Pre-rRNA is first transcribed from ribosomal DNA (rDNA), then cleaved and processed into mature rRNA.
Research suggests that either simultaneous to or immediately following synthesis of pre-rRNA, internal modifications are made at regions in the rRNA components, 18S, 5.8S, and 28S, which vary depending on cell type.
There is thought that the base-pairing of snoRNA to pre-rRNA acts as a chaperone in the folding of mature rRNA.
[4] To form mature rRNA 18S, 5.8S, and 28S, pre-rRNA 40S (Xenopus) and 45S (mammals) must go through a series of cleavages to remove the external and internal spacers (ETS/ITS).
[7] Nucleolin, an abundant phosphoprotein, binds to the pre-rRNA immediately after transcription and facilitates the base-pairing between the U3 snoRNA hinges and the ETS.
[8] The area where 5’-ETS is cross-linked to U3 is known as site A’, and is sometimes cleaved in a primary processing event in mammalian pre-rRNA.
[11] The cleavage occurs at site 3, which is near the end of ITS1 and subsequently forms 32S pre-rRNA, a long-lived intermediate.
It is hypothesized that site 3 may serve as a link between 18S and 28S rRNA processing pathways in higher organisms.
Eubacteria contain 16S and 23S rRNA that reside at the top of long base-paired stems that serve as the site for processing of RNase III cleavage.