Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Alternative RNA Splicing

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

The molecular determinants of PABPC-mediated deadenylation rate.

bioRxiv : the preprint server for biology·2026

Same author

CD4+ T Cells Sensitize Quasimesenchymal Breast Tumors Lacking CD73 to Anti-CTLA4 Immune Checkpoint Blockade Therapy.

Cancer research communications·2026

Same author

Global stabilization of the transcriptome in mitotic cells.

The EMBO journal·2026

Same author

mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth.

Genes & development·2026

Same author

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation.

Nature·2026

Same author

RSRC2 is a novel RNA-binding protein that safeguards mitotic fidelity by interacting with the lncRNA C1QTNF1-AS1.

Nucleic acids research·2026

Same journal

Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.

Genome research·2026

Same journal

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution.

Genome research·2026

Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026

Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026

Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026

Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 21, 2026

Generation of Maternal Mutants Using zpc:cas9 Knock-in Zebrafish

Generation of Maternal Mutants Using zpc:cas9 Knock-in Zebrafish

Published on: July 22, 2025

Extensive alternative polyadenylation during zebrafish development.

Igor Ulitsky¹, Alena Shkumatava, Calvin H Jan

¹Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.

Genome Research

|June 23, 2012

Summary

This summary is machine-generated.

Zebrafish messenger RNA (mRNA) 3' untranslated regions (3' UTRs) were mapped using 3P-seq, revealing extensive alternative cleavage and polyadenylation (CPA) across development. This provides a comprehensive resource for understanding gene regulation in vertebrates.

More Related Videos

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

Published on: October 19, 2013

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Published on: March 25, 2009

Related Experiment Videos

Last Updated: May 21, 2026

Generation of Maternal Mutants Using zpc:cas9 Knock-in Zebrafish

Generation of Maternal Mutants Using zpc:cas9 Knock-in Zebrafish

Published on: July 22, 2025

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

Published on: October 19, 2013

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Published on: March 25, 2009

Area of Science:

Molecular Biology
Developmental Biology
Genomics

Background:

The 3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) critically regulate their post-transcriptional fate.
Cleavage and polyadenylation (CPA) of pre-mRNAs defines these 3' UTRs.
Understanding 3' UTR dynamics is essential for deciphering gene expression control.

Purpose of the Study:

To comprehensively map poly(A) sites and characterize 3' UTRs in zebrafish across multiple developmental stages and tissues.
To identify instances of alternative CPA and their regulatory implications.
To provide an improved annotation of zebrafish 3' UTRs for future research.

Main Methods:

Poly(A)-position profiling by sequencing (3P-seq) was employed to map poly(A) sites.
Analysis of over 60 million 3P-seq reads was performed.
Existing 3' UTR annotations were substantially improved and expanded.

Main Results:

3' UTR annotations were confidently identified for over 79% of zebrafish protein-coding genes.
Most zebrafish genes exhibit alternative CPA, with over a thousand genes showing stage-specific dominant 3' UTRs.
3' UTR length varies significantly, being shortest in ovaries and longest in the brain, with implications for maternal mRNA stability.

Conclusions:

The study provides a high-resolution map of zebrafish 3' UTRs, significantly enhancing the existing annotation.
Alternative CPA is a widespread mechanism in zebrafish, contributing to stage-specific gene regulation.
The findings offer valuable insights into mRNA processing, stability, and evolution, serving as a crucial resource for vertebrate developmental studies.