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Related Concept Videos

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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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...
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...
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...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: 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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Using the E1A Minigene Tool to Study mRNA Splicing Changes
10:25

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

Prioritizing single-nucleotide variations that potentially regulate alternative splicing.

Mingxiang Teng1, Yadong Wang, Guohua Wang

  • 1School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China. ydwang@hit.edu.cn.

BMC Proceedings
|March 1, 2012
PubMed
Summary
This summary is machine-generated.

Synonymous genetic variations can impact gene regulation and disease. This study identifies functional synonymous single-nucleotide variations (SNVs) affecting RNA-binding protein affinity and alternative splicing, offering a new approach for disease research.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • Complex diseases often stem from genetic variations influencing gene expression.
  • Nonsynonymous variations are typically studied, but synonymous variations also impact disease through RNA processing and translation.
  • RNA-binding proteins (RBPs) play crucial roles in gene regulation.

Purpose of the Study:

  • To systematically investigate the impact of synonymous single-nucleotide variations (SNVs) on RNA-binding protein (RBP) binding affinity.
  • To develop a workflow for identifying regulatory SNVs affecting alternative splicing from exome-sequencing data.
  • To identify functional SNVs associated with quantitative traits in a simulated dataset.

Main Methods:

  • Analysis of 10,113 synonymous SNVs from the 1,000 Genomes Project (GAW17).
  • Identification of SNVs in alternatively spliced exons affecting RBP binding affinity using known 7-mer RNA binding preferences.
  • Application of a proposed workflow to exome-sequencing data and simulated quantitative traits (Q1, Q2).

Main Results:

  • Identified 182 synonymous SNVs significantly altering RBP binding affinity in alternatively spliced exons.
  • Found minor allele frequencies of these SNVs comparable to nonsynonymous SNVs, suggesting functionality.
  • Identified 2 and 4 SNVs predicted to be involved in alternative splicing regulation for traits Q1 and Q2, respectively.

Conclusions:

  • Synonymous SNVs can functionally impact RBP binding and alternative splicing.
  • The developed workflow can identify phenotype-associated regulatory SNVs potentially missed by traditional studies.
  • This research highlights the importance of considering synonymous variations in genetic studies of complex diseases.