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Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

Characterization of mRNA structure during the zebrafish maternal-to-zygotic transition identifies the ribosome as a major RNA structure remodeler in vivo and reveals that structural dynamics can affect gene expression, partly by modulating miRNA activity.

Jean-Denis Beaudoin
Eva Maria Novoa
Antonio J. Giraldez
Research30 Jul 2018
Nature Structural & Molecular Biology

Volume: 25, P: 677-686
NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development

The cis-regulatory elements encoded in the sequence and structure of mRNAs determine their translational output. Here the authors develop NaP-TRAP, an assay to measure translation in a frame-specific manner, revealing dynamic regulatory elements in zebrafish embryos and HEK293T cells.

Ethan C. Strayer
Srikar Krishna
Antonio J. Giraldez
ResearchOpen Access30 Dec 2024
Nature Communications

Volume: 15, P: 1-21
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Nano3P-seq presents a nanopore-based sequencing tool to profile polyA-tailed and non-polyA-tailed transcripts, as well as capture polyA tail length and composition.

Oguzhan Begik
Gregor Diensthuber
Eva Maria Novoa
ResearchOpen Access19 Dec 2022
Nature Methods

Volume: 20, P: 75-85
Extreme conservation encodes the structural dynamics and function of 5′ UTRs

RNA is dynamic and can fold into multiple alternative conformations. A new study shows that cells control mRNA translation by regulating the stoichiometry of alternative RNA structures formed from extremely conserved sequences of 5′ untranslated regions and that this control may contribute to embryonic development.

Amit Gupta
Jean-Denis Beaudoin
News & Views22 Apr 2021
Nature Genetics

Volume: 53, P: 591-592
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

An sgRNA-scoring algorithm (CRISPRscan) based on molecular features that enhance activity allows users to predict the most efficient sgRNA for in vivo targets.

Miguel A Moreno-Mateos
Charles E Vejnar
Antonio J Giraldez
Research31 Aug 2015
Nature Methods

Volume: 12, P: 982-988

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Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Extreme conservation encodes the structural dynamics and function of 5′ UTRs

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

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