1.GENE HYBRID Kua-UBE2V1

DESCRIPTION

Co-transcription of the gene UBE2V1 (Ubiquitin-conjugating E2 enzyme variant 1) with the neighboring upstream gene Kua generates a rare transcript (Kua-UEV), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. Kua-UEV is a two-domain protein, where domain B comes from Kua, and confers the hybrid protein its cytoplasmic localization. This results in the fusion protein Ubiquitin-conjugating E2 enzyme variant Kua. The genes are located in chromosome 20q13.2. In strand minus.

Fig1. Representation of the fusion gene Kua-UEV in chromosome 20. From NCBI.

GENE STRUCTURE

The gene encodes for two different transcripts due to alternative splicing:

Transcript variant 1: longer isoform

• ENSEMBL ID: ENST 00000341698
• Length: 72598bp
• Number of exons: 8
  • First five exons are from Kua
  • Last three exons from UBE2V1
• Translation lenght: 370aa
  • 231aa from Kua
  • 139aa from UBE2V1
• Protein ENSEMBL ID: ENSP00000344166
  View transcript and protein sequences
  

Transcript variant 2: shorter isoform

• ENSEMBL ID: ENST 00000371658
• Length: 48520bp
• Number of exons: 5
  • Exons 4 and 5 from Kua
  • Last three exons from UBE2V1
  • This variant lacks three alternate exons in the coding region and the 5'UTR compared to variant 1
• Translation lenght: 221aa
  • Different N-terminal compared to variant 1
• Protein ENSEMBL ID: ENSP00000360721
  View transcript and protein sequences

Different isoforms are a result of the alternative splicing process. In all alternative isoforms generated from this gene the reading frame is mantained, since the resulting protein has the same aminoacid sequence in all the isoforms.

HOMOLOGY STUDY

List of orthologues from NCBI:

IMAGE	SPECIE	GENE	PROTEIN HOMOLOGY(%)	DNA HOMOLOGY(%)
	P.troglodytes	LOC458329	99.7%	99.8%
	P.falciparum	MAL3P2.20	54.8%	49.3%
	O.sativa	OSJNBb003	50.4%	55.9%
	A.thaliana	AT1G23260	54.5%	56.5%

In humans Kua and UBE2V1 are located contiguously in the same chromosome. Meanwhile, in other species which are very separated phylogenetically from humans (like D. melanoganster and C.elegans) the gene for Kua is unlinked to the gene for the corresponding UEV protein, and Kua and UEV are always expressed as separate proteins. However, there is certain homology in primates such as P. troglodytes.

We have also found orthologues in plasmodium and two plants. This is quite abnormal, because considering that the fusion has probably occured in a recent evolution stage we should have not been able to find the hybrid gene in such species. Therefore, to explain this controversy (if the orthology data is correct, and the co-expresion does really exist in these species) we have hypothezised that the fusion could have also occured in these plants and plasmodium in a parallel way to that in humans. Because plants have a high rate of genomic duplications, this could increase the probability of the fusion between two different genes in different loci. Refered to plasmodium, because it is a parasit with a small genome, it is possible for the genes to be concentrated in the same chromosome, and thereby, near enough to co-express.

GENE EXPRESSION

In order to characterize the gene expression in human cell types and tissues, some miroarray chips from UCSC Genome Browser have been analyzed. The figures show the ratios of two of these experiments, where red colour indicates the gene is highly expressed in the tissue and green that it is underexpressed.

Normal Human Tissue cDNA Microarrays

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

According to the data from the expression tables from UCSC, Kua-UBE2V1 is quite homogenicaly expressed. However, we can highlight that it is highly expressed in immune and blood cells, salivary gland, and the respiratory system like the trachea and lungs. It is detected at low levels mainly in pancreas, brain, bone and ovaries.

Comparing the expression of the hybrid protein with the expression of the two individual genes, it can be seen that tissues where there is over- or underexpression of Kua-UEV also have the same levels of expression either of UBE2V1 or of Kua. Because the function of the hybrid protein and the individual proteins is similar, it is logical to observe this correlation.

GENE FUNCTION

The Kua-UEV mRNA is an infrequent but naturally occurring co-transcribed product of the neighboring Kua and UBE2V1 genes. Two alternative transcripts encoding different isoforms have been described. The proteins produced by these transcripts have UEV1 B domains but the proteins are localized to the cytoplasm rather than to the nucleus. The significance of these co-transcribed mRNAs and the function of their protein products have not yet been determined.

PROMOTER REGION

The characterizations of the gene's promoter region and the transcription factors that are likely to bind to it has been done by two ways: with the program PROMO and with a PERL program developed by ourselves.

1.Perl program:
The folowing items are needed:
- The promoter sequence of the gene Kua-UEV
- Document TFs matrices, which contains 13 selected TFs matrices
- Perl program PERL PROGRAM(identificacio_de_lufs.pl), which has been developed by the authors.

The program has to be executed in Linux terminal by typing:

We have reduced the list of TFs provided by PROMO by selecting the ones with smaller RE-equally values (using a 0,1 cutoff). RE-equally gives the number of expected occurrences of the match in a random sequence of the same length as the query sequence according to the dissimilarity index (15%) consifering equiprobability for the 4 nucleotides.

We can compare the results obtained with the two different methods, bearing in mind however that the program is just a very simple approach to the problem, and hence has a limited predictability.

The coincident TFs are the following: NF-AT1, NF-kappaB and RXR-alpha.