The role of the TNF (rs1800629), TNFB (rs2239704) and TNFRSF1B (rs652625) genes polymorphic variants in the allergic and infectious disease's development

В настоящем исследовании установлены ассоциации полиморфных вариантов генов TNF (rs1800629), TNFB (rs2239704) и TNFRSF1B (rs652625) с развитием бронхиальной астмы и туберкулеза. Различия в характере транскрипции гена TNF в зависимости от генотипа и воздействия стимуляторов микробного/немикробного происхождения (LPS, IFN-γ) предполагают функциональную значимость однонуклеотидной замены G>A (rs1800629) в гене TNF. In the present study, we established associations of the genes TNF (rs1800629); TNFB (rs2239704) and TNFRSF1B (rs652625) with the development of bronchial asthma and tuberculosis. Differences in the TNF gene transcription pattern depending on the genotype and the effect of stimulators of microbial/non-microbial origin (LPS, IFN-γ) suggest the functional significance of the single nucleotide substitution G>A (rs1800629) of the TNF gene.

Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype

Background Clonal chromosome changes are often found in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS). The most frequent ones include an isochromosome of the long arm of chromosome 7, i (7)(q10), and an interstitial deletion of the long arm of chromosome 20, del (20)(q). These two imbalances are mechanisms of somatic genetic rescue. The literature offers few expression studies on SDS. Results We report the expression analysis of bone marrow (BM) cells of patients with SDS in relation to normal karyotype or to the presence of clonal chromosome anomalies: del (20)(q) (five cases), i (7)(q10) (one case), and other anomalies (two cases). The study was performed using the microarray technique considering the whole transcriptome (WT) and three gene subsets selected as relevant in BM functions. The expression patterns of nine healthy controls and SDS patients with or without chromosome anomalies in the bone marrow showed clear differences. Conclusions There is a significant difference between gene expression in the BM of SDS patients and healthy subjects, both at the WT level and in the selected gene sets. The deletion del (20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells led to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields a pattern similar to healthy subjects. Hence, the benign prognostic value of del (20)(q). The case of i (7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.

Follicular environment as a predictive tool for embryo development and kinetics in cattle

Follicular fluid composition and the transcription pattern of granulosa cells were analysed to better comprehend associations between embryo development and morphokinetics. Bovine follicles were punctured and their respective follicular fluid and granulosa cells were collected. Cumulus–oocyte complexes derived from these follicles were matured and fertilised invitro. Embryo morphology and kinetics were evaluated at 40h after insemination, when embryos were classified as fast (FCL, four or more cells), slow (SCL, 2–3 cells) or non-cleaved (NCL). Their development was followed until the blastocyst stage. Glucose, pyruvate, cholesterol and oestradiol were quantified in the follicular fluid and the transcription pattern of 96 target genes was evaluated in granulosa cells by large-scale quantitative reverse transcription polymerase chain reaction. Follicular fluid from the blastocyst group had increased levels of glucose, total cholesterol and pyruvate compared to the non-blastocyst group, whereas higher levels of oestradiol were observed in the follicular fluid of embryos and blastocysts with fast cleavage. The transcriptional pattern revealed altered metabolic pathways between groups, such as lipid metabolism, cellular stress and cell signalling. In conclusion, both follicular fluid and granulosa cells are associated with the possibility of identifying follicles that may generate embryos with high potential to properly develop to the blastocyst stage.

Heritable, Allele-Specific Chromosomal Looping between Tandem Promoters Specifies Promoter Usage of SHC1

ABSTRACT One-half of the genes in the human genome contain alternative promoters, some of which generate products with opposing functions. Aberrant silencing or activation of such alternative promoters is associated with multiple diseases, including cancer, but little is known regarding the molecular mechanisms that control alternative promoter choice. The SHC1 gene encodes p46 Shc /p52 Shc and p66 Shc , proteins oppositely regulating anchorage-independent growth that are produced by transcription initiated from the upstream and downstream tandem promoters of SHC1 , respectively. Here we demonstrate that activation of these promoters is mutually exclusive on separate alleles in single primary endothelial cells in a heritable fashion, ensuring expression of both transcripts by the cell. Peripheral blood lymphocytes that do not transcribe p66 Shc transcribed p52 Shc biallelically. This distinct monoallelic transcription pattern is established by allele-specific chromosomal looping between tandem promoters, which silences the upstream promoter. Our results reveal a new mechanism to control alternative promoter usage through higher-order chromatin structure.

Transcription Pattern of Catalase Gene from Gynostemma pentaphyllum (Thunb.) Makino during Various Abiotic Stresses

<p>Catalase (CAT) is a group of enzymes that protect cells against oxidative damage generated by reactive oxygen species. A CAT cDNA was previously isolated and characterized from 3-month-old hydroponically cultured <em>Gynostemma pentaphyllum</em> (Thunb.) Makino plants. The ORF is 1.479 bp with a deduced amino acid sequence of 492 residues. CAT from <em>G. pentaphyllum </em>has a molecular mass of 56.97 kDa with an isoelectric point (pI) of 6.95. The temporal expression analysis of leaf samples demonstrated that <em>GpCAT</em> expression could be up-regulated by various environmental stresses such as jasmonic acid electro, oxidative, salt, heavy metal, chilling and heat stress in a certain time period. A three-dimensional structural model of <em>G. pentaphyllum </em>based on its <em>GpCAT</em> cDNA sequence. The temporal expression pattern suggests that the <em>GpCAT</em> could play a role in the molecular defense response of <em>G. pentaphyllum</em> to abiotic stresses.</p>

The G-box transcriptional regulatory code in Arabidopsis

ABSTRACTPlants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes—these expansions are linked to adaptation to environmental stressors (1, 2). Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determine that the flanking sequences near G-boxes help determine in vitro specificity, but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we construct a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the gene expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a website that provides interactive visualisations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.