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Pre-mRNA Processing: RNA Splicing01:36

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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 Processing02:01

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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 to it (7-Methyl...
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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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Related Experiment Video

Updated: Sep 11, 2025

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
08:53

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

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Pervasive noise in human splice site selection.

Eraj S Khokhar1, Kaitlyn Brokaw1, Zachary J Kartje1

  • 1RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA.

Biorxiv : the Preprint Server for Biology
|August 12, 2025
PubMed
Summary
This summary is machine-generated.

Biological noise significantly impacts RNA splicing, leading to cryptic splicing and low-fidelity splice site usage. Rapid nuclear degradation highlights extensive RNA quality control mechanisms in human cells.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Historically, RNA splicing was considered highly efficient and accurate.
  • Recent findings suggest biological noise contributes to transcriptome diversity.
  • Quantitative analysis of stochastic splicing variations is difficult due to transcript degradation.

Purpose of the Study:

  • To investigate stochastic variations in RNA splicing.
  • To quantify cryptic splicing and low-fidelity splice site usage.
  • To understand the degradation pathways of non-productive RNA transcripts.

Main Methods:

  • Ultra-deep sequencing across cellular RNA compartments.
  • Tracking of splicing intermediates in human cells.
  • Analysis of genomic features associated with splicing noise.

Main Results:

  • Abundant cryptic splicing linked to genomic features promoting splicing noise was observed.
  • Pervasive use of low-fidelity splice sites, likely due to spliceosome stochasticity, was detected.
  • Evidence suggests rapid nuclear degradation of non-productive transcripts, not translation-dependent degradation.

Conclusions:

  • RNA processing mechanisms exhibit a significant propensity for error.
  • Widespread surveillance and rapid quality control mechanisms exist for non-productive RNA transcripts.
  • Findings offer new insights into alternative splice site regulation across genes.