A functional eukaryotic promoter is contained within the first intron of the hGH-N coding region

A two-promoter system of gene expression in C. elegans

The development of multicellular organisms requires precise spatiotemporal gene expression and the expression of cell/tissue specific isoforms of some genes. This task may require more efficient genome organization in Caenorhabditis elegans and other organisms with relatively small genome size. The SL1 leader sequence is trans-spliced to many mRNAs in C. elegans. We hypothesize that introns coupled to internal SL1 acceptors contain independent promoters. We identify 238 genes that have introns coupled to internal SL1 acceptors. We find that the mean length of the internal SL1-coupled introns is significantly longer than the genome mean. For twelve of the genes, evidence exists that the intronic promoter provides tissue specificity different from that of the primary promoter. We estimate that 2.7% of the genome is regulated through this two-promoter system. We propose that internal SL1-coupled introns function as independent promoters and that this two-promoter system represents a major mechanism in C. elegans, in addition to alternative splicing, that serves to promote tissue-specific expression of protein isoforms. Our finding of the frequent coupling between an internal SL1 and a large immediately upstream intron will make promoters and transcription start sites predictable.

A functional promoter region of the CKLFSF2 gene is located in the last intron/exon region of the upstream CKLFSF1 gene

The genes for CKLFSF1 (chemokine-like factor super family member 1) and CKLFSF2 (chemokine-like factor super family member 2) are very closely linked, within 312 bp of each other. Here, we present evidence that the last intron/exon region of the CKLFSF1 gene contains a novel eukaryotic promoter capable of directing the expression of the downstream gene, CKLFSF2. We identified two segments of the upstream region of the CKLFSF2 gene, 2146 bp (-2134/+12, relative to ATG +1) and 1483 bp (-2134/-652), that were capable of efficiently driving expression of a linked reporter gene upon transient transfection into several kinds of cell lines. The 1483 bp segment exhibited more than a two-fold increase in luciferase activity relative to the 2146 bp segment. By analyzing 5'-deletion mutants of the 1483 bp segment, we identified a 195 bp segment (-846/-625) located in the last intron/exon region of the CKLFSF1 gene that was critical for promoter activity. DNA decoy experiments revealed that a 122 bp (-846/-725) fragment markedly inhibited CKLFSF2 mRNA transcription. Furthermore, we found that the putative promoter region of the CKLFSF2 gene is separated from the transcription start site by about 500 bp. Accumulating reports suggest that introns have many functions, including the modulation of regulation and structure. This work provides evidence that a eukaryotic gene promoter sequence from one gene located in an intron/exon of another.

Usage of an intronic promoter for stable gene expression in Saccharomyces cerevisiae

AIMS

To construct expression vectors capable of switching promoters under different metabolic circumstances to obtain stable gene expression.

METHODS AND RESULTS

In this study, we designed a series of constructs for the expression of the chicken lactate dehydrogenase (cldh) gene under the control of galactose-inducible GAL1 promoter and the high glucose-inducible HXT1 promoter in Saccharomyces cerevisiae. In one construct, the HXT1 promoter was placed between artificial splicing sequences to function as an intronic promoter. We checked all constructs for the usage of promoters by reverse transcriptional polymerase chain reaction and assayed the expression level of the reporter gene under different culturing conditions. In the presence of galactose, when the GAL1 promoter was linked with the intronic HXT1 promoter, the cldh gene showed 1.5-fold activity compared with single GAL1 promoter, while in the presence of glucose, the construct showed over twofold activity compared with that without splicing sequences.

CONCLUSION

The intronic HXT1 promoter could be induced by the presence of high glucose concentration.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report detailing the use of an intronic promoter in the construction of stable expression vectors and the novel system could serve as a model of expression vectors for fermentation or other purposes.

Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene

The genes for chemokine-like factor (CKLF) and four chemokine-like factor super family members (CKLFSF1-4) are tightly linked on chromosome 16, with only 325 bp separating CKLF and CKLFSF1. We used Northern blotting and RT-PCR to show that these two genes are expressed independently of one another. We then used a novel computational promoter prediction method based on the interaction among transcription factor binding sites (TFBSs) to identify a putative promoter region for the CKLFSF1 gene. Our method predicted a promoter region in the last intron of the upstream gene, CKLF. We PCR amplified the predicted promoter region and used a luciferase assay to show that the region was able to drive the luciferase gene. DNA decoy experiments indicated that 214 bp fragment neighboring the TATA box markedly inhibited CKLFSF1 gene expression. Sequence analysis of the region revealed a typical TATA box (TATATAA) and multiple potential transcription factor binding sites, providing further evidence for this being a functional promoter for CKLFSF1. This work provides the first evidence of a promoter from one gene located in an intron of another.

The first intron of the murine beta-casein gene contains a functional promoter

Caseins are the major milk proteins in most mammals. Together with calcium and phosphate they form the casein micelle. The corresponding casein genes are clustered in mammalian genomes and their expression is coordinately regulated with regard to developmental and tissue specificity. Casein gene promoters are responsive to lactogenic hormones, cell-matrix, and cell-cell interactions. Transcriptional enhancer elements are found in the 5(') upstream regions of casein genes but have also been detected in the first intron of the bovine beta-casein gene. We show here that the first intron of the murine beta-casein gene has three discernible functions. First, transcriptional enhancer elements present in the intron increase the basal activity of the beta-casein promoter. In addition, these intronic enhancer elements augment the induction of the beta-casein promoter by lactogenic hormones. Finally, we demonstrate that the first intron of the murine beta-casein gene contains a functional promoter.

Human growth hormone 1 (GH1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region

The proximal promoter region of the human pituitary expressed growth hormone (GH1) gene is highly polymorphic, containing at least 15 single nucleotide polymorphisms (SNPs). This variation is manifest in 40 different haplotypes, the high diversity being explicable in terms of gene conversion, recurrent mutation, and selection. Functional analysis showed that 12 haplotypes were associated with a significantly reduced level of reporter gene expression whereas 10 haplotypes were associated with a significantly increased level. The former tend to be more prevalent in the general population than the latter (p<0.01), possibly as a consequence of selection. Although individual SNPs contributed to promoter strength in a highly interactive and non-additive fashion, haplotype partitioning was successful in identifying six SNPs as major determinants of GH1 gene expression. The prediction and functional testing of hitherto unobserved super-maximal and sub-minimal promoter haplotypes was then used to test the efficacy of the haplotype partitioning approach. Electrophoretic mobility shift assays demonstrated that five SNP sites exhibit allele-specific protein binding. An association was noted between adult height and the mean in vitro expression value corresponding to an individual's GH1 promoter haplotype combination (p=0.028) although only 3.3% of the variance of adult height was found to be explicable by reference to this parameter. Three additional SNPs, identified within sites I and II of the upstream locus control region (LCR), were ascribed to three distinct LCR haplotypes. A series of LCR-GH1 proximal promoter constructs were used to demonstrate that 1) the LCR enhanced proximal promoter activity by up to 2.8-fold depending upon proximal promoter haplotype, and that 2) the activity of a given proximal promoter haplotype was also differentially enhanced by different LCR haplotypes. The genetic basis of inter-individual differences in GH1 gene expression thus appears to be extremely complex.

On biased distribution of introns in various eukaryotes

We conducted comprehensive analyses on intron positions in the Mus musculus genome by comparing genomic sequences in the GenBank database and cDNA sequences in the mouse cDNA library recently developed by Riken Genomic Sciences Center. Our results confirm that introns have a tendency to be located toward the 5' end of the gene. The same type of analysis was conducted in the coding region of seven eukaryotes (Saccharomyces cerevisiae, Plasmodium falciparum, Caenorhabditis elegans, Drosophila melanogaster, M. musculus, Homo sapiens, Arabidopsis thaliana). Introns in genes with a single intron have a locational bias toward the 5' end in all species except A. thaliana. We also measured the distance from the start codon to the position of the intron, and found that single introns prefer the location immediately after the start codon in S. cerevisiae and P. falciparum. We discuss three possible explanations for these findings: (1) they are the consequence of intron loss by reverse-transcriptase; (2) they are necessary to accommodate the function; and (3) they are concerned with the mechanism of pre-mRNA splicing.

Species-specific alternative splicing of transgenic RNA in the mammary glands of pigs, rabbits, and mice

Gene-farming techniques provide an effective tool for the production of recombinant proteins in livestock. Transgenes consisting of genomic DNA sequences are as a rule more efficiently expressed than those in which the product of interest is encoded by a cDNA. However, the processing of pre-mRNA from genomic constructs may yield unexpected messenger RNAs and subsequently protein variants. We describe the appearance of different alternative mRNA splice patterns of a gene construct in which a mutant human growth hormone (hGH-N) gene is transcriptionally controlled by 2.5 kb of mouse whey acidic protein (WAP2) regulatory sequences in the mammary gland of different livestock species. Compared to the transcription products in transgenic mice harboring the same gene construct and to cell transfection experiments, expression analysis in transgenic pigs and rabbits revealed different mRNA splice patterns with regard to the proportion of the processed transcripts. Apart from already-known physiological mRNA splice products, previously undescribed processed hGH transcripts were observed in these species. Sequence analysis of the transgenes suggests that the species-specific hGH mRNA patterns may be caused by species- and tissue-specific differences in trans-acting splice factors.