Evolutionarily conserved features of the retained intron in alternative transcripts of the &amp;lt;i&amp;gt;nxf1&amp;lt;/i&amp;gt; (nuclear export factor) genes in different organisms

Ludmila A Mamon,Sergey F Kliver,Elena V Golubkova

doi:10.4236/ojgen.2013.33018

Abstract

One of the features of intron-containing genes of the nxf (nuclear export factor) family in different organisms 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 inthe genes that are orthologous to nxf1 in vertebrates, and intron 5 -6 inthe genes that are orthologous to nxf1 in Drosophilidae. The alignment of sequences of cassette introns in nxf1 genes in vertebrates has revealed four evolutionarily conserved 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 alignment demonstrate a similarity between cassette introns of nxf1 in Drosophilidae in two poly(A) sequences. The prevalence of Dm nxf1 transcripts containing cassette intron 5-6 under completely spliced transcripts in the heads of adult Drosophila melanogaster suggests a functional importance of transcripts 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.

Highlights

The nxf gene family was named after the function of the universal gene nxf1 responsible for the nuclear-cytoplasmic transport of most mRNAs [1,2,3]
A feature specific to nxf1 genes is the existence of alternative transcripts with a retained intron flanked by evolutionarily conserved exons: 110 nt upstream and 37 nt downstream of the respective intron
We have demonstrated that the transcript with cassette intron 5 - 6 in the head tissues of adult fruit flies exceeds the universal, completely spliced transcript of the gene Dm nxf1, in its relative content (Figure 3) [57]

Summary

Introduction

The nxf Gene Family and Functions of the nxf Gene. The nxf (nuclear export factor) gene family was named after the function of the universal gene nxf responsible for the nuclear-cytoplasmic transport of most mRNAs [1,2,3]. This path of mRNA export is RanGTP-independent [4]. Genes of the nxf family have been found in eukaryotic organisms of the Opisthokonta group, and are characterized by evolutionary conservation [1,5,8]. Nxf genes are the most evolutionarily conserved in the nxf family. What is even more interesting is that nxf genes across different species of mammals exhibit a much greater degree of similarity than Mm nxf and Mm nxf or Hs nxf and Hs nxf exhibit between themselves (Figure 1)

Methods

Results

Conclusion