Splicing diversity revealed by reduced spliceosomes inC. merolaeand other organisms

Abstract

Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5′ splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms.

Extracellular RNA profiles with human age

“…We next ascertained and annotated the potential circRNAs using custom scripts based on circExplorer and found 133 circRNAs with >3 reads total in serum (Figure 5a,b; Supporting Information Table S6). Of these 133 circRNAs, 122 of them were present in the circRNA database, circBase (Figure 5c) (Hudson, Stark, Fast, Russell & Rader, 2015). The 11 circRNAs we identified that are not annotated in circBase are hg19_circ_chr12_46764960_46765162_R, hg19_circ_chr5_131034609_131055110_R, hg19_circ_chr9_100823063_100840629_F, hg19_circ_chr7_65945380_65953025_R, hg19_circ_chr10_12272946_12280484_F, hg19_circ_chr8_82583173_82593819_R, hg19_circ_chr16_69718789_69728142_F, hg19_circ_chr9_139341423_139341678_R, hg19_circ_chr17_29164223_29167799_F, hg19_circ_chr21_30434648_30434736_R, and hg19_circ_chr5_169108747_169122942_F (Supporting Information Table S6).…”

Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

“…3a) with a four-way junction and a terminal stem-loop 38 . However, the sequence of their SL1 and SL2 loops, which are key sites for snRNP specific proteins binding, differ significantly from their S. cerevisiae and human homologs and lack recognizable U1-70k (GAUCRYGARR) and U1A (YUGCAYUY) canonical protein binding sites 39 . In agreement with motifs present at intron boundaries in Encephalitozoon , U1 snRNA displays a conserved human-like ACUUACC 5′ splicing site (SS) motif.…”

“…The spliceosome of E. cuniculi was predicted based on genome data to be much simpler than that of other eukaryotes and to be composed of only 37 proteins 39 , 41 , 42 compared to its human (∼200) and yeast (∼100) counterparts, yet it clearly remains functional as indicated by splicing studies 44 , 45 . However, up until now, many ncRNA components considered vital to the function of the eukaryotic spliceosome were missing from microsporidian annotations.…”

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

“…Alternatively, CWC16a may have a less essential and more specialized role than CWC16b in splicing. Interestingly, the "dramatically reduced" spliceosome in the red alga Cyanidioschyzon merolae contains an ortholog of Yju2/CWC16b/CCDC94 but not Smu1 (Hudson et al 2015;Stark et al 2015). This may suggest a core spliceosomal function for Yju2/CWC16b/CCDC94 and more advanced regulatory roles for CWC16a/CCDC130 and Smu1 in alternative splicing in higher eukaryotes.…”