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PubMed2000

Identification and mapping of swine cyclin-dependent kinase inhibitor CDKN2A and CDKN2B exon 2 sequences.

We have isolated the swine homologs of human CDKN2A and CDKN2B exon 2 sequences. As in the human and mouse genomes, the exon 2 sequences of these two genes present a high level of sequence homology and are tightly linked. Using fluorescence in situ hybridization, we have mapped swine CDKN2A and CDKN2B to chromosome 1q25. This confirms the comparative mapping data among man, mouse, and swine, showing a conserved synteny among chromosome segments 9p21, 4C3-C6, and 1q25, respectively.

Animals↗
PubMed1997

Characterization of the rat insulin-like growth factor I gene promoters and identification of a minimal exon 2 promoter.

Insulin-like growth factor I (IGF-I) promoter activity was characterized in C6, GH3, OVCAR-3, and Chinese hamster ovary (CHO) cells. Maximal exon 1 promoter activity was present in the region extending from -133 to +362 (where +1 is the first transcription start site). Promoter activity was higher in the +75/+362 fragment, which contains exon 1 transcription start sites 3 and 4, than in the -133/+74 fragment, which contains exon 1 transcription start sites 1 and 2. Promoter activity was also observed in constructs containing sequences from -133 to +192, which includes start sites 1, 2, and 3. Inclusion of sequences upstream of -133 inhibited exon 1 proximal promoter activity in a cell type-specific manner. Exon 2 promoter activity was observed in all cell lines with a construct containing 73 bp of 5'-flanking sequence and 44 bp of exon 2. Exon 2 promoter activity was abolished when only 36 bp of 5'-flanking sequence and 44 bp of exon 2 were present, suggesting that an essential minimal promoter element(s) is contained within the -73 to -36 region. A putative CACCC box was observed within this region at -53. Upstream sequence regulated exon 2 promoter activity in a cell type-specific manner. Electrophoretic mobility shift assays revealed a single specifically bound band when the +75/+362 fragment of the exon 1 promoter was used with nuclear extracts from C6 and GH3 cells. Multiple specifically bound bands with slower mobility were observed when the -236/+44 exon 2 promoter fragment was incubated with C6, GH3, CHO, and OVCAR-3 cell nuclear extracts. The exon 1 and exon 2 promoter regions were able to inhibit each other's binding in electrophoretic mobility shift assay using GH3 cell and OVCAR-3 cell nuclear extracts, respectively. Oligonucleotides containing consensus activating protein-1 (AP-1) and AP-3 sequences inhibited exon 1 promoter binding by GH3 cell nuclear extracts. AP-2 and AP-3 sites inhibited exon 2 promoter binding. Our data suggest that the sequence surrounding and including start site 3 in exon 1 functions as a minimal independent promoter. The minimal exon 2 promoter is contained within the 73 bp upstream and 44 bp downstream of the transcription start site cluster. These minimal promoters contain similar and distinct elements that are important for basal transcription. Upstream sequences may contain cell type-specific silencer elements.

Animals↗
PubMed1998

Enhancer elements activate the weak 3' splice site of alpha-tropomyosin exon 2.

We have identified four purine-rich sequences that act as splicing enhancer elements to activate the weak 3' splice site of alpha-tropomyosin exon 2. These elements also activate the splicing of heterologous substrates containing weak 3' splice sites or mutated 5' splice sites. However, they are unique in that they can activate splicing whether they are placed in an upstream or downstream exon, and the two central elements can function regardless of their position relative to one another. The presence of excess RNAs containing these enhancers could effectively inhibit in vitro pre-mRNA splicing reactions in a substrate-dependent manner and, at lower concentrations of competitor RNA, the addition of SR proteins could relieve the inhibition. However, when extracts were depleted by incubation with biotinylated exon 2 RNAs followed by passage over streptavidin agarose, SR proteins were not sufficient to restore splicing. Instead, both SR proteins and fractions containing a 110-kD protein were necessary to rescue splicing. Using gel mobility shift assays, we show that formation of stable enhancer-specific complexes on alpha-tropomyosin exon 2 requires the presence of both SR proteins and the 110-kD protein. By analogy to the doublesex exon enhancer elements in Drosophila, our results suggest that assembly of mammalian exon enhancer complexes requires both SR and non-SR proteins to activate selection of weak splice sites.

Alternative Splicing↗
PubMed1993

Identification of an alternatively spliced transcript of human interleukin-4 lacking the sequence encoded by exon 2.

The expression of interleukin-4 (IL-4) mRNA of human peripheral blood mononuclear cells stimulated with phytohemagglutinin (PHA) for 15 hours was analyzed by reverse transcription and subsequent polymerase chain reaction (RT/PCR). These analyses revealed an additional smaller fragment that hybridizes with an IL-4 cDNA probe and an oligonucleotide that is specific for a fragment lacking the sequence encoded by exon 2. Sequencing of this fragment demonstrates that it is generated from an alternatively spliced transcript of the IL-4 gene with the sequence encoded by exon 2 being skipped. Skipping of exon 2 does not result in a frame shift but would delete part of the mature protein (48 bp coding for amino acid residues 22 to 37), including Cys24 but not a region directly involved in receptor binding. Differential splicing of other exons or exon combinations has not been observed. The data suggest that the alternatively spliced transcript is not generated by a splicing or PCR error and is not detectable solely because of the high sensitivity of RT/PCR, but in contrast, argue for a physiological role of the transcript and its potentially encoded protein.

Alternative Splicing↗
PubMed1994

Detection of point mutations in exon 2 of the G6PD gene in Chinese G6PD variants.

In the past few years, a total of 6 different mutations of the G6PD gene have been reported in China. One of these, the C6 mutation (A95-->G), accounted for about 15.4% of the Chinese G6PD variants. In order to develop a strategy for rapid detection of mutation-containing exons of the G6PD gene, we applied the single-strand conformation polymorphism (SSCP) technique to the detection of mutations in exon 2 of this gene. We observed four patients with abnormal migration patterns of the exon 2 band among 20 cases of G6PD variants. Direct PCR sequencing confirmed a T to C substitution in exon 2 that has previously been reported. This procedure is therefore of particular importance for the rapid detection of mutation-containing exons in the G6PD gene.

Base Sequence↗
PubMed1997

Exon 2 of human cathepsin B derives from an Alu element.

Transcripts for the cysteine protease cathepsin B are alternatively spliced in the untranslated regions (UTRs). We show that a cathepsin B probe containing 5'-UTR sequences hybridized to an RNA of approximately 300 nt in addition to the typical 2.2 and 4.0 kbp mRNAs. Within this 5'-UTR, exon 2 was found to be homologous to Alu repetitive elements. Specifically, exon 2 was part of an Alu element interspersed with the cathepsin B gene. The approximately 300 nt band that hybridized to our cathepsin B probe likely corresponds to Alu transcripts, which are known to accumulate in human cells. Indeed, a similarly migrating band was detected with an authentic Alu probe. Thus, we suggest that primary transcripts for cathepsin B contain Alu sequences which are preserved as exon 2 in some fully spliced mRNAs.

Alternative Splicing↗
PubMedDate not supplied

Clinical variability of Stickler syndrome: role of exon 2 of the collagen COL2A1 gene.

Stickler syndrome (progressive arthro-ophthalmopathy) is a genetically heterogeneous disorder resulting from mutations in at least three collagen genes. The most common disease-causing gene is COL2A1, a 54-exon-containing gene coding for type II collagen. At least 17 different mutations causing Stickler syndrome have been reported in this gene. Phenotypically, it is also a variably expressed disorder in which most patients present with a wide range of eye and extraocular manifestations including auditory, skeletal, and orofacial manifestations. Some patients, however, present without clinically apparent systemic findings. This observation has led to difficulty distinguishing this Stickler phenotype from other hereditary vitreoretinal degenerations, such as Wagner syndrome and Snowflake vitreoretinal degeneration. In this regard, review of the literature indicates type II collagen exists in two forms resulting from alternative splicing of exon 2 of the COL2A1 gene. One form, designated as type IIB (short form), is preferentially expressed in adult cartilage tissue. The other form, designated as type IIA (long form), is preferentially expressed in the vitreous body of the eye. Because of this selective tissue expression, mutations in exon 2 of the COL2A1 gene have been hypothesized to produce this Stickler syndrome phenotype with minimal or absent extraocular findings. We review the evidence for families with exon 2 mutations of the collagen COL2A1 gene presenting in a distinct manner from families with mutations in the remaining 53 exons, as well as other hereditary vitreoretinal degenerations without significant systemic manifestations.

Collagen Type II↗
PubMedDate not supplied

Purification and characterization of an exon 2-deleted human beta-tropomyosin constructed by the polymerase chain reaction.

We deleted exon 2 in human skeletal beta-tropomyosin (h beta-SK tropomyosin) using an improved adaptation of polymerase chain reaction (PCR) technology. The first PCR product was used to prime the full-length cDNA, leading to an exon 2-deleted h beta-SK tropomyosin. This new protein, des-(39-80)-tropomyosin, could then be expressed in Escherichia coli and purified to homogeneity. At the nucleotide level, the junction between exons 1 and 3 has been precisely made in the PCR product. The mutated protein was purified using high-performance liquid chromatography. Des-(39-80)-tropomyosin revealed new immunological properties but was still recognized by certain antitropomyosin antibodies. Furthermore, the structural characteristics of the mutated tropomyosin fit those of the full-length tropomyosin. This new adaptation of PCR technology appears to be suitable for every kind of mutation inside a cloned DNA molecule, and one mutation primer per mutation is sufficient.

Base Sequence↗
PubMed2000

Deletion and tandem duplication of exons 2 - 7 in the epidermal growth factor receptor gene of a human malignant glioma.

The epidermal growth factor receptor (EGFR) gene is frequently amplified and rearranged in malignant gliomas with expression of oncogenic deletion mutants (DM). The most common mutant EGFRvIII, which contains a deletion of exons 2 - 7, is constitutively autophosphorylated and inefficiently downregulated. Other less common EGFR mRNA species in gliomas contain tandem duplication of exons, which encode the tyrosine kinase (TK) and calcium mediated receptor internalization (CAIN) domains of the molecule. We examined a panel of human malignant gliomas and found one tumor that expressed four related EGFR proteins, including 125-, 140-, 170-, and 180-kDa species. This tumor also contained four EGFR-related mRNA species, including both wild type EGFR and EGFRvIII transcripts. A third transcript contained a deletion of exons 2 - 7 and 12 - 13 corresponding to the 125-kDa protein. A fourth transcript contained an in-frame, tandem duplication of exons 2 - 7 (EGFR.TDM/2 - 7). The 180-kDa, tandem duplication mutant (TDM) exhibited enhanced basal phosphorylation and impaired downregulation. In contrast to the 140-kDa EGFRvIII; however, phosphorylation of the 180-kDa EGFR.TDM/2 - 7 was strongly induced by ligand. Expression of both deletion and tandem duplication mutants in the same tumor suggests that the mechanisms responsible for DM and TDM formation might be closely related. Oncogene (2000) 19, 4542 - 4548.

Central Nervous System Neoplasms↗
PubMed2004

High variability of peptidylarginine deiminase 4 (PADI4) in a healthy white population: characterization of six new variants of PADI4 exons 2-4 by a novel haplotype-specific sequencing-based approach.

Seven single nucleotide polymorphisms (SNPs) of the peptidylarginine deiminase 4 (PADI4) gene have recently been reported to be strongly associated with rheumatoid arthritis in Japanese individuals. These SNPs are located in or close to exons 2-4 of PADI4 and are organized in at least four different haplotypes. However, a detailed sequencing-based characterization of the PADI4 gene in other populations is still lacking. We therefore analyzed exons 2-4 of the PADI4 gene in 102 healthy white Germans individuals by DNA sequencing and characterized new variants and haplotypes by a novel haplotype-specific sequencing-based approach. The haplotypes 2/3 (padi4_89*G, padi4_90*T, padi4_92*G, padi4_94*T, padi4_104*T, padi4_95*C, padi4_96*C), and haplotype 4 (padi4_89*G, padi4_90*T, padi4_92*G, padi4_94*T, padi4_104*C, padi4_95*G, padi4_96*T) conferring susceptibility to rheumatoid arthritis were detected at frequencies of 30.9% and 7.8%, respectively. In addition, three novel coding SNPs in exons 2, 3, and 4, and three SNPs in introns 2 and 3 located near the exon-intron boundaries were identified in 11 individuals (10.8%). The so-called nonsusceptibility haplotype 1 (padi4_89*A, padi4_90*C, padi4_92*C, padi4_94*C, padi4_104*C, padi4_95*G, padi4_96*T) occurred at a frequency of 58.3%. Additionally, we identified a closely related novel haplotype, haplotype 1B (2.9%), that differs from haplotype 1 only by padi4_92*G/padi4_96*C. This haplotype was not described in the Japanese population. Our results indicate that the PADI4 gene exhibits a remarkable variability and a rather complex haplotypic organization. Further studies on disease association of PADI4 should be performed by haplotype-specific sequencing-based approaches to identify the exact genotype of the PADI4 fragment of interest.

Exons↗
PubMed2003

Disruption of glucocorticoid receptor exon 2 yields a ligand-responsive C-terminal fragment that regulates gene expression.

Mice in which exon 2 of the glucocorticoid receptor (GR) has been disrupted [GR exon 2 knockout (GR2KO)] have been used as a model to study the requirement for this receptor in a number of biological systems. A recent report showed that these mice actually express a truncated ligand-binding GR fragment, prompting us to ask whether this mutation truly results in a glucocorticoid-insensitive phenotype. Based on cDNA microarray analysis of fetal thymocytes, we found that glucocorticoids were able to enhance or repress activation-induced gene expression in GR2KO and wild-type thymocytes to a similar degree. Moreover, although changes in gene expression induced by glucocorticoids alone were blunted, the expression of a substantial number of genes in GR2KO thymocytes was modulated by stimulation with glucocorticoids. Among these genes, as confirmed by quantitative real-time PCR, was the classic glucocorticoid-responsive gene glutamine synthetase as well as genes implicated in T cell development and function such as IL-7 receptor alpha-chain and glucocorticoid-induced leucine zipper (GIL2). Thus, the truncated C-terminal GR2KO product, which lacks the major transactivation domain, retains, to a large extent, the ability to regulate gene expression both positively and negatively in a ligand-responsive manner when expressed in vivo.

Animals↗
PubMed2003

Mutations in exon 2 of GATA1 are early events in megakaryocytic malignancies associated with trisomy 21.

Patients with Down syndrome (DS) frequently develop 2 kinds of clonal megakaryocytosis: a common, congenital, spontaneously resolving, transient myeloproliferative disorder (TMD) and, less commonly, childhood acute megakaryoblastic leukemia (AMKL). Recently, acquired mutations in exon 2 of GATA1, an X-linked gene encoding a transcription factor that promotes megakaryocytic differentiation, were described in 6 DS patients with AMKL. The mutations prevent the synthesis of the full-length GATA1, but allow the synthesis of a shorter GATA1 protein (GATA1s) that lacks the transactivation domain. To test whether mutated GATA1 is involved in the initiation of clonal megakaryoblastic proliferation or in the progression to AMKL, we screened 35 DS patients with either AMKL or TMD and 7 non-DS children with AMKL for mutations in exon 2 of GATA1. Mutations were identified in 16 of 18 DS patients with AMKL, in 16 of 17 DS patients with TMD, and in 2 identical twins with AMKL and acquired trisomy 21. Analysis revealed various types of mutations in GATA1, including deletion/insertions, splice mutations, and nonsense and missense point mutations, all of which prevent the generation of full-length GATA1, but preserve the translation of GATA1s. We also show that the likely mechanism of generation of GATA1 isoforms is alternative splicing of exon 2 rather than, or in addition to, alternative translation initiation, as was proposed before. These findings suggest that acquired intrauterine inactivating mutations in GATA1 and generation of GATA1s cooperate frequently with trisomy 21 in initiating megakaryoblastic proliferation, but are insufficient for progression to AMKL.

Alternative Splicing↗
PubMed2005

Human glucocorticoid receptor alpha transcript splice variants with exon 2 deletions: evidence for tissue- and cell type-specific functions.

Alternative splicing of exon 9 in human glucocorticoid receptor (hGR) transcripts yields two native hGR transcripts and proteins, hGRalpha and hGRbeta. We have now identified four novel hGRalpha transcripts that have various deletions of exon 2 sequences. Among these hGRalpha splice variants, three of them, 1A1/E2dist hGRalpha, 1A2/E2prox hGRalpha, and 1A3/E3 hGRalpha, arise from the hGR 1A promoter, while 1B/E3 hGRalpha comes from the hGR 1B promoter. When fused to Flag and enhanced green fluorescent protein (EGFP) tags at the carboxy terminus, all transcript variants can be correctly translated in vitro and in vivo. The Flag-tagged hGRalpha protein variants can functionally bind to a glucocorticoid response element (GRE) and can mediate hormonal stimulation of a pGRE-luciferase reporter gene. Compared to the "classical", native hGRalpha, these four variants exhibit a cell type-specific activation of a reporter gene, and this is influenced by the hGRalpha 3' untranslated region in the hGR transcript. When equal amounts of the cDNAs for these GRalpha variant proteins are transfected into cells, they can exhibit lower or higher transcriptional activation compared to the classical GR. Furthermore, the EGFP-tagged proteins are nuclear localized, even in the absence of hormone. Using quantitative reverse transcription PCR, we found that these transcripts exist at a low level in CEM-C7 cells and IM-9 cells, although the concentrations of the 1A3/E3 hGRalpha and 1B/E3 hGRalpha transcripts are higher than for hGRbeta transcripts, while 1A1/E2dist hGRalphaand 1A2/E2prox hGRalpha transcript levels are comparable to the 1A1 hGRalpha and 1A2 hGRalpha (without the exon 2 deletions) transcript levels, respectively. Because these novel hGR, N-terminal deleted, protein variants have altered biological activity, their expression could potentially affect the hormone sensitivity or resistance in leukemia and be useful in diagnosing hormone-sensitive or -resistant disease.

Alternative Splicing↗
PubMed2006

Identification of Alu-mediated, large deletion-spanning exons 2-4 in a patient with mitochondrial acetoacetyl-CoA thiolase deficiency.

Mitochondrial acetoacetyl-CoA thiolase (T2) deficiency is a rare inherited metabolic disorder affecting isoleucine catabolism and ketone body metabolism. So far, more than 39 different mutations have been identified in 60 T2-deficient patients. However, no large deletions have been reported. We herein report the first case of a large T2 gene deletion from intron 1 to intron 4 in a T2-deficient patient (GK41). cDNA analysis revealed that an aberrant cDNA with exons 2-5 skipping was a major transcript, associated with a minor transcript of exons 2-4 skipping with a 94-bp insertion composed of an intron 1 sequence. Genomic analysis indicated an absence of PCR amplification of exons 2-4 and gene deletion was revealed by Southern blot analysis. Cloning and sequencing long range PCR products revealed a 6.4kb deletion. Alu element-mediated unequal homologous recombination between an Alu-Sx in intron 1 and another Alu-Y in intron 4 appears to be responsible for this deletion.

Acetyl-CoA C-Acetyltransferase↗
PubMed2003

The alternative use of exons 2 and 3 in cathepsin B mRNA controls enzyme trafficking and triggers nuclear fragmentation in human cells.

Pathological overexpression and trafficking of the cysteine peptidase cathepsin B depend in part on the composition of its mRNA. To investigate the roles of the alternatively spliced exons 2 and 3 in the 5'-untranslated region of cathepsin B mRNA we produced constructs of cathepsin B fused to green fluorescent protein. Expression and trafficking of the fluorescent chimeric products was followed in living human immortalized chondrocytes and HeLa cells. Although synthesized at different rates, proteins encoded by the full transcript and by that missing exon 2 followed a classic route, with the endosomal-lysosomal compartment as the final target. The point-mutated variant missing the glycosylation site for lysosomal targeting followed the secretory pathway. A truncated form of cathepsin B lacking the signal peptide and part of the propeptide, and encoded by the construct missing exons 2 and 3, was neither found in the Golgi apparatus nor in vesicles, but rather in the cytoplasm as patches associated with membranous and short fibrillar elements. This particular form of truncated cathepsin B produced nuclear damage and shrinking of the trans Golgi network and of the acidic compartment. The C-terminal, six-amino acid-long propeptide of cathepsin B did not exhibit a discernible role in protein trafficking.

Alternative Splicing↗
PubMed1993

HLA-B locus DNA typing: detection of B*7801 and seven additional alleles by BW6-specific exon 2 amplification.

A molecular approach to type a new HLA-B5 antigen, HLA-BSNA, characterized by its unusual association with the public determinant BW6, referred to as B*7801, has been designed. Antigens disclosing serological identity with SNA, BX1 and Te76 were also investigated. Based upon HLA-B exon 2 group-specific PCR, the following procedure was established: 5' and 3' primers were designed by targetting the codons 11-12 (AM) and 81-83 (LRG), respectively, in exon 2 (alpha 1 domain). The 5' primer discriminates with HLA-A, -C genes and pseudogenes, while the 3' primer detects the sequence encoding the BW6 epitope (NLRG) and discriminates it from the BW4 epitope. The combination of this pair of primers specifically amplifies 26 HLA-B alleles. Oligotyping for B*7801 was performed using a combination of two non-radioactively labeled SSO probes identifying positions T45 and D74 in exon 2. To resolve ambiguous hybridization patterns, an additional set of probes was used. The specificity of this BW6-group-specific amplification procedure was investigated on 150 genomic DNA samples. Among them, we obtained 94 amplified DNA products which were tested with eight SSOs. Beside B*7801, the following B alleles could be defined: B*0801, B*35, B*5401, B*5501-2, B*5601-2, B*1501-7 (including B62, B75 and B72) and B*4601. SNA, BX1 and Te76 DNA samples gave similar hybridization pattern providing a clue to the identity of these antigens. This "one PCR and two probes" procedure represents a simple oligotyping strategy which can also be applied to type many other HLA-B specificities.

Alleles↗
PubMed2005

The cathepsin D gene exon 2 (C224T) polymorphism and sporadic Alzheimer's disease in European populations.

The cathepsin D gene (CTSD) exon 2 (C224T) polymorphism has been associated with an increased risk for sporadic Alzheimer's disease (AD), but with controversial findings. We studied CTSD exon 2 (C224T) and apolipoprotein E (APOE) genotype frequencies in 168 AD patients and 218 age-matched healthy controls from Southern Italy. No statistically significant differences were found in CTSD allele or genotype frequencies between AD patients and controls, and there were no interactions with sex or APOE genotype. Furthermore, comparing our results with the findings from other European populations, the CTSD*T allele frequency showed a statistically significant increasing trend from Northern to Southern regions of Europe in AD patients and controls (z=2.51, p<.01; z=4.02, p<.001, respectively), with a concomitant inverse trend for CTSD*C allele frequency. The regional differences in CTSD allele frequencies could be related to the different patterns of association between this polymorphism and AD in various European studies.

Aged↗
PubMed1993

C-ski transcripts with and without exon 2 are expressed in skeletal muscle and throughout chick embryogenesis.

Overexpression of v-ski or c-ski cDNAs has a pronounced effect on proliferation, morphological transformation and myogenic differentiation in cells in culture and in transgenic animals. Yet, little is known about expression of the c-ski locus or the relationship between c-ski cDNAs and alternatively spliced c-ski transcripts in chicken tissues, particularly in skeletal muscle or during embryogenesis. We developed a series of probes and oligonucleotide primers specific for the eight coding exons and the long 3' noncoding region found in chicken c-ski mRNAs. The most abundant chicken c-ski mRNAs in a vast array of tissues are 8.5 kb, with additional, but less abundant, mRNAs of 7.5, 6.5 and 4.4 kb. Steady-state levels of c-ski mRNAs, indistinguishable from transcripts in other tissues, accumulate in skeletal muscle from embryonic, newly hatched, and adult chicks. Only exon 2, a small exon of 111 bp, was found to be alternatively spliced in c-ski mRNAs. Transcripts with and without exon 2 appear in all tissues, in somites, and from the earliest stages of chick embryogenesis. Thus, c-ski cDNA sequences, which extend about 4.3 kb, represent either the least abundant form of c-ski mRNAs in tissues or a severely truncated form of the major 8.5 kb transcripts.

Animals↗