PUBLICATION
ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis
- Authors
- Xu, W., Liu, X., Li, J., Sun, C., Chen, L., Zhou, J., Li, K., Li, Q., Meng, A., Sun, Q.
- ID
- ZDB-PUB-240709-3
- Date
- 2024
- Source
- Cell insight 3: 100179100179 (Journal)
- Registered Authors
- Meng, Anming
- Keywords
- Embryogenesis, Embryonic development, Next generation sequencing, R-loop, Zygotic genome activation
- MeSH Terms
- none
- PubMed
- 38974143 Full text @ Cell Insight
Citation
Xu, W., Liu, X., Li, J., Sun, C., Chen, L., Zhou, J., Li, K., Li, Q., Meng, A., Sun, Q. (2024) ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. Cell insight. 3:100179100179.
Abstract
R-loop, a chromatin structure containing one RNA:DNA hybrid and one unpaired single-stranded DNA, plays multiple biological roles. However, due to technical limitations, the landscapes and potential functions of R-loops during embryogenesis remain elusive. Here, we developed a quantitative and high-resolution ultra-low input R-loop profiling method, named ULI-ssDRIP-seq, which can map global R-loops with as few as 1000 cells. By using ULI-ssDRIP-seq, we reveal the R-loop dynamics in the zebrafish from gametes to early embryos. In oocytes, the R-loop level is relatively low in most regions of the nuclear genome, except maternal-inherited rDNA and mitochondrial genome. The correlation between R-loop and CG methylation dynamics during early development is relatively weak. Furthermore, either up- or down-regulation of global R-loops by knockdown or overexpression of RNase H1 causes a delay of embryonic development with dramatic expression changes in zygotic and maternal genes. This study provides comprehensive R-loop landscapes during early vertebrate embryogenesis and demonstrates the implication of R-loops in embryonic development.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping