R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. Issue 13 (15th July 2022)

• Record Type: Journal Article
• Authors: Munden, Alexander; Benton, Mary Lauren; Capra, John A.; Nordman, Jared T.
• Is Part Of: Journal of molecular biology. Volume 434:Issue 13(2022)
• Publication Date: 2022-07-15
• Subjects: Chromatin -- Epigenetics -- RNA; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2022.167645
• Languages: English
• ISSNs: 0022-2836

Abstract

Graphical abstract: Highlights: Do R-loop positions change during development and do R-loops influence development? Absolute levels of R-loops and their localization change across embryogenesis. R-loop resolution is critical for Drosophila embryogenesis. Chromatin associated factors overlapping R-loops is plastic across development. Changes in transcription do not account for variation in R-loop formation. Abstract: R-loops are involved in transcriptional regulation, DNA and histone post-translational modifications, genome replication and genome stability. To what extent R-loop abundance and genome-wide localization is actively regulated during metazoan embryogenesis is unknown. Drosophila embryogenesis provides a powerful system to address these questions due to its well-characterized developmental program, the sudden onset of zygotic transcription and available genome-wide data sets. Here, we measure the overall abundance and genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that absolute R-loop levels change during embryogenesis and that RNaseH1 catalytic activity is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq reveals that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. Importantly, these changes are not driven by changes in the transcriptional program. Negative GC skew and absolute changes in AT skew are associated with R-loop formation in Drosophila. Furthermore, we demonstrate that while some chromatin binding proteins and histone modifications such as H3K27me3 are associated with R-loops throughout development, other chromatin factors associated with R-loops in a developmental specific manner. Our findings highlight the importance and developmental plasticity of R-loops during Drosophila embryogenesis.