Evolutionarily conserved features of the retained intron in alternative transcripts of the nxf1 (nuclear export factor) genes in different organisms

Abstract

One of the features of intron-containing genes of the nxf (nuclear export factor) family in different organ-isms is the presence of an evolutionarily conserved exon-intron block: exon 110nt-intron-exon 37nt. The intron in this evolutionarily conserved block, which we call a " cassette " intron, can be excised or retained in alternative transcripts of nxf1. It corresponds to intron 10 -11 in the genes that are orthologous to nxf1 in vertebrates, and intron 5 -6 in the genes that are orthologous to nxf1 in Drosophilidae. The align-ment of sequences of cassette introns in nxf1 genes in vertebrates has revealed four evolutionarily con-served sequences: 1) 5' flanking sequence, 2) a region containing СТЕ (constitutive transport element), 3) third conserved sequence, and 4) 3' flanking sequence. Introns 5 -6 of nxf1 in Drosophilidae have no similar conserved sequences. The results of sequence align-ment demonstrate a similarity between cassette in-trons of nxf1 in Drosophilidae in two poly(A) se-quences. The prevalence of Dm nxf1 transcripts con-taining cassette intron 5 -6 under completely spliced transcripts in the heads of adult Drosophila melan-ogaster suggests a functional importance of tran-scripts that contain a retained intron. Evolutionary conservation, which in Drosophilidae is evident in the presence of poly(A) sequences in cassette introns of the nxf1 genes, is an adaptive feature: the poly(A) sequences are capable of mimicking the 3'-end of transcripts, promote transport from the nucleus to the cytoplasm, or are involved in NMD control. The ability to form characteristic secondary structures is a common feature of nxf1 cassette introns.