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
Datasets
GEO:GSE183453
MeSH Terms
none
PubMed
38974143 Full text @ Cell Insight
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
Figures
Figure Gallery (6 images)
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Expression
No data available
Phenotype
No data available
Mutations / Transgenics
Allele Construct Type Affected Genomic Region
tsu37
    		Small Deletion
    1 - 1 of 1
    Show
    Human Disease / Model
    No data available
    Sequence Targeting Reagents
    Target Reagent Reagent Type
    rnaseh1CRISPR1-rnaseh1CRISPR
    rnaseh1MO1-rnaseh1MRPHLNO
    tp53MO4-tp53MRPHLNO
    1 - 3 of 3
    Show
    Fish
    No data available
    Antibodies
    Name Type Antigen Genes Isotypes Host Organism
    Ab1-tuba1bmonoclonal
      		IgG2aMouse
      Ab4-h2afxmonoclonalIgGRabbit
      1 - 2 of 2
      Show
      Orthology
      No data available
      Engineered Foreign Genes
      No data available
      Mapping
      No data available
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      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.