Molecular and biochemical studies have shown that gene contains single or combination of different cis-acting regulatory elements are actively controlling the transcriptional regulation of associated genes, downstream effects of these result in the modulation of various biological pathways such as biotic/abiotic stress responses, hormonal responses to growth and development processes and secondary metabolite production. Therefore, the identification of promoters and their cis-regulatory elements is one of intriguing area to study the dynamic complex regulatory network of genes activities by integrating computational, comparative, structural and functional genomics. Several bioinformatics servers or database have been established to predict the cis-acting elements present in the promoter region of target gene and their association with the expression profiles in the TFs. The aim of this study is to predict possible cis-acting regulatory elements that have putative role in the transcriptional regulation of a dynamic network of metabolite gene activities controlling prenylflavonoid and bitter acids biosynthesis in hop (Humulus lupulus). Recent release of hop draft genome enabled us to predict the possible cis-acting regulatory elements by extracting 2kbp of 5' regulatory regions of genes important for lupulin metabolome biosynthesis, using Plant CARE, PLACE and Genomatix Matinspector professional databases. The result reveals the plausible role of cis-acting regulatory elements in the regulation of gene expression primarily involved in lupulin metabolome biosynthesis including under various stress conditions.

• Klíčová slova
• Cis-acting elements, Gene regulation, Humulus lupulus, Transcriptional factor, secondary metabolites,
• MeSH
• Humulus genetika   MeSH
• promotorové oblasti (genetika) * MeSH
• regulace genové exprese u rostlin genetika   MeSH
• regulační elementy transkripční genetika   MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The H-2Kb gene equipped with a minimal promoter (5' deletion up to -61) was fully expressed in transfected fibroblasts, but inactive in transfected embryonal carcinoma cells. A strong transcriptional regulatory element (H2DRE) was identified when a fragment spanning the second exon and second intron was used to activate transient expression of the reporter chloramphenicol acetyltransferase (CAT) gene in mouse Ltk- or NIH3T3 fibroblasts. Its activity was twice that of a construct where the CAT gene was driven by the H-2Kb 5' enhancer region (H2TF1/KBF1 site) and comparable to that of pRSVCAT construct carrying the strong Rous sarcoma virus LTR enhancer. In accord with regulated transcriptional activity of the intact H-2Kb gene, the H2DRE did not activate the CAT expression in P19 mouse embryonal carcinoma cells. The H2DRE did not function as a typical enhancer since its activity was strongly position dependent. Consistent with its anticipated role in transcription regulation, H2DRE displayed more than five target sites for specifically interacting nuclear factors, two of them being present in H-2 positive fibroblasts, but not in H-2 negative teratocarcinoma cells. None of them was cross-competed by sequences of the 5' enhancer. The results of deletion experiments show that H2DRE is the only regulatory region that can activate transcription from the 5' enhancerless H-2Kb gene in mouse L fibroblasts.

• MeSH
• chloramfenikol-O-acetyltransferasa genetika   MeSH
• genetická transkripce MeSH
• H-2 antigeny genetika   MeSH
• hlavní histokompatibilní komplex * MeSH
• jaderné proteiny metabolismus   MeSH
• kultivované buňky MeSH
• messenger RNA metabolismus   MeSH
• myši MeSH
• nádorové buňky kultivované MeSH
• northern blotting MeSH
• regulační oblasti nukleových kyselin * MeSH
• sekvenční delece MeSH
• Southernův blotting MeSH
• zesilovače transkripce MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chloramfenikol-O-acetyltransferasa MeSH
• H-2 antigeny MeSH
• jaderné proteiny MeSH
• messenger RNA MeSH

It has been reported that the major function of the sterol regulatory element binding protein 2 (SREBP-2) is to activate preferentially cholesterol biosynthesis in liver and adipose tissue rather than fatty acid synthesis. In the current study, we analyzed the effects of overexpression of human dominant-positive SREBP-2 transgene under control of PEPCK promoter in the spontaneously hypertensive rat (SHR) on lipid and glucose metabolism. Transgenic overexpression of SREBP-2 was associated with significantly higher hepatic triglycerides (20.4+/-0.9 vs. 17.0+/-0.05 micromol/g, P<0.05) but not cholesterol (10.6+/-0.4 vs. 10.9+/-0.4 micromol/g) and decreased relative weight of epididymal fat pad (0.73+/-0.03 vs. 0.83+/-0.03, P<0.05). In addition, muscle triglyceride (15.8+/-3.7 vs. 8.5+/-1.2 micromol/g, P<0.001) and cholesterol (3.6+/-0.5 vs. 2.1+/-0.1 micromol/g, P<0.05) concentrations were significantly increased in transgenic rats when compared to SHR controls. Ectopic fat accumulation was associated with significantly increased serum glucose levels (6.4+/-0.1 vs. 5.9+/-0.1 mmol/l, P<0.005) and reduced insulin levels (1.78+/-0.33 vs. 2.73+/-0.37 nmol/l, P<0.05) in transgenic rats. These results provide evidence for important role of SREBP-2 in regulation of lipid and glucose metabolism.

• MeSH
• adipogeneze * MeSH
• adipozita * MeSH
• cholesterol metabolismus   MeSH
• fosfoenolpyruvátkarboxykinasa (závislá na GTP) genetika   MeSH
• hypertenze krev   genetika   metabolismus   patofyziologie   MeSH
• intracelulární signální peptidy a proteiny genetika   MeSH
• inzulin krev   MeSH
• játra metabolismus   MeSH
• krevní glukóza metabolismus   MeSH
• lidé MeSH
• modely nemocí na zvířatech MeSH
• potkani inbrední SHR MeSH
• potkani transgenní MeSH
• promotorové oblasti (genetika) MeSH
• protein SREBP2 genetika   metabolismus   MeSH
• triglyceridy metabolismus   MeSH
• tuková tkáň metabolismus   patofyziologie   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cholesterol MeSH
• fosfoenolpyruvátkarboxykinasa (závislá na GTP) MeSH
• intracelulární signální peptidy a proteiny MeSH
• inzulin MeSH
• krevní glukóza MeSH
• Pck1 protein, rat MeSH Prohlížeč
• protein SREBP2 MeSH
• SREBF2 protein, human MeSH Prohlížeč
• triglyceridy MeSH

The previously reported genetic polymorphisms of the stearoyl-CoA desaturase (SCD1) and sterol regulatory element binding protein-1 (SREBP-1) genes were investigated in Fleckvieh bulls using the PCR-RFLP and AS-PCR methods, respectively. The genomic DNA was obtained from a total of 370 bulls. The frequencies of alleles A and V of the single nucleotide polymorphism in exon 5 of the SCD1 gene (SNP 878C>T) were 0.555 and 0.445, respectively. In the 84-bp Ins/Del polymorphism in intron 5 of the SREBP-1 gene, the frequency of the L allele (insertion) was markedly higher (0.920) than that of the S allele (deletion; 0.080). Fatty acid profile was determined in a total of 367 samples of muscle fat (MSF) and 150 samples of subcutaneous fat (SCF). The AA genotype of SCD1 polymorphism showed a lower content of C18:0 (P<0.01) and higher contents of C14:1 cis-9 (P<0.001) and C18:1 cis-9 (P<0.05) in MSF compared to the VV genotype. As a result, the bulls with genotypes AA or AV had lower SFA (P<0.01), higher MUFA (P<0.05) and higher MUFA/SFA (P<0.01) than VV animals. The results obtained for SCF were similar. The SREBP-1 polymorphism was associated with a higher content of C14:1 cis-9 (P<0.01) in the LS compared to LL genotype in SCF. The results of this study demonstrated the existence of the polymorphisms in the SCD1 and SREBP-1 genes in the population of Fleckvieh cattle and their associations with the concentrations of several MSF and SCF fatty acids.

• MeSH
• DNA analýza   MeSH
• exony MeSH
• frekvence genu MeSH
• genom MeSH
• genotyp MeSH
• introny MeSH
• jednonukleotidový polymorfismus * MeSH
• kosterní svaly chemie   MeSH
• kyseliny mastné mononenasycené analýza   MeSH
• mastné kyseliny analýza   genetika   MeSH
• podkožní tuk chemie   MeSH
• polymerázová řetězová reakce metody   MeSH
• protein SREBP1 genetika   MeSH
• skot MeSH
• stearyl-CoA-desaturasa genetika   MeSH
• uhlík MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• kyseliny mastné mononenasycené MeSH
• mastné kyseliny MeSH
• protein SREBP1 MeSH
• stearyl-CoA-desaturasa MeSH
• uhlík MeSH

Iron is an essential element involved in many life-necessary processes. Interestingly, in mammals there is no active excretion mechanism for iron. Therefore iron kinetics has to be meticulously regulated. The most important step for regulation of iron kinetics is absorption. The absorption takes place in small intestine and it is implicated that it requires several proteins. Iron is then released from enterocytes into the circulation and delivered to the cells. Iron movement inside the cell is only partially elucidated and its traffic to mitochondia is not known. Surprisingly, the regulation of various proteins related to iron kinetics and energy metabolism at the molecular level is better described. On contrary, the complex control of iron absorption cannot be fully explicated with present knowledge.

• MeSH
• absorpce MeSH
• lidé MeSH
• proteiny regulující obsah železa metabolismus   MeSH
• tenké střevo metabolismus   MeSH
• železo metabolismus   farmakokinetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• proteiny regulující obsah železa MeSH
• železo MeSH

The paired domain, DNA-binding domain of Pax6 and other Pax transcription factors, is composed of two subdomains (PAI and RED), each recognizing distinct half-sites of the bipartite binding site in adjacent major grooves of the DNA helix. The alternatively spliced Pax6(5a) isoform containing 14 extra amino acids within the PAI domain recognizes the 5aCON sequence consisting of four interdigitated 5' half-sites of the bipartite consensus sequence. A genome database search for similar tetrameric Pax6(A) recognition sequences led to the identification of a Pax6-binding site in the lens-specific enhancer of the mouse E- and F-crystallin genes. This binding site combines the properties of bipartite and tetrameric recognition sequences and, by mutational analysis, is shown to mediate Pax6-dependent regulation of the E- and F-crystallin promoter constructs both in primary chicken lens cells and in chicken embryo fibroblasts. The Pax6-binding site is adjacent to a previously identified retinoic acid response element and is itself required for retinoic acid induction of the F- and E-crystallin genes, suggesting that Pax proteins and retinoic acid receptors cooperate in transcriptional regulation. In summary, our protein-DNA binding and transactivation studies suggest that -crystallin genes are under the control of a multifunctional enhancer element that mediates Pax6 regulation as well as retinoic acid-mediated induction.

• MeSH
• DNA vazebné proteiny genetika   fyziologie   MeSH
• down regulace MeSH
• epitelové buňky metabolismus   MeSH
• homeodoménové proteiny genetika   fyziologie   MeSH
• krystaliny genetika   MeSH
• kultivované buňky MeSH
• kuřecí embryo MeSH
• luciferasy genetika   metabolismus   MeSH
• oční čočka cytologie   metabolismus   MeSH
• oční proteiny MeSH
• plazmidy genetika   MeSH
• promotorové oblasti (genetika) genetika   MeSH
• receptory kyseliny retinové genetika   fyziologie   MeSH
• regulace genové exprese účinky léků   MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• rekombinantní fúzní proteiny genetika   metabolismus   MeSH
• represorové proteiny genetika   fyziologie   MeSH
• retinoidní X receptory MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• transfekce MeSH
• transkripční faktor PAX6 MeSH
• transkripční faktory bHLH MeSH
• transkripční faktory paired box MeSH
• transkripční faktory genetika   fyziologie   MeSH
• tretinoin farmakologie   MeSH
• vazebná místa genetika   MeSH
• zesilovače transkripce genetika   MeSH
• zvířata MeSH
• Check Tag
• kuřecí embryo MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• gro protein, Drosophila MeSH Prohlížeč
• homeodoménové proteiny MeSH
• krystaliny MeSH
• luciferasy MeSH
• oční proteiny MeSH
• Pax6 protein, mouse MeSH Prohlížeč
• receptory kyseliny retinové MeSH
• rekombinantní fúzní proteiny MeSH
• represorové proteiny MeSH
• retinoidní X receptory MeSH
• transkripční faktor PAX6 MeSH
• transkripční faktory bHLH MeSH
• transkripční faktory paired box MeSH
• transkripční faktory MeSH
• tretinoin MeSH

Gene expression regulation during tissue development is extremely complex. A key mechanism of gene regulation is the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in gene promoter regions. Localization of these motifs near the transcription start site (TSS) or translation start site (ATG) is crucial for transcription initiation and rate. Transcription levels of individual genes, regulated by these motifs, can vary significantly across tissues and developmental stages, especially in processes like sexual reproduction. However, the precise localization and visualization of these motifs in relation to gene expression in specific tissues can be challenging. Here, we introduce a freely available tool called GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz), which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life (Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis). The visualization of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution regardless of the transcription level. Additionally, genes with specific CREs at defined positions and high expression in selected tissues can be exported for further analysis. GOLEM's functionality is illustrated by its application to conserved motifs (e.g. TATA-box, ABRE, I-box, and TC-element), hormone-responsive elements (GCC-box, ARR10_binding motif), as well as to male gametophyte-related motifs (e.g., LAT52, MEF2, and DOF_core).

• Klíčová slova
• GOLEM, Gene regulatOry eLEMents, TSS, gametophyte, motif localization, plant genes, promoter elements, technical advance,
• MeSH
• genom rostlinný genetika   MeSH
• počátek transkripce MeSH
• promotorové oblasti (genetika) * genetika   MeSH
• pyl genetika   MeSH
• regulace genové exprese u rostlin * MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH

The aim of this investigation was to discover the promoters that drive expression of the sig genes encoding sigma factors of RNA polymerase in Rhodococcus erythropolis CCM2595 and classify these promoters according to the sigma factors which control their activity. To analyze the regulation of major sigma factors, which control large regulons that also contain genes expressed under exponential growth and non-stressed conditions, we used the R. erythropolis CCM2595 culture, which grew rapidly in minimal medium. The transcriptional start sites (TSSs) of the genes sigA, sigB, sigD, sigE, sigG, sigH, sigJ, and sigK were detected by primary 5'-end-specific RNA sequencing. The promoters localized upstream of the detected TSSs were defined by their -35 and -10 elements, which were identical or closely similar to these sequences in the related species Corynebacterium glutamicum and Mycobacterium tuberculosis. Regulation of the promoter activities by different sigma factors was demonstrated by two independent techniques (in vivo and in vitro). All analyzed sig genes encoding the sigma factors with extracytoplasmic function (ECF) were found to be also driven from additional housekeeping promoters. Based on the classification of the sig gene promoters, a model of the basic sigma transcriptional regulatory network in R. erythropolis was designed.

• Klíčová slova
• Rhodococcus erythropolis, in vitro transcription, RNA-seq, sigma factor, transcriptional regulatory network,
• MeSH
• bakteriální proteiny * metabolismus   MeSH
• genetická transkripce MeSH
• genové regulační sítě MeSH
• regulace genové exprese u bakterií * MeSH
• Rhodococcus MeSH
• sigma faktor metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny * MeSH
• sigma faktor MeSH

The genetic architecture of corneal endothelial dystrophies remains unknown in a substantial number of affected individuals. The proband investigated in the current study was diagnosed in the neonatal period with bilateral corneal opacification due to primary endothelial cell dysfunction. Neither his parents nor his sister had signs of corneal disease. Conventional karyotyping revealed a de novo translocation involving chromosomes 3 and 20, t(3;20)(q25;p11-12). Following genome and targeted Sanger sequencing analysis, the breakpoints were mapped at the nucleotide level. Notably, the breakpoint on chromosome 20 was identified to lie within the same topologically associated domain (TAD) as corneal endothelial dystrophy-associated gene OVOL2, and it is predicted to disrupt distal enhancers. The breakpoint at chromosome 3 is located within intron 2 of PFN2, which is currently not associated with any human disease. Further interrogation of the proband's genome failed to identify any additional potentially pathogenic variants in corneal endothelial dystrophy-associated genes. Disruption of a candidate cis-regulatory element and/or positional effects induced by translocation of OVOL2 to a novel genomic context may lead to an aberrant OVOL2 expression, a previously characterized disease mechanism of corneal endothelial dystrophy. Further research is necessary to explore how disruption of regulatory elements may elucidate genetically unsolved corneal endothelial dystrophies.

• MeSH
• dědičné dystrofie rohovky * genetika   diagnóza   MeSH
• genetická predispozice k nemoci MeSH
• lidé MeSH
• lidské chromozomy, pár 3 genetika   MeSH
• novorozenec MeSH
• regulační oblasti nukleových kyselin * MeSH
• rodokmen MeSH
• transkripční faktory * genetika   MeSH
• translokace genetická MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Ovol2 protein, human MeSH Prohlížeč
• transkripční faktory * MeSH

Analysis of plants bearing a T-DNA insertion is a potent tool of modern molecular biology, providing valuable information about the function and involvement of genes in metabolic pathways. A collection of 12 Arabidopsis thaliana lines with T-DNA insertions in the gene coding for the catalytic subunit of telomerase (AtTERT) and in adjacent regions was screened for telomerase activity [telomere repeat amplification protocol (TRAP) assay], telomere length (terminal restriction fragments), and AtTERT transcription (quantitative reverse transcription-PCR). Lines with the insertion located upstream of the start codon displayed unchanged telomere stability and telomerase activity, defining a putative minimal AtTERT promoter and the presence of a regulatory element linked to increased transcription in the line SALK_048471. Lines bearing a T-DNA insertion inside the protein-coding region showed telomere shortening and lack of telomerase activity. Transcription in most of these lines was unchanged upstream of the T-DNA insertion, while it was notably decreased downstream. The expression profile varied markedly in mutant lines harbouring insertions at the 5' end of AtTERT which showed increased transcription and abolished tissue specificity. Moreover, the line FLAG_385G01 (T-DNA insertion inside intron 1) revealed the presence of a highly abundant downstream transcript with normal splicing but without active telomerase. The role of regulatory elements found along the AtTERT gene is discussed in respect to natural telomerase expression and putative intron-mediated enhancement.

• MeSH
• Arabidopsis genetika   MeSH
• DNA bakterií genetika   MeSH
• genotyp MeSH
• inzerční mutageneze MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• proteiny huseníčku genetika   MeSH
• regulace genové exprese u rostlin MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• telomerasa genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA bakterií MeSH
• proteiny huseníčku MeSH
• T-DNA MeSH Prohlížeč
• telomerasa MeSH
• TERT protein, Arabidopsis MeSH Prohlížeč