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Regulation Network (regulation + network)
Selected AbstractsStudy of PfMyb1 Transcription Factor Regulation Network during Plasmodium falciparum Erythrocytic CycleTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005M. GISSOT During the complex life cycle of Plasmodium falciparum, the regulation of events that occur during the erythrocytic cycle, such as proliferation and differentiation, implies a fine control of transcriptional activities governing the expression profiles of each gene. However, transcriptional regulation and notably its actors, transcription factors and regulation motifs, are poorly described in Plasmodium. In order to decipher the mechanisms implicated in transcriptional regulation, we studied a transcription factor belonging to the trytophan family and showed that the PfMyb1 protein contained in nuclear extracts has a specific DNA binding activity. We took advantage of long pfmyb1 double stranded RNA (dsRNA) to inactivate the cognate messenger and understand the role of PfMyb1 during the erythrocytic cycle. Culture treated with pfmyb1 dsRNA exhibited a 40% growth inhibition and mortality during trophozoite to schizont transition when compared to either untreated control or culture treated with unrelated long dsRNA. We have further demonstrated that pfmyb1 transcript and protein decreased up to 80% in treated trophozoite culture at the time of pfmyb1 expression peak. Thus, we investigated the effect of this partial loss of transcript and protein using a thematic DNA microarray containing PCR products, representative of P. falciparum genes involved in cell cycle and transcriptional regulation. SAM software enabled us to identify several genes over and under-expressed, potentially directly or indirectly regulated by PfMyb1. These alterations of expression were verified by qPCR and Western blotting. We are currently working on the promoters of those genes to decode determinants of gene regulation by Pfmyb1. [source] Coordinated and conserved expression of alphoid repeat and alphoid repeat-tagged coding sequencesDEVELOPMENTAL DYNAMICS, Issue 1 2003Yin-Xiong Li Abstract We have found an alpha-like simple-sequence DNA repeat that is differentially expressed during early embryogenesis in both chick and zebrafish. Before and during the primitive streak stage, transcripts of the alphoid repeat sequence were ubiquitously expressed throughout zebrafish and chick embryos. After headfold formation, expression was limited to the cardiac neural crest, the head, and the heart. Two types of alphoid repeat sequence transcripts were identified: alphoid repeat RNA and alphoid repeat-tagged mRNA (ES,T). Several of the ES,Ts were identified by (1) searching expressed sequence tag databases, (2) arbitrary rapid amplification of cDNA ends (RACE), and (3) screening embryonic cDNA libraries. The alphoid element was located in the 3, untranslated region of one ES,T that was obtained by RACE. The ES,T sequences encoded a variety of different types of proteins, but all were expressed within tissues that were positive for the alphoid repeat RNA. The presence of two types of coordinately expressed alphoid-like repeat transcripts in maternal RNA with subsequent restriction to the head and heart, and the conservation of these features in disparate vertebrate embryos, suggest that the alphoid repeat sequence may serve as a control element in the gene regulation network. Developmental Dynamics 228:72,81, 2003. © 2003 Wiley-Liss, Inc. [source] Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cellsGENES TO CELLS, Issue 6 2010Shinya Sato DNA methylation profile, consisting of tissue-dependent and differentially methylated regions (T-DMRs), has elucidated tissue-specific gene function in mouse tissues. Here, we identified and profiled thousands of T-DMRs in embryonic stem cells (ESCs), embryonic germ cells (EGCs) and induced pluripotent stem cells (iPSCs). T-DMRs of ESCs compared with somatic tissues well illustrated gene function of ESCs, by hypomethylation at genes associated with CpG islands and nuclear events including transcriptional regulation network of ESCs, and by hypermethylation at genes for tissue-specific function. These T-DMRs in EGCs and iPSCs showed DNA methylation similar to ESCs. iPSCs, however, showed hypomethylation at a considerable number of T-DMRs that were hypermethylated in ESCs, suggesting existence of traceable progenitor epigenetic information. Thus, DNA methylation profile of T-DMRs contributes to the mechanism of pluripotency, and can be a feasible solution for identification and evaluation of the pluripotent cells. [source] Decorin and its galactosaminoglycan chain: Extracellular regulator of cellular function?IUBMB LIFE, Issue 11 2008Daniela G. Seidler Abstract A molecular network of extracellular matrix molecules determines the tissue architecture and accounts for mechanical properties like compressibility or stretch resistance. It is widely accepted that the elements of the cellular microenvironment are important regulators of the cellular behavior in vitro and in vivo. One large group comprising these molecules is the family of proteoglycans. Both, the core proteins and, in particular, the attached galactosaminoglycans, contribute to the regulation network as they bind a variety of signaling molecules, e.g. cytokines, chemokines, growth, and differentiation factors. We would like to emphasize specific patterns of epimerization and sulfation within the galactosaminoglycans chains, because these result in "motifs" that are responsible for the modulation of signal factor binding, release and activity. This property is crucial in physiological and pathological conditions, for example development and wound healing. © 2008 IUBMB IUBMB Life, 60(11): 729,733, 2008 [source] Plasticity of a transcriptional regulation network among alpha-proteobacteria is supported by the identification of CtrA targets in Brucella abortusMOLECULAR MICROBIOLOGY, Issue 4 2002Anne-Flore Bellefontaine Summary CtrA is a master response regulator found in many alpha-proteobacteria. In Caulobacter crescentus and Sinorhizobium meliloti, this regulator is essential for viability and is transcriptionally autoregulated. In C. crescentus, it is required for the regulation of multiple cell cycle events, such as DNA methylation, DNA replication, flagella and pili biogenesis and septation. Here, we report the characterization of the ctrA gene homologue in the ,2 -proteobacteria Brucella abortus, a facultative intracellular pathogen responsible for brucellosis. We detected CtrA expression in the main Brucella species, and its overproduction led to a phenotype typical of cell division defect, consistent with its expected role. A purified B. abortus CtrA recombinant protein (His6,CtrA) was shown to protect the B. abortus ctrA promoter from DNase I digestion, suggesting transcriptional autoregulation, and this protection was enhanced under CtrA phosphorylation on a conserved Asp residue. Despite the similarities shared by B. abortus and C. crescentus ctrA, the pathway downstream from CtrA may be distinct, at least partially, in both bacteria. Indeed, beside ctrA itself, only one (the ccrM gene) out of four B. abortus homologues of known C. crescentus CtrA targets is bound in vitro by phosphorylated B. abortus CtrA. Moreover, further footprinting experiments support the hypothesis that, in B. abortus, CtrA might directly regulate the expression of the rpoD, pleC, minC and ftsE homologues. Taken together, these results suggest that, in B. abortus and C. crescentus, similar cellular processes are regulated by CtrA through the control of distinct target genes. The plasticity of the regulation network involving CtrA in these two bacteria may be related to their distinct lifestyles. [source] Concepts and Approaches Towards Understanding the Cellular Redox ProteomePLANT BIOLOGY, Issue 4 2006E. Ströher Abstract: The physiological activity of a significant subset of cell proteins is modified by the redox state of regulatory thiols. The cellular redox homeostasis depends on the balance between oxidation of thiols through oxygen and reactive oxygen species and reduction by thiol-disulfide transfer reactions. Novel and improved methodology has been designed during recent years to address the level of thiol/disulfide regulation on a genome-wide scale. The approaches are either based on gel electrophoresis or on chromatographic techniques coupled to high end mass spectrometry. The review addresses diagonal 2D-SDS-PAGE, targeted identification of specific redox-interactions, affinity chromatography with thioredoxins and glutaredoxins, gel-based and non-gel based labelling techniques with fluorophores (such as Cy3, Cy5, ICy), radioisotopes, or with isotope-coded affinity tags (ICAT), differential gel electrophoresis (DIGE) and combined fractional diagonal chromatography (COFRADIC). The extended methodological repertoire promises fast and new insight into the intricate regulation network of the redox proteome of animals, bacteria, and plants. [source] Brassinosteroids as Metahormones: Evidence for their Specific Influence during the Critical Period in Sorghum DevelopmentPLANT BIOLOGY, Issue 6 2002G. N. Amzallag Abstract: In Sorghum bicolor, the effect of brassinosteroid (BR) treatments on blade elongation depends both on concentration and on the stage of development. A specific period of increase in sensitivity to BR is reported during early vegetative development. It coincides with emergence of a critical period during which the between-organs relationship is readjusted as a function of new developmental events or new environmental conditions. Accordingly, the influence of BR cannot be completely understood without separating its effects during stable phases (phenophases) and during critical periods. A high level of redundancy exists in networks of regulation, so that modifications due to BR treatments generally remain cryptic. Nevertheless, it is shown that BR affects the pattern of relationships between organs, confirming its involvement in emergence of a new network of regulation. It is suggested that, during critical periods, brassinosteroids act as "metahormones" integrating the new emerging regulation network by triggering changes in cellular sensitivity to PGRs. [source] Developmental Changes in Effect of Cytokinin and Gibberellin on Shoot K+ and Na+ Accumulation in Salt-Treated Sorghum PlantsPLANT BIOLOGY, Issue 4 2001G. N. Amzallag Abstract: The effect of cytokinin (CK) and/or gibberellin (GA) treatments on shoot accumulation of Na+ and K+ was investigated in Sorghum bicolor exposed to 150 mM NaCl. These hormonal treatments modified the shoot content of Na+ and K+, but the effect varied throughout development. Comparison of ion concentration versus ion content in shoots indicates that regulation of shoot concentration of K+ is modified during a transition period of development. This change is concomitant with reorganization of the regulation network for meristem activity, an event also involving changes in sensitivity to CK and GA. This evidence suggests a strong interdependency between dynamic changes in a between-organ network of relations and control of accumulation of monovalent ions in the shoot. Moreover, a new pattern of regulation of shoot Na+ concentration emerges during the transition period. During this process GA appears progressively involved in regulation of Na retranslocation, while CK is rather controlling the root uptake of Na+. Accordingly, the spontaneous emergence of Na-includer and Na-excluder individuals observed from an initially homogeneous population is interpreted as related to variations in sensitivity to GA and CK during differentiation of this newly emerging pathway of regulation. [source] Genomic location analysis by ChIP-SeqJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2009Artem Barski Abstract The interaction of a multitude of transcription factors and other chromatin proteins with the genome can influence gene expression and subsequently cell differentiation and function. Thus systematic identification of binding targets of transcription factors is key to unraveling gene regulation networks. The recent development of ChIP-Seq has revolutionized mapping of DNA,protein interactions. Now protein binding can be mapped in a truly genome-wide manner with extremely high resolution. This review discusses ChIP-Seq technology, its possible pitfalls, data analysis and several early applications. J. Cell. Biochem. 107: 11,18, 2009. © 2009 Wiley-Liss, Inc. [source] | ||||||||||