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Related Concept Videos

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...
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 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...
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...

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Related Experiment Video

Updated: Jun 1, 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

Quantitative evaluation of all hexamers as exonic splicing elements.

Shengdong Ke1, Shulian Shang, Sergey M Kalachikov

  • 1Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

Genome Research
|June 11, 2011
PubMed
Summary

Researchers developed a method to quantify the splicing impact of RNA 6-mers, identifying enhancers (ESEseqs) and silencers (ESSseqs) that influence gene expression. This provides insights into splicing mechanisms and regulatory motifs.

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Using the E1A Minigene Tool to Study mRNA Splicing Changes
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Using the E1A Minigene Tool to Study mRNA Splicing Changes

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Published on: June 24, 2021

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

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • RNA splicing is a critical process in gene expression.
  • Understanding the regulatory elements that control splicing is essential.
  • Previous methods for quantifying splicing factor activity have limitations.

Purpose of the Study:

  • To develop a comprehensive quantitative measure for the splicing impact of all possible RNA 6-mer sequences.
  • To identify and characterize RNA 6-mers as splicing enhancers (ESEseqs) and silencers (ESSseqs).
  • To investigate the influence of sequence context, position, RNA secondary structure, and chromatin structure on splicing regulation.

Main Methods:

  • Deep sequencing of millions of successfully spliced transcripts from a minigene system containing all 4096 RNA 6-mers.
  • Substitution of 6-mers at five positions within two internal exons of a 3-exon minigene.
  • Assignment of relative splicing strength scores (ESRseq scores) to each mutant 6-mer.
  • Analysis of sequence overlaps, positional bias, RNA secondary structure predictions, and nucleosome occupancy scores.

Main Results:

  • A quantitative scoring system (ESRseq) was established for all 4096 RNA 6-mers, classifying them as enhancers or silencers.
  • The splicing effect of 6-mers was context-dependent, often due to overlapping sequences.
  • Positional bias of 6-mers relative to splice sites was observed.
  • RNA secondary structure (single-stranded enhancers/silencers, double-stranded 5' splice sites) and chromatin structure (nucleosome occupancy) correlated with splicing activity.
  • Synergistic effects between 6-mers were identified.

Conclusions:

  • The developed deep sequencing approach provides a robust method for quantifying the splicing impact of RNA sequences.
  • This study identified a comprehensive catalog of RNA 6-mers as splicing enhancers and silencers with associated strength scores.
  • The findings offer significant insights into the mechanisms of RNA splicing regulation, including sequence context, structural, and epigenetic influences.
  • This approach can be broadly applied to define nucleic acid regulatory motifs and potentially replace functional SELEX.