R-loop landscape in mature human sperm: Regulatory and evolutionary implications

Area of Science:

• Genetics
• Epigenetics
• Molecular Biology

Background:

• R-loops (RNA:DNA hybrids with a displaced DNA strand) are crucial for genome regulation but can threaten genome integrity.
• They are linked to histone modifications, influencing chromatin accessibility.
• Male gametogenesis involves extensive transcription, creating opportunities for R-loop formation in germ cells.

Purpose of the Study:

• To investigate the presence and characteristics of R-loops in mature sperm.
• To explore the relationship between R-loops, chromatin structure, and active retroposons in sperm.
• To assess the impact of sperm R-loops on early zygote development and gene regulation.

Main Methods:

• DNA-RNA immunoprecipitation (DRIP) to map R-loops in human and bonobo sperm.
• Comparison of R-loop data with existing DNA methylation and ChIP data.
• Analysis of R-loop influence on zygote transcriptomes before zygotic genome activation.

Main Results:

• R-loops are present in mature human and bonobo sperm, correlating with transcribed regions and chromatin structure.
• R-loops were found in both histone and protamine-packed chromatin, localizing to active retroposons like ALUs and SVAs.
• Sperm R-loops appear to epigenetically reduce SVA methylation and significantly impact early zygote transcriptomes.

Conclusions:

• R-loops in sperm exhibit conserved and species-specific patterns, resembling somatic cell R-loop landscapes.
• R-loops may epigenetically regulate retroposon methylation, particularly SVAs.
• Chromatin accessibility, modulated by R-loops, could be a mechanism for inherited gene regulation.