Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark

Kundnani, D. L.; Yang, T.; Channagiri, T.; Xu, P.; Lee, Y.; Sun, M.; Martinez-Figueroa, F.; Randhawa, S.; Gogate, A.; Jeon, Y.; Marsili, S.; Newnam, G.; Lu, Y.; Park, V.; Tao, S.; Ling, J.; Schinazi, R.; Pursell, Z.; Mohammed, A.; Opresko, P.; Freudenthal, B.; Kim, B.; Yi, S.; Jonoska, N.; Storici, F.

doi:10.1101/2025.06.27.661996

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bioRxiv · 10.1101/2025.06.27.661996

Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark

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Abstract

Ribonucleoside monophosphates (rNMPs) are abundant in DNA, but their distribution and function in human nuclear genomes remain unknown. Here, we mapped nearly one million rNMPs per genome across diverse human cell types, defining a nuclear "ribome" with non-random distribution patterns. rNMPs are enriched in C/G-rich sequences, epigenetically marked regions, and telomeres. Conserved ribonucleotide-enriched zones (REZs) overlap with CpG islands and R-loops. rNMP concentration near transcription start sites (TSSs) correlates positively with gene expression. Wild-type cells display a broader gene-expression range than ribonuclease H2A (RNH2A) knockouts, in which loss of rNMP cleavage causes pronounced retention of embedded rG and strand-biased rC near TSSs, both increasing with gene expression. These findings establish DNA-embedded rNMPs as a novel epigenetic mark that modulates human gene expression.

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Kundnani, D. L., Yang, T., Channagiri, T., Xu, P., Lee, Y., Sun, M., Martinez-Figueroa, F., Randhawa, S., Gogate, A., Jeon, Y., Marsili, S., Newnam, G., Lu, Y., Park, V., Tao, S., Ling, J., Schinazi, R., Pursell, Z., Mohammed, A., Opresko, P., Freudenthal, B., Kim, B., Yi, S., Jonoska, N., Storici, F.. 2025-06-30. Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark. https://doi.org/10.1101/2025.06.27.661996

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