PUBLICATION
CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
- Authors
- Huang, Y., Gao, B.Q., Meng, Q., Yang, L.Z., Ma, X.K., Wu, H., Pan, Y.H., Yang, L., Li, D., Chen, L.L.
- ID
- ZDB-PUB-230120-10
- Date
- 2023
- Source
- Genome biology 24: 1515 (Journal)
- Registered Authors
- Li, Dong
- Keywords
- De novo transcription, Developmental embryos, Modified gRNAs, Post-mitotic, Zygotic microinjection, mRNP export
- MeSH Terms
-
- Active Transport, Cell Nucleus
- Animals
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- RNA*/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Zebrafish*/genetics
- Zebrafish*/metabolism
- PubMed
- 36658633 Full text @ Genome Biol.
Citation
Huang, Y., Gao, B.Q., Meng, Q., Yang, L.Z., Ma, X.K., Wu, H., Pan, Y.H., Yang, L., Li, D., Chen, L.L. (2023) CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome biology. 24:1515.
Abstract
Background Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export.
Results We report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression.
Conclusions This optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping