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Putative Cis (putative + cis)
Selected AbstractsGenomic context of paralogous recombination hotspots mediating recurrent NF1 region microdeletionGENES, CHROMOSOMES AND CANCER, Issue 1 2004Stephen H. Forbes Recombination between paralogs that flank the NF1 gene at 17q11.2 typically results in a 1.5-Mb microdeletion that includes NF1 and at least 13 other genes. We show that the principal sequences responsible are two 51-kb blocks with 97.5% sequence identity (NF1REP-P1-51 and NF1REP-M-51). These blocks belong to a complex group of paralogs with three components on 17q11.2 and another on 19p13.13. Breakpoint sequencing of deleted chromosomes from multiple patients revealed two paralogous recombination hot spots within the 51-kb blocks. Lack of sequence similarity between these sites failed to suggest or corroborate any putative cis -acting recombinogenic motifs. However, the NF1REPs showed relatively high alignment mismatch between recombining paralogs, and we note that the NF1REP hot spots were regions of good alignment bordered by relatively large alignment gaps. Statistical tests for gene conversion detected a single significant tract of perfect match between the NF1REPs that was 700 bp long and coincided with PRS2, the predominant recombination hot spot. Tracts of perfect match occurring by chance may contribute to breakpoint localization, but our result suggests that perfect tracts at recombination hot spots may be a result of gene conversion at sites at which preferential pairing occurs for other, as-yet-unknown reasons. © 2004 Wiley-Liss, Inc. [source] Candidate cis -elements for human renin gene expression in the promoter regionJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 2 2004Tadashi Konoshita Abstract The regulation of renin gene expression, the rate-limiting enzyme of the system, is thought to be fundamental to the total system. Previously, we mapped six putative cis -elements in the promoter region of the human renin gene with nuclear proteins from human chorionic cells and human renal cortex by DNase I protection assay (footprint A,F). Each footprint contains Ets motif like site (A), HOXñPBX recognition sequence (B), unknown sequence as DNA binding consensus (C), CRE (D), COUP-TFII (ARP-1) motif like site (E), and AGE3 like site (F). Footprint D has been characterized by means of functional studies as the genuine human renin gene CRE interacting with CREB in cooperation with the site of footprint B. To obtain further clues to the specific expression in the promoter region, these putative cis -elements were conducted to a consensus-specific binding assay to compare renin-producing and non-renin-producing cells by EMSA and electromobility super-shift assay. Different sequence-specific DNA/protein binding was obtained among the different cell lines with footprint B site, with COUP-TFII (ARP-1) motif like site and possibly with footprint F site. The results implicate these putative cis -elements and each corresponding trans -factor in the specific expression of the human renin gene in the promoter region. Further functional characterization of these elements would provide important data for a better understanding of human renin gene expression. © 2004 Wiley-Liss, Inc. [source] Significance of consensus CYC-binding sites found in the promoters of both ChCYC and ChRAD genes in Chirita heterotricha (Gesneriaceae)JOURNAL OF SYSTEMATICS EVOLUTION, Issue 4 2010Xia YANG Abstract,CYC -like genes are widely conserved in controlling floral dorsoventral asymmetry (zygomorphy) through persistent expression in corresponding domains in core eudicots. To understand how CYC -like gene expression is maintained during flower development, we selected Chirita heterotricha as a material and isolated the promoter sequences of the ChCYC1C and ChCYC1D genes, homologs of CYC, by inverse polymerase chain reaction. Further promoter analyses led to the identification of a putative cis -regulatory element in each promoter matching the consensus DNA binding site for Antirrhinum CYC protein: GGCCCCTC at ,165 for ChCYC1C, and GGCCCCCC at ,163 for ChCYC1D. This indicates that both the ChCYC1C and ChCYC1D genes have probably evolved autoregulatory loops to sustain their expression in developing flowers. We also isolated the coding and promoter sequences of the ChRAD gene, a homolog of Antirrhinum RAD. Promoter analysis showed that the ChRAD gene promoter also contained a putative CYC-binding site (GGCCCAC at ,134). Therefore, ChRAD is likely a direct target of the ChCYC1 genes, which is similar to Antirrhinum RAD. These results imply that the establishment of floral zygomorphy in Chirita may have been achieved by the evolution of an autoregulatory loop for CYC -like genes, which was probably accompanied by simultaneous co-option of the RAD -like gene into their regulatory network. [source] Priming of plant innate immunity by rhizobacteria and ,-aminobutyric acid: differences and similarities in regulationNEW PHYTOLOGIST, Issue 2 2009Sjoerd Van der Ent Summary ,,Pseudomonas fluorescens WCS417r bacteria and ,-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. ,,In this study, we examined the differences and similarities of WCS417r- and ,-aminobutyric acid-induced priming. ,,Both WCS417r and ,-aminobutyric acid prime for enhanced deposition of callose-rich papillae after infection by the oomycete Hyaloperonospora arabidopsis. This priming is regulated by convergent pathways, which depend on phosphoinositide- and ABA-dependent signalling components. Conversely, induced resistance by WCS417r and ,-aminobutyric acid against the bacterial pathogen Pseudomonas syringae are controlled by distinct NPR1-dependent signalling pathways. As WCS417r and ,-aminobutyric acid prime jasmonate- and salicylate-inducible genes, respectively, we subsequently investigated the role of transcription factors. A quantitative PCR-based genome-wide screen for putative WCS417r- and ,-aminobutyric acid-responsive transcription factor genes revealed distinct sets of priming-responsive genes. Transcriptional analysis of a selection of these genes showed that they can serve as specific markers for priming. Promoter analysis of WRKY genes identified a putative cis -element that is strongly over-represented in promoters of 21 NPR1-dependent, ,-aminobutyric acid-inducible WRKY genes. ,,Our study shows that priming of defence is regulated by different pathways, depending on the inducing agent and the challenging pathogen. Furthermore, we demon-strated that priming is associated with the enhanced expression of transcription factors. [source] TERE; a novel cis -element responsible for a coordinated expression of genes related to programmed cell death and secondary wall formation during differentiation of tracheary elementsTHE PLANT JOURNAL, Issue 6 2007Hyunjin Pyo Summary The differentiation of water-conducting tracheary elements (TEs) is the result of the orchestrated construction of secondary wall structure, including lignification, and programmed cell death (PCD), including cellular autolysis. To understand the orchestrated regulation of differentiation of TEs, we investigated the regulatory mechanism of gene expression directing TE differentiation. Detailed loss-of-function and gain-of-function analyses of the ZCP4 (Zinniacysteine protease 4) promoter, which confers TE-specific expression, demonstrated that a novel 11-bp cis -element is necessary and sufficient for the immature TE-specific promoter activity. The 11-bp cis -element-like sequences were found in promoters of many Arabidopsis TE differentiation-related genes. A gain-of-function analysis with similar putative cis -elements from secondary wall formation or modification-related genes as well as PCD-related genes indicated that the cis -elements are also sufficient for TE-specific expression of genes. These results demonstrate that a common sequence, designated as the tracheary-element-regulating cis -element, confers TE-specific expression to both genes related to secondary wall formation or modification and PCD. [source] Molecular characterization, immunohistochemical localization and expression of a ribosomal protein L17 gene from Apis cerana ceranaARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 2 2010Fei Meng Abstract Ribosomal protein L17 (RPL17) is a core protein of the large (60S) ribosomal subunit and plays an important role in protein synthesis. In this report, a RPL17 gene was isolated from Apis cerana cerana, designated as AccRPL17. Alignment analysis showed that AccRPL17 exhibits high homology to other known RPL17s. Moreover, genomic sequence analysis revealed that five exons are splitted by four introns, and the position of the first intron is comparatively conservative, being localized in the 5, untranslated region. Partial putative cis -acting elements related to development were also examined. Quantitative real-time PCR showed that the highest mRNA level was detected in larvae on the fifth day. Simultaneously, immunohistochemical localization showed that AccRPL17 is primarily concentrated in muscular tissues, stigma, body wall, and the surrounding of the eye in the fifth-instar larvae. Further studies suggested that AccRPL17 might be involved in responses to abiotic stresses. This is a report attempting to analyze the expression and distribution of RPL17 in A. cerana cerana. These results indicated that AccRPL17 might play an important role in insect development, and the importance of AccRPL17 in participating in abiotic stresses is discussed. © 2010 Wiley Periodicals, Inc. [source] | ||||||||||