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Related Concept Videos

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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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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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 alternatively spliced transcripts using a proteomic informatics approach.

Rajasree Menon1, Gilbert S Omenn

  • 1Center for Computational Medicine and Biology and National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 11, 2010
PubMed
Summary
This summary is machine-generated.

We developed a new protocol to identify alternatively spliced peptides in mass spectrometry data. This method aids in understanding complex protein changes in diseases like pancreatic cancer.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing is a key mechanism for protein diversity.
  • Identifying alternatively spliced peptides is crucial for understanding cellular function and disease.
  • Existing methods may not fully capture the complexity of alternative splicing in proteomic datasets.

Purpose of the Study:

  • To present a robust protocol for identifying alternatively spliced peptide sequences.
  • To enable the analysis of alternative splicing events using tandem mass spectrometry.
  • To provide a method applicable to both human and mouse proteomic data.

Main Methods:

  • Tandem mass spectrometry datasets were searched using X!Tandem.
  • A modified ECgene resource with all potential translation products was utilized.
  • The Michigan Peptide to Protein Integration (MPPI) scheme was employed for matching peptides to proteins.

Main Results:

  • The protocol successfully identifies alternatively spliced peptide sequences.
  • The method is demonstrated to be effective for human and mouse proteomic datasets.
  • Application to a Kras activation-Ink4/Arf deletion mouse model of pancreatic cancer showcases its utility.

Conclusions:

  • The presented protocol offers a reliable approach for alternative splicing identification in proteomics.
  • This method enhances the understanding of protein isoform diversity.
  • The protocol is valuable for research in cancer biology and other fields involving complex splicing.