in public mouse microarray data.
- To investigate the role of RNA-binding proteins (RBPs) in regulating APA.
- To create a comprehensive resource for APA research.
Main Methods:
- Systematic search and analysis of public mouse microarray data for APA events.
- Construction of a co-expression network between APA events and RBPs.
- Integration of CLIP-seq data to elucidate RBP-APA interactions.
Main Results:
- Hundreds of genes with differential APA events were identified, prevalent in brain and during development, differentiation, and immune responses.
- Differential APA events were widespread in RNA-binding protein genes.
- Nova2 was found to repress and Mbnl1 to promote polyadenylation at proximal poly(A) sites.
Conclusions:
- This study represents the first mammalian microarray meta-analysis on RBP regulation of APA.
- The findings highlight the prevalence of differential APA in specific tissues and biological processes.
- An online resource is provided for the research community, integrating expression data and RBP regulation insights.
Related Concept Videos
02:18Alternative RNA Splicing
20.5K
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...
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...
20.5K
01:36What is Gene Expression?
10.1K
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
10.1K
02:41Chromatin Structure Regulates pre-mRNA Processing
6.6K
In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
The chromatin structure, especially...
6.6K
01:32RNA Splicing
53.3K
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...
53.3K
01:56Riboswitches
8.0K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.0K
01:23Regulation of Expression at Multiple Steps
1.4K
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
1.4K