Abstract
Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing.
Highlights
Nuclear genes of eukaryotes contain introns which are removed from pre-mRNA in a splicing process catalyzed by the spliceosome–a ribonucleoprotein complex assembled from five small nuclear RNAs and a range of proteins
Along with the increasing popularity of whole genome studies, nonconventional introns were disclosed in the genes of other protists, diplonemids
The relative order of intron excision was compared for pairs of introns belonging to different types
Summary
Nuclear genes of eukaryotes contain introns which are removed from pre-mRNA in a splicing process catalyzed by the spliceosome–a ribonucleoprotein complex assembled from five small nuclear RNAs (snRNA) and a range of proteins. Intron removal begins co-transcriptionally– when the pre-mRNA synthesis on the DNA template by RNA polymerase II is yet to be completed [1,2,3,4,5]. This is possible due to the transcribed introns’ sequences becoming available for further processing as the transcription machinery moves down the DNA template along the reading frame. Non-collinear removal of introns from pre-mRNA is observed in transcripts which can undergo alternative splicing. This process takes place when the removal of the first alternative intron is delayed. It has been observed that in alternatively spliced transcripts, constitutive introns are mainly co-transcriptionally removed, whereas alternative introns–post-transcriptionally [3,5]
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