# rRNA processing and modification

[Ribosomal RNA](https://www.edgepedia.org/ribosomal-rna) (rRNA) processing and modification are the two sets of chemical changes that convert a long precursor transcript into the mature rRNAs of functional ribosomes. Processing consists of endonucleolytic and exonucleolytic cleavage of a single polycistronic (one transcript encoding several separate RNA molecules) precursor to release the 18S, 5.8S, and 28S rRNAs (25S in yeast) of the eukaryotic ribosome.<sup>[5](https://reactome.org/content/detail/R-HSA-8868773)</sup> Modification is the site-specific chemical alteration of nucleotides within those rRNAs, chiefly 2′-O-methylation of the ribose and conversion of uridine to pseudouridine, carried out while the precursor is still being transcribed.<sup>[4](https://reactome.org/content/detail/R-HSA-6790901)</sup> Both processes occur in the nucleolus and cytoplasm as the precursor travels through pre-ribosomal particles.

| Key fact | Detail |
|---|---|
| Precursor transcript | A single 47S pre-rRNA (45S in older nomenclature) is cleaved to yield 18S, 5.8S, and 28S rRNA in humans<sup>[5](https://reactome.org/content/detail/R-HSA-8868773)</sup> |
| Yeast precursor | The 35S pre-rRNA, transcribed by RNA polymerase I, is processed into 18S, 5.8S, and 25S rRNA<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup> |
| Modification counts | 45 pseudouridines and 55 2′-O-methylations in yeast rRNA; around 100 of each in human rRNA<sup>[3](https://pmc.ncbi.nlm.nih.gov/articles/PMC7766524/)</sup> |
| Guiding particles | Box C/D snoRNPs catalyze 2′-O-methylation; box H/ACA snoRNPs guide pseudouridylation<sup>[4](https://reactome.org/content/detail/R-HSA-6790901)</sup> |
| Gene copy number | Human rDNA exists as about 300–400 copies per diploid genome on the short arms of the five acrocentric chromosomes<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup> |
| Cytoplasmic maturation | The endonuclease NOB1 produces the 3′ end of mature 18S rRNA in the cytoplasm<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup> |

## Cleavage of the pre-ribosomal RNA

In eukaryotes the three largest rRNAs are transcribed together by [RNA polymerase I](https://www.edgepedia.org/rna-polymerase-i) as one precursor. In humans this is a 47S transcript containing external and internal transcribed spacers that flank the mature sequences; the 18S, 5.8S, and 28S rRNAs are released by a combination of endonucleolytic cuts and exonucleolytic trimming.<sup>[5](https://reactome.org/content/detail/R-HSA-8868773)</sup> In the yeast *Saccharomyces cerevisiae*, the model organism for ribosome biogenesis, the corresponding 35S pre-rRNA is processed into the 18S, 5.8S, and 25S rRNAs.<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup>

Cleavage at defined sites separates the two maturation pathways. Consistently, the endonuclease NOB1 is required for maturation of the 3′ end of the 18S-E pre-rRNA in the cytoplasm.<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup>

Mammalian cells use more than one processing route. Cleavage of the 45S pre-rRNA can begin either in the 5′ external transcribed spacer or in internal transcribed spacer 1, and initial cleavage at site 2 is the major pathway in HeLa cells, judging by the relative abundance of the resulting pre-rRNA species.<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup> Major differences therefore exist between mammalian and yeast processing pathways.<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup>

Large-subunit maturation also depends on spacer removal.

## 2′-O-methylation and pseudouridylation

Two modifications dominate the rRNA modification landscape. 2′-O-methylation adds a methyl group to the hydroxyl on the 2′ carbon of the ribose, and pseudouridylation converts selected uridines to pseudouridine. Both are introduced co-transcriptionally by small nucleolar ribonucleoproteins (snoRNPs): methylation of the 2′ hydroxyl is catalyzed by box C/D snoRNPs, while pseudouridylation is guided by box H/ACA snoRNPs.<sup>[4](https://reactome.org/content/detail/R-HSA-6790901)</sup>

The cataloged site counts differ between species. In *S. cerevisiae*, 45 pseudouridine and 55 2′-O-methylation sites have been identified on rRNAs, and around 100 of each are found in human rRNAs.<sup>[3](https://pmc.ncbi.nlm.nih.gov/articles/PMC7766524/)</sup> These modifications add hydrogen bonding and lead to a more rigid ribosome structure.<sup>[3](https://pmc.ncbi.nlm.nih.gov/articles/PMC7766524/)</sup>

## Revisions to the modification catalog

The inventory of human modification sites is periodically revised as mapping methods improve. An updated inventory of human 2′-O-methylation sites found no evidence for the previously reported 18S-Gm1536 and 18S-Um1602 sites, while newly identifying modifications at 28S-A1868 and 28S-G3771.<sup>[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC5699541/)</sup> Site counts and identities taken from older references may therefore be outdated, and current catalogs should be checked against recent mapping data.<sup>[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC5699541/)</sup>

## Context within ribosome biogenesis

Processing and modification are embedded in the larger assembly program of the ribosome. The mature 80S ribosome consists of a 60S subunit containing the 25S (plants) or 28S (mammals), 5.8S, and 5S rRNAs with 46 ribosomal proteins in yeast and 47 in humans, and a 40S subunit containing the 18S rRNA with 33 ribosomal proteins.<sup>[6](https://doi.org/10.15252/embj.2022112699)</sup> The high rDNA copy number, about 300–400 repeats per diploid human cell, supports the transcriptional demand for precursor rRNA.<sup>[1](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)</sup>

## References

1. [An overview of pre-ribosomal RNA processing in eukaryotes (WIREs RNA, 2015)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4361047/)
2. [Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function](https://pmc.ncbi.nlm.nih.gov/articles/PMC5699541/)
3. [Non-Coding RNA-Driven Regulation of rRNA Biogenesis](https://pmc.ncbi.nlm.nih.gov/articles/PMC7766524/)
4. [Reactome: rRNA modification in the nucleus and cytosol](https://reactome.org/content/detail/R-HSA-6790901)
5. [Reactome: rRNA processing in the nucleus and cytosol](https://reactome.org/content/detail/R-HSA-8868773)
6. [C0tlxbts3sq (exa.ai)](https://doi.org/10.15252/embj.2022112699)

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*Topic: Encyclopedia › Life and health › Biological foundations › RNA and gene regulation › RNA processing, modification, and translation › Transfer RNA, ribosomal RNA, and translation › Ribosomal RNA and ribosome biogenesis › rRNA processing and modification (site-catalogue home)*

*Initially written Sep 17, 2026 · Reviewed: Sep 30, 2026 · Edited: Sep 30, 2026; Oct 25, 2026 · Last review: Sep 30, 2026*

*Copyright 2026 EdgeChat AI, a subsidiary of Biostate AI.*

License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license