HPV induced R-loop formation represses innate immune gene expression while activating DNA damage repair pathways

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• R-loops, trimeric nucleic acid structures, regulate transcription and replication.
• Aberrant R-loops can cause DNA breaks and genomic instability.
• Elevated R-loops are observed in cancers and human papillomavirus (HPV)-infected cells.

Purpose of the Study:

• To investigate changes in R-loop distribution and function between normal keratinocytes and HPV-positive cervical intraepithelial neoplasia (CIN I) cells.
• To understand the impact of enhanced R-loops on gene transcription and associated pathways in HPV-positive cells.

Main Methods:

• Comparative analysis of R-loop levels in normal keratinocytes versus HPV-positive CIN I cells.
• Assessment of gene transcription alterations in response to R-loop presence.
• Correlation analysis between R-loops, histone modifications (H3K36me3, γH2AX), and gene expression pathways.

Main Results:

• R-loop levels were up to 10-fold higher at cellular genes and 500-fold higher at ALU1 elements in HPV-positive cells.
• Enhanced R-loops led to altered gene transcription, with both increases and decreases observed, affecting pathways like innate immunity and DNA damage repair.
• Downregulation of innate immune genes (e.g., DDX58, IL-6) and upregulation of DNA damage repair genes (e.g., ATM, ATRX) were linked to R-loops and specific histone marks in HPV-positive cells.

Conclusions:

• HPV infection significantly increases R-loop formation in cervical cells, impacting gene expression.
• A potential link exists between R-loops, DNA damage repair, and innate immune pathways in HPV-positive cells.
• These R-loop-associated alterations may play a crucial role in HPV pathogenesis and disease progression.