Endogenous DNA damage at sites of terminated transcripts

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• DNA damage is a known driver of cancer, aging, and neurodegenerative diseases.
• Existing knowledge identifies three transcription-related mechanisms causing DNA damage.
• The precise causes and types of DNA damage remain largely unknown.

Purpose of the Study:

• To identify novel DNA damage intermediates and sources.
• To uncover a fourth transcription-related mechanism of DNA damage.
• To investigate the role of transcription termination in DNA damage.

Main Methods:

• Engineered proteins to capture single-stranded DNA (ssDNA) ends with 3' polarity in bacterial and human cells.
• Utilized DirectRNA sequencing and simultaneous 5' and 3' end RNA sequencing (SEnd-seq).
• Employed mutant RNA polymerase (RNAP) that reads through terminators.

Main Results:

• Identified endogenous DNA damage at sites of terminated transcripts as a novel source.
• Observed frequent spontaneous 3'-ssDNA-end foci in Escherichia coli, linked to DNA replication.
• Discovered distinct 3'-ssDNA-end hotspots near transcription-terminator-like sequences, coinciding with RNA 3'-termini.

Conclusions:

• Transcription termination or pausing can directly promote DNA damage.
• This newly identified mechanism contributes to genomic instability.
• Findings offer new insights into DNA damage pathways relevant to disease and aging.