XcisClique: analysis of regulatory bicliques

Background  

Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions.     

Dicer-like (DCL) proteins in plants

Dicer and Dicer-like (DCL) proteins are key components in small RNA biogenesis. DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages, and in response to environmental stresses. In Arabidopsis, AtDCL1, AtDCL2, and AtDCL4 exhibit similar expression pattern during the leaf or stem development, which is distinguished from AtDCL3. However, distinct expression profiles for all DCLs are found during the development of reproductive organs flower and seed. The grape VvDCL1 and VvDCL3 may act sequentially to face the fungi challenge. Overall, the responses of DCLs to drought, cold, and salt are quite different, indicating that plants might have specialized regulatory mechanism in response to different abiotic stresses. Further analysis of the promoter regions reveals a few of cis-elements that are hormone- and stress-responsive and developmental-related. However, gain and loss of cis-elements are frequent during evolution, and not only paralogous but also orthologous DCLs have dissimilar cis-element organization. In addition to cis-elements, AtDCL1 is probably regulated by both ath-miR162 and ath-miR414. Posterior analysis has identified some critical amino acid sites that are responsible for functional divergence between DCL family members. These findings provide new insights into understanding DCL protein functions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Putative cis-elements in the promoter region of the carrot phenylalanine ammonia-lyase gene induced during anthocyanin synthesis

Deletion mutants of the carrot phenylalanine ammonia-lyase gene promoter were used to survey cis-elements for their effect on expression of promoter activity by transient expression. Two putative cis-elements were required to give full activity, but a third might be the most important in regulation of the promoter by 2,4-dichlorophenoxyacetic acid. Electronic Publication     

Evidence that the plastid signal and light operate via the samecis-acting elements in the promoters of nuclear genes for plastid proteins

Nuclear-encoded genes for proteins of the photosynthetic maschinery represent a particular subset of genes. Their expression is cooperatively stimulated by discrete factors including the developmental stage of plastids and light. We have analyzed in transgenic tobacco the plastid- and light-dependent expression of a series of 5 promoter deletions of various nuclear genes from spinach, of fusions of defined promoter segments with the 90-bp 35S RNA CaMV minimal promoter, as well as with mutations in sequences with homologies to characterizedcis-elements, to address the question of whether the plastid signal and light operate via the same or differentcis-acting elements. In none of the 160 different transgenic lines (representing 32 promoter constructs from seven genes) analyzed, could significant differences be identified in the responses to the two regulatory pathways. The data are compatible with the idea that both signals control the expression of nuclear genes for plastid proteins via the samecis-acting elements.     

Functional dissection of a bean chalcone synthase gene promoter in transgenic tobacco plants reveals sequence motifs essential for floral expression

Expression of chalcone synthase (CHS), the first enzyme in the flavonoid branch of the phenylpropanoid biosynthetic pathway in plants, is induced by developmental cues and environmental stimuli. We used plant transformation technology to delineate the functional structure of the French bean CHS15 gene promoter during plant development. In the absence of an efficient transformation procedure for bean, Nicotiana tabacum was used as the model plant. CHS15 promoter activity, evaluated by measurements of -d-glucuronidase (GUS) activity, revealed a tissue-specific pattern of expression similar to that reported for CHS genes in bean. GUS activity was observed in flowers and root tips. Floral expression was confined to the pigmented part of petals and was induced in a transient fashion. Fine mapping of promoter cis-elements was accomplished using a set of promoter mutants generated by unidirectional deletions or by site-directed mutagenesis. Maximal floral and root-specific expression was found to require sequence elements located on both sides of the TATA-box. Two adjacent sequence motifs, the G-box (CACGTG) and H-box (CCTACC(N)₇CT) located near the TATA-box, were both essential for floral expression, and were also found to be important for root-specific expression. The CHS15 promoter is regulated by a complex interplay between different cis-elements and their cognate factors. The conservation of both the G-box and H-box in different CHS promoters emphasizes their importance as regulatory motifs.     

Expression of ethylene response factor JERF1 in rice improves tolerance to drought

Ethylene response factor (ERF) proteins regulate a variety of stress responses in plant. JERF1, a tomato ERF protein, can be induced by abscisic acid (ABA). Overexpression of JERF1 enhanced the tolerance of transgenic tobacco to high salt concentration, osmotic stress, and low temperature by regulating the expression of stress-responsive genes by binding to DRE/CRT and GCC-box cis-elements. In this research, we further report that overexpression of JERF1 significantly enhanced drought tolerance of transgenic rice. The overexpression activated the expression of stress-responsive genes and increased the synthesis of the osmolyte proline by regulating the expression of OsP5CS, encoding the proline biosynthesis key enzyme deltal-pyrroline-5-carboxylate synthetase. JERF1 also activated the expression of two ABA biosynthesis key enzyme genes, OsABA2 and Os03g0810800, and increased the synthesis of ABA in rice. Analysis of cis-elements of JERF1-targeted genes pointed to the existence of DRE/CRT and/or GCC box in their promoters, indicating that JERF1 could activate the expression of related genes in rice by binding to these cis-elements. Unlike some other ERF proteins, constructive overexpression of JERF1 did not change the growth and development of transgenic rice, which makes JEFR1 a potentially useful source in breeding for greater tolerance to abiotic stress.     

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis‐regulatory, rather than the coding, regions of developmental genes. This “cis‐regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis‐regulatory hypothesis. We then test the empirical support for the cis‐regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis‐regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis‐regulatory changes published annually is rapidly increasing. Above the species level, cis‐regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis‐regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis‐regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.     

以转录因子AP-1为靶的decoy核酸体内外抗肿瘤研究

合成了双链寡聚核苷酸——decoy核酸,其与靶转录因子AP-1有高亲和性,可进入细胞作为decoy顺式元件,通过抑制特异的转录因子和调控区域的结合,调控基因转录而改变基因的表达.在体内外抗肿瘤试验中, decoy核酸有显著抑制肿瘤细胞增殖的作用,可以成为潜在性的肿瘤基因治疗药物.