Javascript must be enabled to continue!
Extensive alternative polyadenylation during zebrafish development
View through CrossRef
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3′ UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development.
Cold Spring Harbor Laboratory
Title: Extensive alternative polyadenylation during zebrafish development
Description:
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs.
We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish.
Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish.
mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages.
These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary.
3′ UTRs tend to be shortest in the ovaries and longest in the brain.
Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA.
At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates.
Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development.
Related Results
Overexpression of CPEB4 in glioma indicates a poor prognosis by promoting cell migration and invasion
Overexpression of CPEB4 in glioma indicates a poor prognosis by promoting cell migration and invasion
Glioma is an aggressive malignancy with limited effective treatment and poor prognosis. Cytoplasmic polyadenylation element binding protein 4 is a regulator of gene transcription a...
Alternatives in Animal Research: The Zebrafish Option
Alternatives in Animal Research: The Zebrafish Option
The utilisation of animals in scientific research has been a longstanding subject of debate, with concerns about animal welfare and ethics. In response, researchers have been inves...
Abstract 1273: Adaptive immunity in a zebrafish model of melanoma.
Abstract 1273: Adaptive immunity in a zebrafish model of melanoma.
Abstract
The recent success of the anti-CLTA-4 antibody, ipilimumab, for late stage metastatic melanoma, provides proof of principle that stimulating the immune syst...
Abstract 1581: Tumor suppressor functions of the zebrafish ink4ab: a novel cyclin-dependent kinase inhibitor.
Abstract 1581: Tumor suppressor functions of the zebrafish ink4ab: a novel cyclin-dependent kinase inhibitor.
Abstract
The human INK4b-ARF-INK4a genetic locus encodes two closely related members of the INK4 family of cyclin dependent kinase inhibitors, p15INK4b and p16INK4a ...
Rearranged zebrafish genomic DNA induces zebrafish mutant after microinjection into fertilized egg and preliminary study of the mechanism
Rearranged zebrafish genomic DNA induces zebrafish mutant after microinjection into fertilized egg and preliminary study of the mechanism
Abstract
Genomic DNA of zebrafish was first digested incompletely with
Msp I
, and then the fragments were jo...
A novel nanoluciferase transgenic reporter to measure proteinuria in zebrafish
A novel nanoluciferase transgenic reporter to measure proteinuria in zebrafish
Abstract
The zebrafish is an important animal system for modelling human diseases. This includes kidney dysfunction as the embryonic kidney (pron...
The Zebrafish Neurophenome Database (ZND): a dynamic open‐access resource for zebrafish neuroscience research
The Zebrafish Neurophenome Database (ZND): a dynamic open‐access resource for zebrafish neuroscience research
Zebrafish (Danio rerio) are widely used in neuroscience research, where their utility as a model organism is rapidly expanding. Low cost, ease of experimental manipulations and suf...
Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish
Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish
AbstractExtensive characterisations of the zebrafish genome and proteome have established a foundation for the use of the zebrafish as a model organism; however, characterisation o...

