Ribonucleotide Dynamics in DNA Replication Systems

Ribonucleotides are frequently misincorporated into DNA during replication, arising from imperfect sugar discrimination by DNA polymerases and high intracellular ribonucleotide triphosphate pools. These embedded ribonucleoside monophosphates (rNMPs) alter DNA geometry, compromise strand stability and provoke genome instability if left unrepaired. Cellular surveillance systems mobilise specialised nucleases, notably RNase H enzymes, to excise rNMPs and restore canonical DNA. In eukaryotes, RNase H2 cooperates with replication factors to detect single rNMPs and coordinate their removal, while RNase H1 addresses longer RNA–DNA hybrids. Prokaryotes employ a more diverse suite of ribonucleases that operate at the replication fork or within Okazaki fragment maturation. Emerging evidence further links rNMP dynamics to transcription, mitochondrial genome maintenance and replication restart mechanisms. Understanding the balance between ribonucleotide incorporation, detection and removal is critical for elucidating fundamental replication biology, the aetiology of ribonucleotide‐related diseases and the development of novel genome‐stability therapies.

Research from Nature Portfolio

Recent studies have revealed the importance of regulatory factors in shaping replication‐coupled ribonucleotide removal. In mammalian cells, Replication Termination Factor 2 governs the localisation of RNase H2 at active replisomes, ensuring rapid excision of embedded rNMPs and maintaining replication speed. Unchecked retention of RNase H2 at stalled forks impedes fork restart, which can be rescued by primase‐mediated repriming. In parallel, advances in nanopore sequencing have enabled the direct detection of rNMPs in genomic DNA. Signal patterns characteristic of each ribonucleotide have been exploited to map embedded rNMPs at single‐molecule resolution, paving the way for comprehensive atlases of ribonucleotide distribution in complex genomes without reliance on indirect biochemical assays.

Ribonucleotide Dynamics in DNA Replication Systems publication trend

The graph below shows the total number of articles in ribonucleotide dynamics in dna replication systems across all publications each year (not limited to Nature Index journals).

Technical terms

ribonucleoside monophosphate (rNMP): A single ribonucleotide unit embedded in DNA, comprising a ribose sugar, phosphate and nucleobase.

RNase H1/H2: Enzymes that cleave the RNA strand of RNA–DNA hybrids or remove single embedded rNMPs, respectively.

replisome: The multiprotein complex responsible for DNA strand unwinding and synthesis during replication.

transcription‐coupled repair: A mechanism by which DNA lesions or errors are recognised and repaired preferentially on the transcribed strand by factors associated with RNA polymerase.

Okazaki fragment: Short DNA stretches synthesised on the lagging strand during replication, initially primed by RNA.

ribose‐seq: A sequencing method designed to capture and map the positions of embedded rNMPs in genomic DNA.

References

1. RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell (2023).
2. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nature Communications (2024).
3. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Research (2023).
4. Detection of ribonucleotides embedded in DNA by Nanopore sequencing. Communications Biology (2024).
5. Visual Evidence for the Recruitment of Four Enzymes with RNase Activity to the Bacillus subtilis Replication Forks. Cells (2024).