Human Intron Research Articles

Up-Regulation of Luciferase Gene Expression with Antisense Oligonucleotides: Implications and Applications in Functional Assay Development

HeLa Tet-Off cells were transfected transiently as well as stably with a recombinant plasmid (pLuc/705) carrying the luciferase gene interrupted by a mutated human beta-globin intron 2 (IVS2-705). The mutation in the intron causes aberrant splicing of luciferase pre-mRNA, preventing translation of luciferase. However, treatment of the cells with a 2'-O-methyl-oligoribonucleotide targeted to the aberrant splice sites induces correct splicing, restoring luciferase activity. The effects are sequence-specific, depend on the concentration of the oligonucleotide, and can be modulated by the pretreatment of the cell line, Luc/705, with tetracycline. Thus, the cell line provides, among others, a novel functional assay system superior to other procedures that are based on protein down-regulation. In particular, the system would be ideal in assessing the cellular delivery efficiency of antisense oligonucleotides.

Genomic DNA sequence of Rhesus (M. mulatta) cystic fibrosis (CFTR) gene.

Cystic fibrosis is a common human genetic disease caused by mutations in CFTR, a gene that codes for a chloride channel that is regulated by phosphorylation and cytosolic nucleotides. As part of a program to discover natural animal models for human genetic diseases, we have determined the genomic sequence of CFTR in the Rhesus monkey, Macaca mulatta. The coding region of rhesus CFTR is 98.3% identical to human CFTR at the nucleotide level and 98.2% identical and 99.7% similar at the amino acid level. Partial sequences of flanking introns (5582 base pair positions analyzed) revealed 91.1% identity with human introns. Relative to rhesus intronic sequence, the human sequences had 27 insertions and 22 deletions. Primer sequences for amplification of rhesus genomic CFTR sequences are provided. The accession number is AF013753 (all 27 exons and some flanking intronic sequence).

Intradermal immunization with a bovine herpesvirus-1 DNA vaccine induces protective immunity in cattle.

Although intramuscular (i.m.) injection of DNA encoding glycoprotein D (gD) of bovine herpesvirus-1 (BHV-1) induces immune responses in cattle, this route of delivery is inefficient. Here we assessed three parameters that may enhance the efficacy of a gD DNA vaccine in cattle. First, the immune response generated by i.m. injected plasmid expressing a secreted form of gD (tgD) was determined and found to be very similar in magnitude to the response induced by gD-expressing plasmid. Secondly, gD- and tgD-expressing plasmids were administered by intradermal (i.d.) immunization, which resulted in a superior immune response to the secreted form, but no improvement in the response to the membrane-associated form. However, the form of gD used for immunization did not influence the immunoglobulin subtype, the ratio of antigen-specific IgG1 to IgG2 being approximately 4:1. Finally, the effect of promoter strength was assessed by replacing the Rous sarcoma virus (RSV) promoter, which was used in the original experiments, with the human cytomegalovirus immediate early promoter and first intron A (HCMV/IA). Although upon transfection in vitro the HCMV/IA promoter appeared to be stronger than the RSV promoter, there was only a 2-fold higher antibody response in vivo upon i.d. injection of cattle. Protection against virus challenge was obtained in the calves immunized i.d. with tgD-encoding plasmid, as shown by a significant reduction in weight loss, virus excretion, temperature response and clinical disease. No significant protection was observed in the animals vaccinated i.d. with the gD-expressing plasmid, which correlates with the lower level of immunity pre-challenge.

G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection.

Splicing of small introns in lower eucaryotes can be distinguished from vertebrate splicing by the inability of such introns to be expanded and by the inability of splice site mutations to cause exon skipping-properties suggesting that the intron rather than the exon is the unit of recognition. Vertebrates do contain small introns. To see if they possess properties similar to small introns in lower eucaryotes, we studied the small second intron from the human alpha-globin gene. Mutation of the 5' splice site of this intron resulted in in vivo intron inclusion, not exon skipping, suggesting the presence of intron bridging interactions. The intron had an unusual base composition reflective of a sequence bias present in a collection of small human introns in which multiple G triplets stud the interior of the introns. Each G triplet represented a minimal sequence element additively contributing to maximal splicing efficiency and spliceosome assembly. More importantly, G triplets proximal to a duplicated splice site caused preferential utilization of the 5' splice site upstream of the triplets or the 3' splice site downstream of the triplets; i.e., sequences containing G triplets were preferentially used as introns when a choice was possible. Thus, G triplets internal to a small intron have the ability to affect splice site decisions at both ends of the intron. Each G triplet additively contributed to splice site selectivity. We suggest that G triplets are a common component of human 5' splice sites and aid in the definition of exon-intron borders as well as overall splicing efficiency. In addition, our data suggest that such intronic elements may be characteristic of small introns and represent an intronic equivalent to the exon enhancers that facilitate recognition of both ends of an exon during exon definition.

Sequence, splice site and population frequency distribution analyses of the polymorphic human tryptophan hydroxylase intron 7.

A human tryptophan hydroxylase intron seven polymorphism previously associated with low CSF 5-HIAA and suicidal behavior was sequenced and characterized for its potential role in TPH pre-mRNA splicing. Two polymorphic sites were identified: A218C and A779C. The 779A allelic frequency in various populations ranged from 0.43 to 0.61 and was in strong linkage disequilibrium with the A218C site. A218C provides a site for restriction fragment length polymorphism analysis. TPH mRNA was reverse-transcribed and sequenced. No aberrant splice products from the 779A or 779G TPH genes were detected nor were any other polymorphic nucleotides found.

An Evolutionarily Conserved Region in the Second lntron of the Human Nestin Gene Directs Gene Exmession to CNS Progenitor Cells and to Early Neural Ciest Cells

Central nervous system (CNS) progenitor cells transiently proliferate in the embryonic neural tube and give rise to neurons and glial cells. A characteristic feature of the CNS progenitor cells is expression of the intermediate filament nestin and it was previously shown that the rat nestin second intron functions as an enhancer, directing gene expression to CNS progenitor cells. In this report we characterize the nestin enhancer in further detail. Cloning and sequence analysis of the rat and human nestin second introns revealed local domains of high sequence similarity in the 3' portion of the introns. Transgenic mice were generated with the most conserved 714 bp in the 3' portion of the intron, or with the complete, 1852 bp, human second intron, coupled to the reporter gene lacZ. The two constructs gave a very similar nestin-like expression pattern, indicating that the important control elements reside in the 714 bp element. Expression was observed starting in embryonic day (E)7.5 neural plate, and at E10.5 CNS progenitor cells throughout the neural tube expressed lacZ. At E12.5, lacZ expression was more restricted and confined to proliferating regions in the neural tube. An interesting difference, compared to the rat nestin second intron, was that the human intron at E10.5 mediated lacZ expression also in early migrating neural crest cells, which is a site of endogenous nestin expression. In conclusion, these data show that a relatively short, evolutionarily conserved region is sufficient to control gene expression in CNS progenitor cells, but that the same region differs between rodents and primates in its capacity to control expression in neural crest cells.

Differences in dinucleotide frequencies of human, yeast, and Escherichia coli genes.

Nucleotide sequences coding proteins in human, yeast and Escherichia coli genes were analyzed in terms of dinucleotide occurrences. Every gene is plotted as a point in the dinucleotide space, which is spanned by 16 axes corresponding to the 16 components of the dinucleotide. The metric unit in the space is defined using the log-odds ratio of dinucleotide occurrences in a gene. The distribution of points showed that genes from the same organism are clustered in the space. The clusters of human and E. coli are completely separated, and the yeast cluster sits between, implying that individual genes are classified into the three sources from their location. In fact, they could be identified with accuracy of 90%, using the DNA data alone. Even genes encoding homologous proteins belonging to the same protein superfamily were discriminated by the DNA data, and were correctly identified into their sources with the same accuracy as above. DNA sequences of non-coding regions, including human introns, as well as human genes of GC-rich and GC-poor types, were also analyzed in the same manner. The most significant finding is that human genomic DNA sequences, including genes and introns together, exhibit the largest deviation of dinucleotide occurrence from the random expectation. Possible origins for this phenomenon are discussed.

The introns of the canine rod opsin gene show higher sequence homology to the human than to the rodent introns.

Using genomic DNA from late-onset retinal degenerate and wild type Labrador Retrievers as templates and canine exon-specific oligonucleotides as primers in polymerase chain reaction, all four introns of opsin were cloned and sequenced. Dot-matrix comparisons were made for human, murine and canine introns. Selected sequences containing either intronic or coding sequences were aligned and used for phylogenetic relationship analysis. The opsin gene introns are conserved between the human, the mouse and the dog with regards to number and length. In addition there is an astonishingly high degree of sequence homology between the second and fourth introns. Introns 2(1277 bp in dog) and 4 (863 bp in dog) are 72% and 71% homologous to the human introns, and 57% and 52% homologous to the mouse introns, respectively. The coding sequence (CDS) of the dog shows 93% homology to human CDS and 88% homology to mouse CDS. A phylogenetic analysis of the intronic sequences 2 and 4 confirms the higher relatedness between dog and human than between mouse and human opsin genes. As there are good reasons to believe that the primate and rodent lineages are closer to each other than to the Canis familiaris, there must be some functional constraints on the evolution of human and dog opsins.

Genomic Organization and Transcript Analysis of ICAp69, a Target Antigen in Diabetic Autoimmunity

Islet cell antigen p69 (ICAp69) is a target self-antigen in autoimmune (insulin-dependent) diabetes mellitus. Distributed over more than 100 kb on chromosome 6 (6{A1-A2}), the single murine genomic locus contains 14 coding exons, 39–271 bp in length. The identified human and mouse intron–exon junctions are identical, with intron sizes ranging from 94 bp to 24 kb and with conserved flanking region intron sequences. cDNA cloning identified alternatively spliced ICAp69 mRNA transcripts. The predominating α-transcripts lack exon 4, while β-transcripts include this exon, which codes translation termination in all reading frames and a truncated molecule followingin vitroexpression. γ-Transcripts show splice removal of exons 8–12, while δ-transcripts exclude exon 11. Transcripts use alternative polyadenylation signals including a less frequent ATTAAA sequence. 5′-Untranslated cDNA and genomic sequencing and long PCR analysis suggest the presence of more noncoding exons. All splice variants encode the conserved T-cell epitope (in exon 2) recognized by autoreactive T cells in diabetic children and diabetes-prone NOD mice.

Human and fungal 3′ splice sites are used by Trypanosoma brucei for trans splicing

In Trypanosoma brucei, pre-mRNAs are joined to a 5′ 39 nt spliced leader sequence by trans splicing, a process that has not been well characterized. We have asked whether the 3′ splice site regions of human and yeast introns are able to substitute in vivo for the 3′ spliced leader acceptor regions of trypanosome pre-mRNA sequences. The ability of heterologous sequences to participate in trans splicing in trypanosomes was assayed by chloramphenicol acetyltransferase (CAT) enzyme activity and/or the detection of spliced CAT mRNA. Four out of the six heterologous 3′ splice site regions (human β-globin intervening sequence (IVS)2, human c-myc IVS2, human factor-VIII IVS1, and yeast actin IVS) functioned as 3′ spliced leader acceptor regions in T. brucei, while two did not show significant or detectable levels of CAT activity (human β-globin IVS1 and human c-myc IVS1). In the case of the human β-globin IVS1 however, lengthening of the polypyrimidine tract as a result of single purine to pyrimidine transversions produced an active acceptor in which the spliced leader addition site coincides with the 3′ splice site of the β-globin exon 2. These studies indicate that some, but not all 3′ acceptor regions in humans can function as spliced leader addition sites in trypanosomes.

Chapter 26 Cholinergic drug resistance and impaired spatial learning in transgenic mice overexpressing human brain acetylcholinesterase

Publisher Summary This chapter focuses on the cholinergic drug resistance and impaired spatial learning in transgenic mice overexpressing human brain acetylcholinesterase. Appropriate functioning of the cholinergic synapse requires a precise balance of its elements. Important contributors toward this balance are the acetylcholine (ACh) synthesizing enzyme choline acetyltransferase, the hydrolyzing enzyme acetylcholinesterase (AChE), and ACh receptors. Balanced cholinergic neurotransmission is disrupted in several pathological situations. Expression of human AChE under control of the authentic human promoter and first intron is observed in central nervous system neurons of transgenic mice. This expression changed responses to hypothermia-inducing drugs acting on cholinergic and probably serotonergic receptors. In addition, it created a progressive spatial learning and memory impairment. In contrast, the open field behavior of these transgenic animals remained normal. These findings suggest that subtle alterations in the cholinergic balance may cause physiologically observable changes and contribute by itself to the memory deterioration in at least a part of the patients with cholinergic deficits.

The Complete Exon-Intron Structure of the 156-kb Human Gene NFKB1, Which Encodes the p105 and p50 Proteins of Transcription Factors NF-κB and IκB-γ: Implications for NF-κB-Mediated Signal Transduction

The NFKB1 gene encodes three proteins of the NF-κB/Rel and IκB families: p105, p50, and (in mouse) IκB-γ. We determined the complete genomic structure of human NFKB1. NFKB1 spans 156 kb and has 24 exons with introns varying between 40,000 and 323 bp in length. Although NFKB2 , which encodes p100 and p52, also has 24 exons and has a comparable exon-intron structure, it is 20 times shorter (8 kb; Fracchiola et al. (1993) Oncogene 8, 2839-2845) than NFKB1. We propose that the long size of NFKB1 is important for transient activation of NF-κB complexes containing p50. IκB-γ corresponds to the carboxyl-terminal half of p105. DNA sequence analysis showed that the 3′-end of human intron 11 and the 5′-end of exon 12 of NFKB1 are colinear with the 5′-untranslated region of mouse IκB-γ cDNA. IκB-γ is thus likely to be generated by transcription starting within intron 11 and not by alternative splicing of the mouse mRNA encoding p105 and p50.

A densely methylated DNA Island is associated with a chromosomal replication origin in the humanRPS14 locus

We describe a 258-bp densely methylated DNA island (DMI) and chromosomal origin of bidirectional DNA replication within the transcribed portion of the human RPS14 intron 1. Together with the DMIs previously detected in two functional Chinese hamster replication origins [see Ref. 1, pp. 5636-5644], observations described in this report strengthen the correlation between densely methylated DNA islands and active mammalian chromosomal replication origins. Accordingly, DMIs may prove to be reliable physical markers for origins of bidirectional DNA replication in complex genomic DNAs of higher animals.

Comparison of repetitive elements in the third intron of human and rodent mitochondrial benzodiazepine receptor-encoding genes

The third intron of the mitochondrial benzodiazepine receptor (MBR)-encoding gene was sequenced from hamster, mouse and human. The rodent species were found to include an Alu-like sequence, as was first discovered in the rat gene. Differences with the rat intron were evident by an insertion of an additional B1 element in the hamster and the introduction of a complete and two partial B2 sequences in the mouse intron. The human intron contained a cluster of four Alu sequences; however, all of these repetitive elements were found to be in the opposite orientation relative to the Alu-like sequence present in the rodent genes. These findings support the possibility that the rodent Alu-like sequence is a remnant of a retropositional insertion in this gene prior to the divergence of rodent species. Because the human intron does not contain the same Alu remnant, it cannot be concluded that the rodent sequence represents an insertion of a primordial Alu element prior to the divergence of rodent and primate lineages

The baboon expresses the calbindin‐D9k gene in intestine but not in uterus and placenta: Implication for conservation of the gene in primates

Expression of the Calbindin-D9k (CaBP-9k) gene was studied in the baboon. Northern blot analysis using a human CaBP-9k cDNA probe detected expression in duodenum but not in uterus and placenta. Reverse transcription/polymerase chain reaction (RT/PCR) confirmed this expression pattern and indicated a high degree of identity between the baboon and human CaBP-9k mRNAs. PCR was employed to amplify the intron A region of the baboon CaBP-9k gene using human-derived primers and baboon genomic DNA. The baboon intron was closely related to the human CaBP-9k intron A, including the presence a complete Alu-repetitive element. Most significantly, a 13 nucleotide long element at the 5' end of the baboon intron matched exactly the human sequence. This element represents a nonfunctional variation of an estrogen response element found at the same location in the rat CaBP-9k gene. The rat element functions as an enhancer and mediates uterine and possibly placental CaBP-9k expression in the rat and probably most other mammals. The finding of a modified ERE in baboon as in human suggests that during primate evolution the expression of this mammalian-specific gene has been eliminated in uterus and placenta. This scenario raises the question of the role of CaBP-9k in these reproductive tissues.

Regulation of human RPS14 transcription by intronic antisense RNAs and ribosomal protein S14.

RNase protection studies reveal two stable RNAs (250 and 280 nucleotides) transcribed from the antisense strand of the human ribosomal protein gene RPS14's first intron. These transcripts, designated alpha-250 and alpha-280, map to overlapping segments of the intron's 5' sequence. Neither RNA encodes a polypeptide sequence, and both are expressed in all human cells and tissues examined. Although alpha-280 is detected among both the cells' nuclear and cytoplasmic RNAs, the great majority of alpha-250 is found in the cytoplasmic subcellular compartment. As judged by its resistance to high concentrations of alpha-amanitin, cell-free transcription of alpha-250 and alpha-280 appears to involve RNA polymerase I. Tissue culture transfection and cell-free transcription experiments demonstrate that alpha-250 and alpha-280 stimulate S14 mRNA transcription, whereas free ribosomal protein S14 inhibits it. Electrophoretic mobility shift experiments indicate specific binary molecular interactions between r-protein S14, its message and the antisense RNAs. In light of these data, we propose a model for fine regulation of human RPS14 transcription that involves RPS14 intron 1 antisense RNAs as positive effectors and S14 protein as a negative effector.

Mutation analysis in two newly identified rat p53 pseudogenes.

We have analysed the genomic organization of the rat p53 gene in normal intestinal rat cells. Exons 5-8 of the p53 gene were amplified by PCR from rat genomic DNA using primers complementary to stretches of nucleotides identical in rat and human cDNAs. Two amplification products of 727 and 339 bp were obtained from the rat DNA. The PCR products were subcloned into M13mp18 and sequenced. By comparison with the rat cDNA sequence the 727 bp band was identified as the functional p53 gene containing exons 5, 6 7 and 8 and introns 5 and 7. The sequences corresponding to human intron 6 are absent from the rat p53. The second amplification product was a mixture of two different 'processed' pseudogenes, in which 42 mutations accumulated in a sequence corresponding to the cDNA between exons 5 and 8. Analysis of these mutations shows that in both pseudogenes the vast majority is constituted by base substitutions, with transitions being more frequent than transversions. The most prominent mutational class is formed by G-->A transitions which are predominantly located at CpG sites. Since a high level of homology is present between the rat and the human cDNA, the type and the positions where mutations occur in the two rat pseudogenes is discussed in relation to the possible origin of these mutations in human tumors.

An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken beta-tropomyosin pre-mRNA.

Computer analysis of human intron sequences have revealed a 50 nucleotide (nt) GC-rich region downstream of the 5' splice site; the trinucleotide GGG occurs almost four times as frequently as it would in a random sequence. The 5' part of a beta-tropomyosin intron exhibits six repetitions of the motif (A/U)GGG. In order to test whether these motifs play a role in the splicing process we have mutated some or all of them. Mutated RNAs show a lower in vitro splicing efficiency when compared with the wild-type, especially when all six motifs are mutated (> 70% inhibition). Assembly of the spliceosome complex B and, to a lesser extent, of the pre-spliceosome complex A also appears to be strongly affected by this mutation. A 55 kDa protein within HeLa cell nuclear extract is efficiently cross-linked to the G-rich region. This protein is present in the splicing complexes and its cross-linking to the pre-mRNA requires the presence of one or several snRNP. Altogether our results suggest that the G-rich sequences present in the 5' part of introns may act as an enhancer of the splicing reaction at the level of spliceosome assembly.

Specific combinations of human serum albumin introns direct high level expression of albumin in transfected COS cells and in the milk of transgenic mice.

A new series of expression vectors, each comprised of the beta-lactoglobulin (BLG) promoter driving one of a variety of human serum albumin (HSA) minigenes or the entire gene, were evaluated for their ability to direct expression of HSA in vitro in COS tissue culture cells and into the milk of transgenic mice. Vectors directed a hierarchy of expression levels in vitro, dependent upon the specific complement of HSA introns included. HSA introns acted in a synergistic manner. In addition, minigenes comprised of specific subsets of introns were more efficacious than the entire HSA gene with all of its introns. Transgenic mice expressed as much as 10 mg ml-1 of HSA in their milk. Vectors comprised of specific intron subsets directed levels at 1 mg ml-1 or greater in the milk of 20% of generated transgenics. A statistical correlation between the expression level trend in vitro with the trend of expression in vivo (% which express) at detectable levels (p = 0.0015) and at the level of greater than 0.1 mg ml-1 (p = 0.0156) was demonstrated. A weak correlation existed (p = 0.0526) at in vivo levels of 1 mg ml-1 or greater. These new vectors are expected to direct the production of high levels of HSA in the milk of a large percentage of generated transgenic dairy animals.

Presence of regulatory sequences within intron 4 of human and murine c-myb genes

The molecular mechanisms that modulate c-myb mRNA transcription in hematopoietic cells appear to involve intron regulatory sequences. We have characterized the fourth of ten introns from both human and murine c-myb genes in regard to nucleotide sequence and specific protein binding. For this approach complete genomic c-myb intron 4 fragments were isolated from mouse and human DNA using PCR amplification with flanking exon-primers derived from the mouse gene. Comparison of the obtained sequences revealed strong homology between the two species. Using crude nuclear protein extracts from mouse and human myb expressing cells (70Z/3B; Molt4) and gel shift experiments we found specific protein interaction for both introns and to determine the protein binding site in detail, we performed DNase I footprinting. Our results indicate that the binding factor is absent in control cell lines without c-myb transcriptional activity, suggesting a possible positive regulatory function of the DNA-protein complex. To confirm these findings we introduced the human c-myb intron 4 DNA sequence into the EcoRI site of the pCAT ™-Promoter plasmid and transfected Molt4 cells with this chimeric construct. The transient expression studies revealed that intron 4 sequences possess enhancer activity. Thus, we have demonstrated that intron 4 sequences can be important for the regulation of c-myb proto-oncogene expression.