Promoter choice influences alternative splicing and determines the balance of isoforms expressed from the mouse bcl-X gene

Regulation of Bcl-xL expression by H2O2 in cardiac myocytes

Oxidative stress promotes cardiac myocyte apoptosis through the mitochondrial death pathway. Since Bcl-2 family proteins are key regulators of apoptosis, we examined the effects of H2O2 on the expression of principal Bcl-2 family proteins (Bcl-2, Bcl-xL, Bax, Bad) in neonatal rat cardiac myocytes. Protein expression was assessed by immunoblotting. Bcl-2, Bax, and Bad were all down-regulated in myocytes exposed to 0.2 mm H2O2, a concentration that induces apoptosis. In contrast, although Bcl-xL levels initially declined, the protein was re-expressed from 4-6 h. Bcl-xL mRNA was up-regulated from 2 to 4 h in neonatal rat or mouse cardiac myocytes exposed to H2O2, consistent with the re-expression of protein. Four different untranslated first exons have been identified for the Bcl-x gene (exons 1, 1B, 1C, and 1D, where exon 1 is the most proximal and exon 1D the most distal to the coding region). All were detected in mouse or rat neonatal cardiac myocytes, but exon 1D was not expressed in adult mouse hearts. In neonatal mouse or rat cardiac myocytes, H2O2 induced the expression of exons 1B, 1C, and 1D, but not exon 1. These data demonstrate that the Bcl-x gene is selectively responsive to oxidative stress, and the response is mediated through distal promoter regions.

Dynamic regulation of alternative ATP-binding cassette transporter A1 transcripts

The ATP-binding cassette transporter A1 (ABCA1) gene, a major regulator of high-density lipoprotein (HDL) metabolism, utilizes several transcriptional start sites. The pattern of transcripts among tissues and cells differed significantly. The longest (class 1) transcripts were abundant in adult brain and fetal tissues. Class 2 transcripts predominated in most other tissues. The shortest (class 3) transcripts were present mainly in adult liver and lung. To study the biochemical significance of changes in transcript distribution, two cell models were compared. In primary human fibroblasts, upregulation of mRNA levels by oxysterols and retinoic acid increased the relative proportion of class 2 transcript compared to class 1. Phorbol ester stimulated human macrophage-derived THP-1 cells increased the abundance of class 1 transcripts relative to class 2. In both cell lines class 3 transcript levels were minimal and unchanged. It is shown here for the first time that the regulation of ABCA1 mRNA levels exploits the use of alternative transcription start sites.

The function of the bcl-x promoter in erythroid progenitor cells

The protein Bcl-x(L) is essential for survival of erythroid progenitor cells, and it increases substantially during late erythrocyte differentiation due to an increase of mRNA. We mapped the transcription start sites of bcl-x mRNA in mouse and human erythroblasts, and we analyzed the function of the mouse bcl-x promoter by transient and stable transfection assays in a mouse erythroid cell line using plasmids containing the bcl-x promoter fused to a luciferase reporter gene. In mouse erythroblasts, a cluster of start sites at positions -664, -655, and -644 relative to the ATG initiation codon account for almost all transcripts. Human erythroblasts exhibit a start site at -654 that is homologous to the triplet in the mouse. A short sequence element in the mouse bcl-x promoter that includes nucleotides -1804 through -1734 was identified as very important for transcription. This element also showed strong enhancerlike activity in concert with the SV40 promoter in an enhancer test vector. Analyses of mutations indicated that 2 short sequences within the element, about 15 base pair apart, are necessary for full enhancer activity. Gel shift experiments with oligonucleotides representing these sequences revealed specific binding of nuclear proteins from erythroblasts. Some of these proteins are regulated during the late erythroid differentiation.

The human caspase-2 gene: alternative promoters, pre-mRNA splicing and AUG usage direct isoform-specific expression

Caspases have been shown to play important roles in apoptotic cell death, cytokine maturation and cell differentiation. However, the transcriptional regulation of the corresponding CASP genes remains poorly known. We describe a 5.1 kb fragment located upstream of the first translated exon in the human CASP-2 gene, which is known to encode caspase-2L and -2S protein isoforms. Transient transfection experiments, together with transcription start site mapping and transcript analysis, demonstrate that each caspase mRNA is initiated from separate promoter regions, and produced from alternative splicing events in these regions. The CASP-2L promoter is much stronger than the CASP-2S promoter, in good agreement with the respective transcript levels of the two caspases. In addition, several in-frame translational start sites can be identified for each isoform, one of which is common to both, present in the second common exon, and used efficiently. Surprisingly, the short isoform may also be initiated at a downstream AUG codon within the same exon. Thus, promoter strength, alternative transcriptional initiation and 5'-splicing events regulate the expression of the main caspase-2 isoforms that may be translated from alternative translation initiation codons.

New Otx2 mRNA isoforms expressed in the mouse brain

The mouse Otx2 gene is essential throughout head and brain development, from anterior-posterior polarity determination and neuroectoderm induction to post-natal sensory organ maturation. These numerous activities must rely on a very finely tuned regulation of expression. In order to understand the molecular control of the Otx2 gene, we set out to isolate its promoter. During this quest, we identified three remote transcription start sites, two defining two new upstream exons and one mapping within the previously reported first exon. The three transcripts differed in their 5' non-coding region but encoded the same protein. The transcription start nucleotides of each mRNA species have been mapped by RNase protection assays and by an RNA circularization technique. We have demonstrated that they are all used and linked to functional promoters. In addition to leader versatility, we also detected alternative splicing within the coding sequence that gives rise to a new protein endowed with an 8 amino-acid insertion upstream of the homeodomain. Combined analysis of the relative abundance of Otx2 mRNA isoforms in representative tissues and in situ hybridization studies revealed distinct spatial and temporal, although partially overlapping, expression patterns of the mRNA isoforms. These findings provide new clues to a better understanding of the relationships between Otx2 gene architecture and its complex regulatory requirements.

The prodomain of interleukin 1alpha interacts with elements of the RNA processing apparatus and induces apoptosis in malignant cells

Interleukin 1alpha (IL-1alpha), a 33 kDa precursor, is cleaved releasing the 17 kDa carboxyl-terminal cytokine IL-1alpha to which all of the biological properties of IL-1alpha have been attributed. We investigated the potential independent properties of the remaining 16 kDa IL-1alpha amino-terminal propiece by expression in human tumor and primary human cell lines. The IL-1alpha propiece produced apoptosis in malignant but not normal cell lines. A minimal fragment comprised of amino acids 55-108 was required for apoptosis. Deletion and mutation studies identified an extended nuclear localization sequence required for nuclear localization, induction of apoptosis and concentration of the IL-1alpha propiece in interchromatin granule clusters, concentrations of proteins in the RNA splicing and processing pathways. The IL-1alpha propiece interacted with five known components of the RNA splicing/processing pathway, suggesting that the mechanism of action may involve changes in RNA splicing or processing. Expression of the IL-1alpha propiece caused a shift in the ratio of Bcl-Xl/Bcl-Xs toward the apoptotic direction. Our findings indicate that the IL-1alpha propiece induces apoptosis in a range of tumor cells and likely operates through a mechanism involving the RNA processing apparatus and the alternate splicing of apoptosis regulatory proteins.

Expression, alternative splicing and haplotype analysis of transcribed testis specific protein (TSPY) genes

Testis specific protein (TSPY) is a human Y-chromosome derived gene with numerous functional and non-functional copies. Specific expression patterns in testis and testicular tumors, as in prostate cancer samples and cell lines led to the postulation of a potential role in cell proliferation, supported by the presence of a suppressor of variegation, enhancer of zeste and Trithorax/nucleosome assembling protein (nucleosome assembly protein) domain in the mature protein. Expression studies have now identified two transcripts of variable length, termed TSPY-S and -L, which differ in their 3'-translated region due to alternative splicing, and in the quantitative level of transcripts, with TSPY-S being at least 3-4-fold more abundant. In immunoblot experiments on human testis and LNCaP protein extracts using an anti-peptide-antiserum against the TSPY-L specific C-terminus TSPY-L was characterized as a functional variant on the protein level. As there are at least three intragenic positions differing between various TSPY genes and thus defining certain haplotypes, the alternatively spliced TSPY transcripts were analysed for their haplotypes in order to link them to well defined TSPY loci. Surprisingly, no evidence of a G-G-18 haplotype was found for the TSPY-L transcript, while this haplotype makes up almost 50% of all TSPY-S transcripts. This excludes the corresponding TSPY-1 locus from alternative splicing. The only significant differences between the TSPY-1 locus and eight other loci were identified in the promotor region as revealed by detailed sequence comparisons. Thus one might speculate that the alternative splicing could be influenced by elements binding to the promotor region.

The role of the Ets2 transcription factor in the proliferation, maturation, and survival of mouse thymocytes

In this study, we investigated the effects of Ets2 expression on the proliferation, maturation, and survival of thymocytes by establishing transgenic mice that specifically express Ets2 or a dominant negative form of Ets2, Deltaets2, in the thymus. We show that, in young animals, there are fewer T cells in Deltaets2 transgenic thymi and that the maturation of these T cells is affected at the CD4(-)CD8(-) double-negative to CD4(+)CD8(+) double-positive transition compared with wild-type littermate mice. Partial recovery in the number of thymocytes and full T cell maturation are restored with increasing age of Deltaets2 transgenic animals. However, thymocytes from adult Deltaets2 transgenic mice cultured ex vivo are more sensitive to cell death and to glucocorticoid-induced apoptosis than are T cells from control littermate mice. We also show that T cells from adult ets2 transgenic mice proliferate faster than their wild-type littermates. The proliferation and survival of these T cells are clearly affected upon apoptotic signals: glucocorticoid-induced apoptosis induces T cells from ets2 transgenic mice to continue to proliferate in vivo and to survive better ex vivo than T cells from control littermates. It has been shown that c-Myc expression is required for thymic proliferation and improves thymocyte survival of dexamethasone-treated animals. We show that the expression of c-Myc, an Ets2 target, is elevated in T cells freshly isolated from thymi of ets2 transgenic mice pretreated with dexamethasone. Together, these results show that Ets2 plays a role in the proliferation and survival of thymocytes, implicating a Myc-dependent pathway.

Pushing the limits of the scanning mechanism for initiation of translation

Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5' end plays a dominant role in identifying the start codon. This "position effect" is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream site. The position effect is evident also in cases where a silent internal AUG codon is activated upon being relocated closer to the 5' end. Two mechanisms for escaping the first-AUG rule--reinitiation and context-dependent leaky scanning--enable downstream AUG codons to be accessed in some mRNAs. Although these mechanisms are not new, many new examples of their use have emerged. Via these escape pathways, the scanning mechanism operates even in extreme cases, such as a plant virus mRNA in which translation initiates from three start sites over a distance of 900 nt. This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. The opposite problem occurs in the case of hereditary thrombocythemia: translational efficiency is increased by mutations that remove or restructure a small upstream open reading frame in thrombopoietin mRNA, and the resulting overproduction of the cytokine causes the disease. This and other examples support the idea that 5' leader sequences are sometimes structured deliberately in a way that constrains scanning in order to prevent harmful overproduction of potent regulatory proteins. The accumulated evidence reveals how the scanning mechanism dictates the pattern of transcription--forcing production of monocistronic mRNAs--and the pattern of translation of eukaryotic cellular and viral genes.

Alternative promoters drive the expression of the gene encoding the mouse axonal glycoprotein F3/contactin

F3/Contactin is a neuronal glycoprotein which mediates axonal growth control via complex interactions with a number of cell surface or matrix components. As part of this developmental role, its expression undergoes differential regulation during the maturation of definite neuronal populations within the central and peripheral nervous tissue. To elucidate the underlying molecular mechanisms we study here the organization of the regulatory region of the mouse F3/Contactin gene. We show that this region displays peculiar features in that it spans more than 80 kb, bears very large introns and includes four untranslated exons which undergo complex splicing events leading to 11 potential arrangements of the F3/Contactin mRNA 5' end. Within this region we identify three alternative neurospecific promoters which, as deduced from the developmental profile of the associated 5' exons (A1,C1,0), drive two different patterns of F3/Contactin gene expression. The activity of the A1 exon-associated promoter displays only minor developmental changes and is likely to contribute to the basal level of the F3/Contactin gene expression; by contrast, the activities of the exon C1- and exon 0-associated promoters are significantly upregulated at the end of the first postnatal week. The data indicate that differential regulation of the F3/Contactin expression during development may depend upon alternative utilization of distinct promoter elements and may involve complex splicing events of the 5' untranslated exons. Several consensuses for homeogene transcription factors are scattered within the identified regulatory region, in agreement with the general assumption of homeotic gene regulation of neural morphoregulatory molecules.