Among computationally predicted and experimentally validated plant miRNAs, several are conserved across species boundaries in the plant kingdom. In this study, a combined experimental-in silico computational based approach was adopted for the identification and characterization of miRNAs in Humulus lupulus (hop), which is widely cultivated for use by the brewing industry and apart from, used as a medicinal herb. A total of 22 miRNAs belonging to 17 miRNA families were identified in hop following comparative computational approach and EST-based homology search according to a series of filtering criteria. Selected miRNAs were validated by end-point PCR and quantitative reverse transcription-polymerase chain reaction (qRT-PCR), confirmed the existence of conserved miRNAs in hop. Based on the characteristic that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences, a total of 47 potential miRNA targets were identified in hop. Strikingly, the majority of predicted targets were belong to transcriptional factors which could regulate hop growth and development, including leaf, root and even cone development. Moreover, the identified miRNAs may also be involved in other cellular and metabolic processes, such as stress response, signal transduction, and other physiological processes. The cis-regulatory elements relevant to biotic and abiotic stress, plant hormone response, flavonoid biosynthesis were identified in the promoter regions of those miRNA genes. Overall, findings from this study will accelerate the way for further researches of miRNAs, their functions in hop and shows a path for the prediction and analysis of miRNAs to those species whose genomes are not available.

• Klíčová slova
• Comparative genomics, Expressed sequence tags, Humulus lupulus, Posttranscriptional gene regulation, microRNA,
• MeSH
• databáze genetické MeSH
• exprimované sekvenční adresy * MeSH
• genové regulační sítě genetika   MeSH
• Humulus genetika   MeSH
• mikro RNA genetika   MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• regulace genové exprese u rostlin genetika   MeSH
• rostlinné geny genetika   MeSH
• software * MeSH
• stanovení celkové genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mikro RNA MeSH

BACKGROUND: Large sets of well-characterized promoter sequences are required to facilitate the understanding of promoter architecture. The major sequence databases are a prospective source of upstream regulatory regions, but suffer from inaccurate annotation. The software tool PRESTA (PRomoter EST Association) presented in this study is designed for efficient recovery of characterized and partially verified promoters from GenBank and EMBL libraries. RESULTS: The PRESTA algorithm examines the putative GenBank/EMBL promoters and automatically removes most of the poorly annotated entries. The remaining records are connected to expressed sequence tags (ESTs) through a high-stringency BLAST search. The frequency and source of recovered ESTs provide an estimate of the activity and expression pattern of the promoter, and the ESTs' 5' ends assist in transcription start-site verification. The PRESTA database provides easy access to non-redundant upstream regulatory regions recently extracted by the PRESTA algorithm. The current size of this resource is 552 human and 241 mouse promoters. Surprisingly, no overlap between the PRESTA database and the Eukaryotic Promoter Database (EPD) was detected by sequence comparison. CONCLUSIONS: The PRESTA algorithm demonstrates the principle of promoter verification by mapping EST 5' ends. The publicly available PRESTA database collects hundreds of characterized and partially verified promoter sequences and is complementary to other promoter databases.

• MeSH
• algoritmy MeSH
• databáze nukleových kyselin MeSH
• exprese genu genetika   MeSH
• exprimované sekvenční adresy MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• myši MeSH
• on-line systémy MeSH
• promotorové oblasti (genetika) genetika   MeSH
• software * MeSH
• stanovení celkové genové exprese metody   MeSH
• ukládání a vyhledávání informací metody   MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

RNA interference (RNAi) is a suitable method for sequence-specific post-transcriptional gene silencing for a number of model systems. Here, we describe selection of the target sequence for efficient RNAi knockdown in mouse.

• MeSH
• 3' nepřekládaná oblast MeSH
• databáze genetické MeSH
• dvouvláknová RNA metabolismus   MeSH
• exprimované sekvenční adresy MeSH
• genetické techniky * MeSH
• komplementární DNA metabolismus   MeSH
• malá interferující RNA metabolismus   MeSH
• messenger RNA metabolismus   MeSH
• myši MeSH
• posttranskripční úpravy RNA MeSH
• RNA interference * MeSH
• umlčování genů MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3' nepřekládaná oblast MeSH
• dvouvláknová RNA MeSH
• komplementární DNA MeSH
• malá interferující RNA MeSH
• messenger RNA MeSH

SMAD5, a transducer of TGF-beta/BMP inhibitory signals and a tumor suppressor candidate, localizes to the region of invariant loss in human myeloid neoplasms, on chromosome 5q31.1. Recent evidence indicates a gene-dosage effect along the TGF-beta/BMP signaling pathways. We have identified a novel transcript designated DAMS, whose 3' exonic sequences contain in part an alternate 5' exon of SMAD5, in the antisense orientation. Expressed sequenced tags (ESTs) for DAMS are found in fetal tissues (heart, adrenal glands, and total fetus) and pancreatic tumor cDNA libraries. In contrast to SMAD5, DAMS expression is not readily detectable in adult and fetal tissues. Semiquantitative PCR suggests that the stoichiometry between SMAD5 and DAMS transcripts ranges between 15 and 120 in normal and malignant hematopoietic cells. The findings raise the possibility that DAMS may be a fail-safe mechanism for precise regulation of SMAD5 transcript levels that may be critical in maintaining normal homeostasis.

• MeSH
• 5' nepřekládaná oblast genetika   MeSH
• antisense RNA genetika   MeSH
• DNA vazebné proteiny genetika   MeSH
• fosfoproteiny genetika   MeSH
• genetická transkripce genetika   MeSH
• hematopoéza genetika   MeSH
• lidé MeSH
• lidské chromozomy, pár 5 genetika   MeSH
• messenger RNA metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• myeloidní leukemie genetika   MeSH
• nádorové buňky kultivované MeSH
• polymerázová řetězová reakce MeSH
• protein Smad5 MeSH
• regulace genové exprese u nádorů genetika   MeSH
• RNA dlouhá nekódující MeSH
• RNA nádorová genetika   MeSH
• trans-aktivátory genetika   MeSH
• transkripční faktory genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Názvy látek
• 5' nepřekládaná oblast MeSH
• antisense RNA MeSH
• DNA vazebné proteiny MeSH
• fosfoproteiny MeSH
• messenger RNA MeSH
• protein Smad5 MeSH
• RNA dlouhá nekódující MeSH
• RNA nádorová MeSH
• SMAD5 protein, human MeSH Prohlížeč
• SMAD5-AS1 lncRNA, human MeSH Prohlížeč
• trans-aktivátory MeSH
• transkripční faktory MeSH

(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.

• Klíčová slova
• A↔T transversion, C↔T transition, EST, indel, nucleotide substitution, potential SNP,
• MeSH
• exprimované sekvenční adresy MeSH
• jednonukleotidový polymorfismus * MeSH
• mapování chromozomů MeSH
• nukleotidy MeSH
• šlechtění rostlin * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• nukleotidy MeSH

Several lines of evidence suggest that the X chromosome of various animal species has an unusual complement of genes with sex-biased or sex-specific expression. However, the study of the X chromosome gene content in different organisms provided conflicting results. The most striking contrast concerns the male-biased genes, which were reported to be almost depleted from the X chromosome in Drosophila but overrepresented on the X chromosome in mammals. To elucidate the reason for these discrepancies, we analysed the gene content of the Z chromosome in chicken. Our analysis of the publicly available expressed sequence tags (EST) data and genome draft sequence revealed a significant underrepresentation of ovary-specific genes on the chicken Z chromosome. For the brain-expressed genes, we found a significant enrichment of male-biased genes but an indication of underrepresentation of female-biased genes on the Z chromosome. This is the first report on the nonrandom gene content in a homogametic sex chromosome of a species with heterogametic female individuals. Further comparison of gene contents of the independently evolved X and Z sex chromosomes may offer new insight into the evolutionary processes leading to the nonrandom genomic distribution of sex-biased and sex-specific genes.

• MeSH
• exprimované sekvenční adresy MeSH
• genetická vazba MeSH
• kompenzace dávky (genetika) MeSH
• kur domácí genetika   MeSH
• mapování chromozomů MeSH
• pohlavní chromozomy genetika   MeSH
• sexuální faktory MeSH
• stanovení celkové genové exprese MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Here we describe a C-SWAT library for high-throughput tagging of Saccharomyces cerevisiae open reading frames (ORFs). In 5,661 strains, we inserted an acceptor module after each ORF that can be efficiently replaced with tags or regulatory elements. We validated the library with targeted sequencing and tagged the proteome with bright fluorescent proteins to quantify the effect of heterologous transcription terminators on protein expression and to localize previously undetected proteins.

• MeSH
• DNA fungální genetika   MeSH
• genom fungální * MeSH
• genomová knihovna * MeSH
• místa se sekvenční adresou MeSH
• otevřené čtecí rámce MeSH
• proteom genetika   MeSH
• proteomika MeSH
• Saccharomyces cerevisiae - proteiny genetika   MeSH
• Saccharomyces cerevisiae genetika   MeSH
• sekvenční analýza DNA MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH
• Názvy látek
• DNA fungální MeSH
• proteom MeSH
• Saccharomyces cerevisiae - proteiny MeSH

Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

• Klíčová slova
• Chromosome 4D survey sequence, Gene annotation, Gene content, Synteny, Triticum aestivum, Virtual gene order,
• MeSH
• chromozomy rostlin * MeSH
• exprimované sekvenční adresy chemie   MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• pořadí genů * MeSH
• pšenice genetika   MeSH
• sekvenční analýza DNA MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Euglena gracilis possesses secondary plastids of green algal origin. In this study, E. gracilis expressed sequence tags (ESTs) derived from polyA-selected mRNA were searched and several ESTs corresponding to plastid genes were found. PCR experiments failed to detect SL sequence at the 5'-end of any of these transcripts, suggesting plastid origin of these polyadenylated molecules. Quantitative PCR experiments confirmed that polyadenylation of transcripts occurs in the Euglena plastids. Such transcripts have been previously observed in primary plastids of plants and algae as low-abundance intermediates of transcript degradation. Our results suggest that a similar mechanism exists in secondary plastids.

• Klíčová slova
• EST, Euglenozoa, Plastid, Polyadenylation, Quantitative PCR, Trans-splicing,
• MeSH
• Euglena gracilis genetika   metabolismus   účinky záření   MeSH
• exprimované sekvenční adresy MeSH
• genom plastidový MeSH
• messenger RNA genetika   metabolismus   MeSH
• plastidy genetika   metabolismus   MeSH
• polyadenylace * MeSH
• protozoální geny MeSH
• RNA protozoální genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• messenger RNA MeSH
• RNA protozoální MeSH

Gene duplication is an important evolutionary mechanism and no eukaryote has more duplicated gene families than the parasitic protist Trichomonas vaginalis. Iron is an essential nutrient for Trichomonas and plays a pivotal role in the establishment of infection, proliferation, and virulence. To gain insight into the role of iron in T. vaginalis gene expression and genome evolution, we screened iron-regulated genes using an oligonucleotide microarray for T. vaginalis and by comparative EST (expressed sequence tag) sequencing of cDNA libraries derived from trichomonads cultivated under iron-rich (+Fe) and iron-restricted (-Fe) conditions. Among 19,000 ESTs from both libraries, we identified 336 iron-regulated genes, of which 165 were upregulated under +Fe conditions and 171 under -Fe conditions. The microarray analysis revealed that 195 of 4,950 unique genes were differentially expressed. Of these, 117 genes were upregulated under +Fe conditions and 78 were upregulated under -Fe conditions. The results of both methods were congruent concerning the regulatory trends and the representation of gene categories. Under +Fe conditions, the expression of proteins involved in carbohydrate metabolism, particularly in the energy metabolism of hydrogenosomes, and in methionine catabolism was increased. The iron-sulfur cluster assembly machinery and certain cysteine proteases are of particular importance among the proteins upregulated under -Fe conditions. A unique feature of the T. vaginalis genome is the retention during evolution of multiple paralogous copies for a majority of all genes. Although the origins and reasons for this gene expansion remain unclear, the retention of multiple gene copies could provide an opportunity to evolve differential expression during growth in variable environmental conditions. For genes whose expression was affected by iron, we found that iron influenced the expression of only some of the paralogous copies, whereas the expression of the other paralogs was iron independent. This finding indicates a very stringent regulation of the differentially expressed paralogous genes in response to changes in the availability of exogenous nutrients and provides insight into the evolutionary rationale underlying massive paralog retention in the Trichomonas genome.

• MeSH
• cysteinové proteasy genetika   metabolismus   MeSH
• duplikace genu MeSH
• exprimované sekvenční adresy MeSH
• genom protozoální MeSH
• genová dávka MeSH
• genová knihovna MeSH
• glykolýza genetika   MeSH
• molekulární evoluce MeSH
• proteiny obsahující železo a síru genetika   metabolismus   MeSH
• protozoální geny * MeSH
• regulace genové exprese * MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• transkriptom * MeSH
• Trichomonas vaginalis genetika   metabolismus   MeSH
• železo metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cysteinové proteasy MeSH
• proteiny obsahující železo a síru MeSH
• železo MeSH