Hi DNAunion
There are in some cases, expressed introns
DNA Res. 2000 Feb 28; 7(1): 27-30. Related Articles, Links
mRNAs encoding zinc finger protein isoforms are expressed by alternative splicing of an in-frame intron in fission yeast.
Okazaki K, Niwa O.
Kazusa DNA Research Institute, Kisarazu, Chiba, Japan. kokazaki@kazusa.or.jp
We report here that a gene encoding a protein with three zinc fingers is expressed predominantly to produce a protein containing only two zinc fingers in the fission yeast Schizosaccharomyces pombe. A third zinc finger resides within the in-frame intron that is normally spliced out. By RT-PCR analysis, we detected a minor transcript encoding a protein with three zinc fingers. Such alternative splicing for assortment of zinc finger domains have been reported in animals and implicated in switching of the target genes expressed specifically during development. This is the first report of the occurrence of such zinc finger assortment in lower eucaryotes.
Another issue, if one studies gene expression, one can examine total RNA or mRNA. Total RNA will measure transcripts containing introns which have been expressed, hence gene expression. This is different from actually making a protein which does not necessarily correlate all that well with total mRNA levels in any case.
There are even functional genes in introns
Biochem J. 2002 Aug 1; 365(Pt 3): 833-40. Related Articles, Links
An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease.
Cioffi AV, Ferrara D, Cubellis MV, Aniello F, Corrado M, Liguori F, Amoroso A, Fucci L, Branno M.
Biochemistry and Molecular Biology Laboratory, Stazione Zoologica A. Dohrn, Villa Comunale 80121 Naples, Italy.
Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.
RNA. 2000 Apr; 6(4): 616-27. Related Articles, Links
Expression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme.
Decatur WA, Johansen S, Vogt VM.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
NaSSU1 is a complex nuclear group I intron found in several species of Naegleria, consisting of a large self-splicing group I ribozyme (NaGIR2), which itself is interrupted by a small, group I-like ribozyme (NaGIR1) and an open reading frame (ORF) coding for a homing endonuclease. The GIR1 ribozyme cleaves in vitro transcripts of NaSSU1 at two internal processing sites about 400 nt downstream of the 5' end of the intron, proximal to the endonuclease ORF. Here we demonstrate that self-cleavage of the excised intron also occurs in vivo in Naegleria gruberi, generating an ORF-containing RNA that possesses a short leader with a sequence element likely to be involved in gene expression. To assess the functional significance of self-cleavage, we constructed a genetic system in Saccharomyces cerevisiae. First, a mutant yeast strain was selected with a mutation in all the rRNA genes, rendering the rDNA resistant to cleavage by the Naegleria endonuclease. Active endonuclease, which is otherwise lethal, could be expressed readily in these cells. Endonuclease activity also could be detected in extracts of yeast harboring plasmids in which the endonuclease ORF was embedded in its native context in the intron. Analysis of the RNA from these yeast cells showed that the excised intron RNA was processed as in N. gruberi. A mutant intron constructed to prevent self-cleavage of the RNA failed to express endonuclease activity. These results support the hypothesis that the NaGIR1-catalyzed self-cleavage of the intron RNA is a key event in expression of the endonuclease.
The problem with science textbooks is they are too general and usually take to long to update given the rapid pace of science and the near futility of keeping up with the primary literature.
RE: chimp human comparisons, as I understand it, how the comparisons are made is still controversial. Some only compare expressed sequences like EST sequences. Whether the initial studies will include transposons, HERVs, microsatellites, etc. is not clear..but inclusion will be essential ultimately in getting an accurate measure of the human-chimp genomic differences.
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