Altered dynamics of scaRNA2 and scaRNA9 in response to stress correlates with disrupted nuclear organization

Abstract

Small Cajal body-specific RNAs (scaRNAs) are part of small Cajal body-specific ribonucleoproteins (scaRNPs) that modify small nuclear RNA (snRNA) in Cajal bodies (CBs). Several scaRNAs (scaRNA 2, 9 and 17) have been found to generate smaller, nucleolus-enriched fragments. We hypothesize that the fragments derived from scaRNA 2, 9 and 17 form regulatory RNPs that influence the level of modifications within rRNA by altering small nucleolar RNP (snoRNP) activity. Here we show that external factors such as DNA damaging agents can alter the scaRNA9 full length to processed fragment ratio. We also show that full-length scaRNA2 levels are likewise impacted by DNA damage, which correlates with the disruption of SMN, coilin and WRAP53 co-localization in CBs. The dynamics of scaRNA9 were also shown to be affected by Drosha levels, which suggests that this protein may participate in the biogenesis and processing of this non-coding RNA. Identification of factors that contribute to scaRNA 2, 9 and 17 processing may facilitate an assessment of how external stress can lead to changes in rRNA modifications.

Synergistic interactions between Cajal bodies and the miRNA processing machinery

“…Our previously published data ( Logan et al , 2018 ), and that shown in Figure 3 , support a role for Drosha and SYNCRIP in the processing of primary-scaRNA. To directly show that the Drosha/DGCR8 complex can process scaRNAs, we conducted in vitro processing assays using two different in vitro transcribed scaRNA9 transcripts.…”

“…In contrast, WRAP53 knockdown does not result in a significant change in the amount of the mgU2-30 fragment derived from ectopically expressed primary-scaRNA9. These findings demonstrate that CB proteins differentially impact the processing of a specific primary-scaRNA, and SYNCRIP, which is part of the miRNA biogenesis machinery, contributes toward scaRNA fragment generation as does Drosha ( Logan et al , 2018 ).…”

“…Interestingly, stem/loop fragments derived from certain scaRNAs (small Cajal body [CB]-specific RNAs) are approximately the same size (70–80 nt) ( Tycowski et al , 2004 ) as precursor-miRNAs generated by Drosha/DGCR8, suggesting that some scaRNAs may be unorthodox substrates for the miRNA processing machinery. We have published data in support of this hypothesis ( Logan et al , 2018 ). CBs are subnuclear domains involved in small nuclear ribonucleoprotein (snRNP) biogenesis ( Darzacq et al , 2002 ; Kiss, 2004 ).…”

“…Namely, mgU2-19 serves as a methylation guide for nucleotide 19 in U2 snRNA and mgU2-30 guides the ribose methylation of U2 snRNA at nucleotide 30 ( Tycowski et al , 2004 ). We have published that the processing of primary-scaRNA9 is reduced on SMN or Drosha knockdown ( Logan et al , 2018 ), which suggests that components of the CB and the miRNA processing machinery together contribute toward the processing of specific primary-scaRNAs. To extend these studies, we evaluated the level of the mgU2-30 fragment generated from ectopically expressed scaRNA9 by Northern blotting in conditions with reduced levels of TDP-43, SYNCRIP, or WRAP53 ( Figure 3B ).…”

Time-restricted feeding alters lipid and amino acid metabolite rhythmicity without perturbing clock gene expression

“…Transcripts with a 12 h circadian period showed an enrichment for transcriptional activity, and for PI3K regulatory activity. Additionally, transcripts with differential rhythmicity were involved in RNA processing [35][36][37] and transcriptional regulation [38][39][40] , as well as PI3K/AKT signaling 41 . These findings corroborate results from rodent studies showing that fasted circadian sampling regulates skeletal and cardiac muscle anabolic signaling 27 .…”