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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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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...
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RNA Splicing01:32

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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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Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

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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 (7-methyl guanosine). This 5' cap helps...
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Related Experiment Video

Updated: Feb 19, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Comprehensive Characterization of Alternative Polyadenylation in Human Cancer.

Yu Xiang1, Youqiong Ye1, Yanyan Lou2

  • 1Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX.

Journal of the National Cancer Institute
|November 7, 2017
PubMed
Summary
This summary is machine-generated.

Alternative polyadenylation (APA) plays a key role in cancer, with 3'UTR shortening observed in cell lines. This study identifies clinically relevant APA events and regulators, offering insights into cancer drug mechanisms.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Alternative polyadenylation (APA) is a critical post-transcriptional gene regulation mechanism implicated in human diseases.
  • The functional role of APA in human cancers remains incompletely understood, with a lack of large-scale analyses in cancer cell lines.

Purpose of the Study:

  • To conduct a comprehensive, large-scale analysis of global APA profiles in cancer cell lines and patient samples.
  • To investigate the correlation between APA factors and APA events across various cancer types.
  • To explore the impact of APA on drug sensitivity and identify clinically relevant APA events.

Main Methods:

  • Characterized global APA profiles from 6398 The Cancer Genome Atlas (TCGA) patient samples and 739 Cancer Cell Line Encyclopedia (CCLE) cell lines.
  • Employed linear regression to model APA factor-event correlations and Spearman correlation to assess APA's effect on drug sensitivity.
  • Utilized Wilcoxon rank-sum test or Cox proportional hazards model to identify clinically relevant APA events.

Main Results:

  • Observed significant global 3'UTR shortening in cancer cell lines compared to tumor samples.
  • Identified PABPN1 as a potential master regulator of APA profiles across cancer types.
  • Demonstrated that APA events influence drug sensitivity, particularly for chromatin modifier-targeting drugs, and identified 1971 clinically relevant APA events.

Conclusions:

  • APA significantly reshapes cellular pathways and gene expression in human cancer.
  • APA alterations in clinically actionable genes suggest potential clinical utility for APA profile analysis.
  • This study provides novel insights into APA's role in cancer biology and cancer drug mechanisms.