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  3. Genome-wide Ribonucleotide Detection In Archaea.

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Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
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Genome-wide ribonucleotide detection in Archaea.

Yann Moalic1, Maurane Reveil1, Deepali L Kundnani2

  • 1Univ Brest, Ifremer, BEEP, F-29280 Plouzané, France.

Nucleic Acids Research
|November 22, 2025

View abstract on PubMed

Summary
This summary is machine-generated.

Cells incorporate ribonucleotides (rNMPs) into DNA, challenging genome stability. Archaeal Ribonucleases H (RNases H) remove these rNMPs, revealing specific repair pathways and replication insights.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Genome integrity is threatened by ribonucleotide monophosphate (rNMP) incorporation during DNA synthesis.
  • Ribonucleases H (RNases H) are crucial enzymes for removing rNMPs from DNA to maintain genome stability.

Purpose of the Study:

  • Investigate the role of RNase H types 1 and 2 in processing embedded rNMPs in archaea.
  • Characterize archaeal mechanisms of rNMP incorporation and repair.

Main Methods:

  • Genome-wide nucleotide-resolution mapping of embedded rNMPs.
  • Analysis of rNMP profiles in wild-type and mutant archaeal strains (Haloferax volcanii, Thermococcus barophilus).

Main Results:

  • Identified strand-switching profiles in H. volcanii ΔrnhB, indicating DNA replication origins.
  • Defined archaeal sequence-context rules for rNMP embedment.
  • Confirmed RNase HII as the primary enzyme for rNMP removal, with evidence of compensatory repair.

    • Conclusions:

    • Uncovered archaeal-specific mechanisms for rNMP incorporation and repair.
    • Demonstrated the link between rNMP incorporation patterns and cellular nucleotide pools.
    • Highlighted the implications for DNA replication and genome stability in archaea.