Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells

Abstract

Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H–based fragmentation analysis and 3΄-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5–44 at the 3΄ end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.

Impaired telomere integrity and rRNA biogenesis in PARN‐deficient patients and knock‐out models

“…Unlike what was observed in human cells however, Parn haploinsufficiency also induced a moderate accumulation of 12S pre‐rRNAs, along with slightly shorter precursors (ITS2 probes). This could be indicative of an involvement of mouse PARN in 12S pre‐rRNA early processing or a quality control process, not found in human cells (Ishikawa et al , ; Montellese et al , ). Altogether, our data attest for a biological impact of Parn haploinsufficiency in MEFs and suggest a conserved function for mouse Parn in 18S rRNA biogenesis.…”

“…Recently, PARN was identified as the exonuclease that trims the 3′ end of 18S‐E pre‐ribosomal RNA (pre‐rRNA; Ishikawa et al , ; Montellese et al , ), the last precursor to the 18S rRNA. The full‐length 18S‐E pre‐rRNA (18S‐E FL ) generated by endonucleolytic cleavage by hUTP24 at site E is then submitted to exonucleolytic trimming by PARN before export to the cytoplasm (; Wells et al , ).…”

“…PARN is a ribonuclease from the DEDDh subfamily of nucleases that deadenylates poly(A) tails of RNA and therefore participates in the controlling of mRNA stability and gene expression (Balatsos et al , ). Moreover, two independent laboratories recently identified PARN as a factor involved in rRNA biogenesis in cultured human cell lines after PARN depletion by siRNA (Ishikawa et al , ; Montellese et al , ). Additionally, PARN deadenylates other non‐coding RNAs including miRNAs, piRNAs, scaRNAs, snoRNAs, and the human telomerase RNA component h TR/TERC (Berndt et al , ; Katoh et al , ; Moon et al , ; Nguyen et al , ; Tseng et al , ; Zhang et al , ; Shukla et al , , ; Ishikawa et al , ; Montellese et al , ).…”

“…Moreover, two independent laboratories recently identified PARN as a factor involved in rRNA biogenesis in cultured human cell lines after PARN depletion by siRNA (Ishikawa et al , ; Montellese et al , ). Additionally, PARN deadenylates other non‐coding RNAs including miRNAs, piRNAs, scaRNAs, snoRNAs, and the human telomerase RNA component h TR/TERC (Berndt et al , ; Katoh et al , ; Moon et al , ; Nguyen et al , ; Tseng et al , ; Zhang et al , ; Shukla et al , , ; Ishikawa et al , ; Montellese et al , ). PARN depletion was initially reported to reduce h TR stability by impacting its 3′‐end maturation regulation (Moon et al , ; Nguyen et al , ; Tseng et al , ).…”

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

“…Further processing of pre‐18S in higher eukaryotes apparently differs from the yeast model. Plant 18S‐A2 and human 18S‐E(2a) species can be cleaved endoribonucleolytically like in yeast, but they can also be trimmed by exonucleases (Fig. ).…”