Polymorphisms in the TNFA promoter region is not associated with palmoplantar pustulosis
Hironori NiizekiT. NaruseKazuhiro HashigucciM. YokoyamaY. YamasakiKumiko AkiyaTaiki TojoT. UrushibaraYukinao YamazakiH. InokoT. Níshikaẃa
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Polymorphisms of the 5′‐flanking promoter/enhancer region of the TNFA gene were determined in 80 Japanese patients with pulmoplantar pustulosis (PPP). The 5′‐flanking region of the TNFA gene from –1107 to –66 was amplified by polymerase chain reaction (PCR) method. Nucleotide sequencing data from the PCR products revealed that 5 single nucleotide polymorphisms at position –1031, –863, –857, –307 and –237. None of the nucleotide substitutions were significantly increased in PPP patients when compared with those in controls. To clarify the linkage among the neighboring genetic marker, we analyzed the association between the polymorphisms in the TNFA promoter region and the Nco I polymorphism in the first intron of the TNFB gene as well as HLA‐DR9 . The genotype at –1031C is strongly associated with TNFB1 and negatively associated with TNFB2 which is reported to be associated with PPP. These data indicate that TNFA gene centromeric to TNFB is not associated with PPP and the susceptible gene of PPP is located between TNFB and HLA‐B .This chapter deals with natural and synthetic promoters frequently used in yeast. It describes principles and strategies exploited to produce synthetic promoters and their cognate transcription factors. The chapter points out the essential structural and functional features of yeast promoters. It highlights some examples of both regulated and constitutive natural yeast promoters. The characterization of these sequences allowed for the identification of structural and functional features that are exploited to build synthetic promoters and heterologous transcription factors. Modification of the binding affinity between the transcription factor and its cognate transcription factor binding site (TFBS) results in promoter strength modulation. The chapter discusses two main groups of synthetic promoters. One includes modified versions of natural promoters, and the other contains hybrid promoters. The chapter also describes Saccharomyces cerevisiae promoters. The characterization of S. cerevisiae promoters began by using them to drive expression of reporter genes.
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The fission yeast, Schizosaccharomyces pombe, is an important model species with a low intron density. Previous studies showed extensive intron losses during its evolution. To test the models of intron loss and gain in fission yeasts, we conducted a comparative genomic analysis in four Schizosaccharomyces species. Both intronization and de-intronization were observed, although both were at a low frequency. A de-intronization event was caused by a degenerative mutation in the branch site. Four cases of imprecise intron losses were identified, indicating that genomic deletion is not a negligible mechanism of intron loss. Most intron losses were precise deletions of introns, and were significantly biased to the 3′ sides of genes. Adjacent introns tended to be lost simultaneously. These observations indicated that the main force shaping the exon-intron structures of fission yeasts was precise intron losses mediated by reverse transcriptase. We found two cases of intron gains caused by tandem genomic duplication, but failed to identify the mechanisms for the majority of the intron gain events observed. In addition, we found that intron-lost and intron-gained genes had certain similar features, such as similar Gene Ontology categories and expression levels.
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Efficient expression of many mammalian genes depends on the presence of at least one intron. We previously showed that addition of almost any of the introns from the mouse thymidylate synthase (TS) gene to an intronless TS minigene led to a large increase in expression. However, addition of intron 4 led to a reduction in minigene expression. The goal of the present study was to determine why TS intron 4 was unable to stimulate expression. Insertion of intron 4 into an intron-dependent derivative of the ribosomal protein L32 gene did not lead to a significant increase in expression, suggesting that its inability to stimulate expression was due to sequences within the intron. Deleting most of the interior of intron 4, improving the putative branch point, removing purines from the pyrimidine stretch at the 3' end of the intron, or removing possible alternative splice acceptor or donor sites within the intron each had little effect on the level of expression. However, when the splice donor sequence of intron 4 was modified so that it was perfectly complementary to U1 snRNA, the modified intron 4 stimulated expression approximately 6-fold. When the splice donor site of TS intron 1 (a stimulatory intron) was changed to that of TS intron 4, the modified intron 1 was spliced very inefficiently and lost the ability to stimulate mRNA production. Our observations support the idea that introns can stimulate gene expression by a process that depends directly on the splicing reaction.
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在其他的拼接， intron 保留在老鼠和老鼠的组织安 H3 受体，或者被切除的短抄本 isoforms 拼接 introns 容易被检测在一在老鼠很低级并且在用常规 PCR 协议的老鼠是无法发现的。Theretained introns 普通 5 ′拼接地点并且不同 3 ′拼接地点。为拼接的特殊选择的详细机制仍然保持大部分不清楚。在这研究，我们开发了拼接的微型基因概括受体的自然其他的拼接的系统并且调查了 5 ′和 3 ′的效果拼接在 HeLa 房间的 intron 保留上的地点。变异弱 5 ′和 3 ′拼接向正规一致序列的或者拼接的 introns 的地点支持了在老鼠和 mouseminigenes 相应 introns 拼接。效果拼接地点力量是上下文依赖者并且为 3 ′更重要拼接更长其他的 intron 的地点比为 3 ′拼接更短的其他的 intron 的地点并且普通 5 ′拼接地点；它比在老鼠微型基因在 ratminigene 也是更重要的。变异 3 ′拼接更长其他的 intron 的地点导致了 intron 的几乎完全的拼接并且做了相应 isoform 在老鼠微型基因成为将近独占的抄本。
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Intronic gene regions are mostly considered in the scope of gene expression regulation, such as alternative splicing. However, relations between basic statistical properties of introns are much rarely studied in detail, despite vast available data. Particularly, little is known regarding the relationship between the intron length and the intron phase. Intron phase distribution is significantly different at different intron length thresholds. In this study, we performed GO enrichment analysis of gene sets with a particular intron phase at varying intron length thresholds using a list of 13823 orthologous human-mouse gene pairs. We found a specific group of 153 genes with phase 1 introns longer than 50 kilobases that were specifically expressed in brain, functionally related to synaptic signaling, and strongly associated with schizophrenia and other mental disorders. We propose that the prevalence of long phase 1 introns arises from the presence of the signal peptide sequence and is connected with 1-1 exon shuffling.
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Journal Article The inconsistent distribution of introns in the T-even phages indicates recent genetic exchanges Get access S.M. Quirk, S.M. Quirk 1New York State Department of Health, Wadsworth Center for Laboratories and ResearchPO Box 509, Empire State Plaza, Albany, NY 12201 Search for other works by this author on: Oxford Academic PubMed Google Scholar D. Bell-Pedersen, D. Bell-Pedersen 1New York State Department of Health, Wadsworth Center for Laboratories and ResearchPO Box 509, Empire State Plaza, Albany, NY 122012Department of Biological Sciences, State University of New YorkAlbany, NY 12222, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Tomaschewski, J. Tomaschewski 3JRuhr-Universitat Bochum, Arbeitsgruppe Molekulare GenetikPostfach 102148, 4630 Bochum 1, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar W. Rüger, W. Rüger 3JRuhr-Universitat Bochum, Arbeitsgruppe Molekulare GenetikPostfach 102148, 4630 Bochum 1, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Belfort M. Belfort 1New York State Department of Health, Wadsworth Center for Laboratories and ResearchPO Box 509, Empire State Plaza, Albany, NY 122014Department of Biomedical Sciences, School of Public Health, State University of New York and New York State Department of HealthAlbany, NY 12201, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 1, 11 January 1989, Pages 301–315, https://doi.org/10.1093/nar/17.1.301 Published: 11 January 1989 Article history Received: 19 August 1988 Revision received: 19 October 1988 Accepted: 19 October 1988 Published: 11 January 1989
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Bidirectional promoters lie between adjacent genes, which are transcribed from opposite strands of DNA. The functional mechanisms underlying the activation of bidirectional promoters are currently uncharacterised. To define the core promoter elements of bidirectional promoters in human, we mapped motifs for TATA, INR, BRE, DPE, INR, as well as CpG-islands. We found a consistently high correspondence between C+G content, CpG-island presence and an average expression level increasing the median level for all genes in bidirectional promoters. These CpG-rich promoters showed discrete initiation patterns rather than broad regions of transcription initiation, as are typically seen for CpG-island promoters. CpG-islands encompass both TSSs within bidirectional promoters, providing an explanation for the symmetrical co-expression patterns of many of these genes. In contrast, TATA motifs appear to be asymmetrically positioned at one TSS or the other. Our findings demonstrate that bidirectional promoters utilize a variety of core promoter elements to initiate transcription. CpG-islands dominate the regulatory landscape of this group of promoters.
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Splice site mutation
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