Analysis of whole-genome binding patterns of GAGA and CNC transcription factors during Drosophila melanogaster development

On the basis of available data of ChIP-seq and ChIPchip experiments performed using antibodies against GAGA and CNC transcription factors, genome-wide binding mapping of these factors at hours 0–12 and 16–24 of Drosophila embryogenesis, as well as on white pre-pupae stage, was conducted. It was shown that the bulk of GAGA and CNC binding falls into promoter regions and introns, with the maximal density of peaks in the vicinity of the transcription start site. Moreover, in both 0–12 and 16–24 hour old embryos GAGA and CNC are frequently co-localized, while on white pre-pupae stage there is no co-localization of these factors on a genome–wide scale. In order to select a set of genes potentially co-regulated by GAGA and CNC, the study of their co-binding in annotated regulatory regions (promoter areas and segments corresponding to the 5’-UTR and 3’-UTR of mRNA) was performed. The results obtained clearly demonstrated that the sets of genes characterized by co-binding of both factors vary greatly at different stages. Thus from 353 genes with overlapped GAGA and CNC binding loci on the 0–12 hour old embryos and 611 genes on the 0–12 hour old embryos only 61 genes “belong” to both stages. For an explanation it is proposed that different sets of target genes are regulated by combinations of various GAGA and CNC isoforms, which are characterized by distinct expression patterns during drosophila embryogenesis. Functional annotation analysis of genes, in whose regulatory regions both GAGA and CNC were found at all investigated stages, demonstrates enrichment by genes controlling embryogenesis, neurogenesis and wing development. The data obtained suggest the interaction of GAGA and CNC during D. melanogaster embryogenesis

The ultradian rhythm of glucocorticoid secretion and the time course of target gene regulation

Glucocorticoid hormones (cortisol in humans and corticosterone in rodents) are secreted in discrete pulses during a day with a periodicityof approximately 1 h (ultradian rhythm), and this pattern is also maintained in plasma and extracellular fluid. However, the vast majority of studies on gene regulation by glucocorticoids typically assess gene responses regardless the ultradian rhythm. These experiments are usually performed using long-term stimulation with synthetic hormones (dexamethasone and triamcinolone), which form much more stable complexes with glucocorticoid receptor (GR) then natural hormones. This review summarizes the current scarce information, obtained in experiments mimicking the ultradian mode of natural hormone secretion in cultured cells and in animal models. The results of these experiments clearly demonstrate that ultradian stimulation by natural hormones induces rapid GR exchange with glucocorticoid response elements and leads to cyclic GR mediated transcriptional regulation (gene pulsing) at the level of nascent RNA. In contrast, synthetic glucocorticoids, having much higher receptor affinity, fail to disengage from nuclear receptors with sufficient speed to support the ultradian cycles, thereby uncoupling extracellular hormone fluctuations from appropriate receptor function at response elements. This alters RNA accumulation profiles dramatically. These findings suggest potentially important consequences of ultradian secretion. The transcriptional program induced by hormone pulses differs significantly from that generated by constant hormone treatment. Thus, treatment with synthetic glucocorticoids may not provide an accurate assessment of physiological hormone action

Application of alternative <i>de novo</i> motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites

The most popular model for the search of ChIP-seq data for transcription factor binding sites (TFBS) is the positional weight matrix (PWM). However, this model does not take into account dependencies between nucleotide occurrences in different site positions. Currently, two recently proposed models, BaMM and InMoDe, can do as much. However, application of these models was usually limited only to comparing their recognition accuracies with that of PWMs, while none of the analyses of the co-prediction and relative positioning of hits of different models in peaks has yet been performed. To close this gap, we propose the pipeline called MultiDeNA. This pipeline includes stages of model training, assessing their recognition accuracy, scanning ChIP-seq peaks and their classif ication based on scan results. We applied our pipeline to 22 ChIP-seq datasets of TF FOXA2 and considered PWM, dinucleotide PWM (diPWM), BaMM and InMoDe models. The combination of these four models allowed a signif icant increase in the fraction of recognized peaks compared to that for the sole PWM model: the increase was 26.3 %. The BaMM model provided the main contribution to the recognition of sites. Although the major fraction of predicted peaks contained TFBS of different models with coincided positions, the medians of the fraction of peaks containing the predictions of sole models were 1.08, 0.49, 4.15 and 1.73 % for PWM, diPWM, BaMM and InMoDe, respectively. Thus, FOXA2 BSs were not fully described by only a sole model, which indicates theirs heterogeneity. We assume that the BaMM model is the most successful in describing the structure of the FOXA2 BS in ChIP-seq datasets under study

Detection of new regulatory SNPs associated with colorectal cancer predisposition

A new approach to the search for regulatory SNPs (rSNPs) based on the use of ENCODE project data on ChIP-seq and RNA-seq experiments was developed. The approach was successfully used for the detection of rSNPs associated with colorectal cancer susceptibility. To start out with, we used raw sequence data of 15 independent ChIP-seq experiments run on colorectal cancer cell line HCT-116, which allowed us to generate the initial pool of 7985 SNPs located in regulatory regions. For further selection of functional SNPs, we used the ChIP-seq binding bias analysis and revealed 775 SNPs that are more likely to influence transcription regulation in HCT-116 cells. Then the RNA-seq bias analysis in HCT-116 cells was performed. As a result, we confirmed the functionality of 231 SNPs, which were classified as rSNPs. In order to select rSNPs potentially associated with colorectal cancer we chose those in strong linkage disequilibrium with SNPs asso-ciated with this pathology according to GWAS and ClinVar data. Functional annotation analysis of genes containing the rSNPs selected confirmed the involvement of BAIAP2L1 and BUB3 genes in colorectal cancer predisposition. We also found two genes (RRAGD and FZD6) playing a role in the RAS/MAРK and WNT signaling pathways. Although the involvement of the RAS/MAРK and WNT pathways in colon cancer is a well-known fact, these two genes are still unknown candidates. Moreover, we found 14 new candidate genes with promise for further study of colorectal cancer predisposition

Glucocorticoid receptor: translocation from the cytoplasm to the nuclei, chromatin and intranuclear chaperone cycles

Glucocorticoid receptor (GR) is a ligand-dependent transcription factor, involved in the regulation of hundreds of genes. In the absence of any ligand, GR resides in the cytoplasm where it is sequestered in a multimeric chaperone complex consisting of hsp90, hsp70, p23, Hop, FKBP51, FKBP52, etc. As part of this multiprotein complex, GR undergoes conformational changes that allow glucocorticoid hormone binding. Upon ligand binding, GR dissociates from chaperon complex and translocates into the nucleus, where it interacts with specific DNA sequences (GREs) in the regulatory regions of target genes and modulates their expression. Then unliganded GR is exported to the cytoplasm, completing the nuclear-cytoplasmic cycle. Recent evidence suggests that, in addition to this cycle, chromatin and chaperone GR cycles exist within the nuclei. The chromatin cycle implies repeated interactions of ligand-bound GR with GREs in the chromatin context lasting for few seconds. The chaperone cycle starts after dissociation of the hormone–receptor complex, when GR binds to the nuclear chaperone machinery. As a result, its hormone-binding affinity is regained. Upon hormone binding, GR releases from chaperon complex and binds to GREs again. It is assumed that the chaperone cycle is mainly responsible for prolonged GR retention in nuclei (half-life within 8–12 h upon steroid withdrawal). In this review, we summarize and critically analyze the published data on chromatin and intranuclear chaperone GR cycles

The functional insight into the genetics of cardiovascular disease: results from the post-GWAS study

Cardiovascular diseases (CVDs), the leading cause of death worldwide, generally refer to a range of pathological conditions with the involvement of the heart and the blood vessels. A sizable fraction of the susceptibility loci is known, but the underlying mechanisms have been established only for a small proportion. Therefore, there is an increasing need to explore the functional relevance of trait-associated variants and, moreover, to search for novel risk genetic variation. We have reported the bioinformatic approach allowing effective identification of functional non-coding variants by integrated analysis of genome-wide data. Here, the analysis of 1361 previously identified regulatory SNPs (rSNPs) was performed to provide new insights into cardiovascular risk. We found 773,471 coding co-segregating markers for input rSNPs using the 1000 Genomes Project. The intersection of GWAS-derived SNPs with a relevance to cardiovascular traits with these markers was analyzed within a window of 10 Kbp. The effects on the transcription factor (TF) binding sites were explored by DeFine models. Functional pathway enrichment and protein– protein interaction (PPI) network analyses were performed on the targets and the extended genes by STRING and DAVID. Eighteen rSNPs were functionally linked to cardiovascular risk. A significant impact on binding sites of thirteen TFs including those involved in blood cells formation, hematopoiesis, macrophage function, inflammation, and vasoconstriction was found in K562 cells. 21 rSNP gene targets and 5 partners predicted by PPI were enriched for spliceosome and endocytosis KEGG pathways, endosome sorting complex and mRNA splicing REACTOME pathways. Related Gene Ontology terms included mRNA splicing and processing, endosome transport and protein catabolic processes. Together, the findings provide further insight into the biological basis of CVDs and highlight the importance of the precise regulation of splicing and alternative splicing

Effect of neonatal dexamethasone treatment on cognitive abilities of adult male mice and gene expression in the hypothalamus

The early postnatal period is critical for the development of the nervous system. Stress during this period causes negative long-term effects, which are manifested at both behavioral and molecular levels. To simulate the elevated glucocorticoid levels characteristic of early-life stress, in our study we used the administration of dexamethasone, an agonist of glucocorticoid receptors, at decreasing doses at the first three days of life (0.5, 0.3, 0.1 mg/kg, s.c.). In adult male mice with neonatal dexamethasone treatment, an increase in the relative weight of the adrenal glands and a decrease in body weight were observed, while the basal level of corticosterone remained unchanged. Dexamethasone treatment in early life had a negative impact on the learning and spatial memory of adult mice in the Morris water maze. We analyzed the effect of elevated glucocorticoid levels in early life on the expression of the Crh, Avp, Gr, and Mr genes involved in the regulation of the HPA axis in the hypothalami of adult mice. The expression level of the mineralocorticoid receptor gene (Mr) was significantly downregulated, and the glucocorticoid receptor gene (Gr) showed a tendency towards decreased expression (p = 0.058) in male mice neonatally treated with dexamethasone, as compared with saline administration. The expression level of the Crh gene encoding corticotropin-releasing hormone was unchanged, while the expression of the vasopressin gene (Avp) was increased in response to neonatal administration of dexamethasone. The obtained results demonstrate a disruption of negative feedback regulation of the HPA axis, which involves glucocorticoid and mineralocorticoid receptors, at the level of the hypothalamus. Malfunction of the HPA axis as a result of activation of the glucocorticoid system in early life may cause the development of cognitive impairment in the adult mice

Steps Toward Determination of the Size and Structure of the Broad-Line Region in Active Galactic Nuclei. XVI. A Thirteen-Year Study of Spectral Variability in NGC 5548

We present the final installment of an intensive 13-year study of variations of the optical continuum and broad H-beta emission line in the Seyfert 1 galaxy NGC 5548. The data base consists of 1530 optical continuum measurements and 1248 H-beta measurements. The H-beta variations follow the continuum variations closely, with a typical time delay of about 20 days. However, a year-by-year analysis shows that the magnitude of emission-line time delay is correlated with the mean continuum flux. We argue that the data are consistent with the simple model prediction that the size of the broad-line region is proportional to the square root of the ionizing luminosity. Moreover, the apparently linear nature of the correlation between the H-beta response time and the nonstellar optical continuum arises as a consequence of the changing shape of the continuum as it varies, specifically with the optical (5100 A) continuum luminosity proportional to the ultraviolet (1350 A) continuum luminosity to the 0.56 power.Comment: 20 pages plus 4 figures. Accepted for publication in The Astrophysical Journa

A Spectroscopic and Photometric Study of Short-Timescale Variability in NGC5548

Results of a ground-based optical monitoring campaign on NGC5548 in June 1998 are presented. The broad-band fluxes (U,B,V), and the spectrophotometric optical continuum flux F_lambda(5100 A) monotonically decreased in flux while the broad-band R and I fluxes and the integrated emission-line fluxes of Halpha and Hbeta remained constant to within 5%. On June 22, a short continuum flare was detected in the broad band fluxes. It had an amplitude of about ~18% and it lasted only ~90 min. The broad band fluxes and the optical continuum F_lambda(5100 A) appear to vary simultaneously with the EUV variations. No reliable delay was detected for the broad optical emission lines in response to the EUVE variations. Narrow Hbeta emission features predicted as a signature of an accretion disk were not detected during this campaign. However, there is marginal evidence for a faint feature at lambda = 4962 A with FWHM=~6 A redshifted by Delta v = 1100 km/s with respect to Hbeta_narrow.Comment: 12 pages, 7 figures, accepted for publishing in A&

EFFECT AUTOMOBILE WHEEL RIM ROLLING DISK OF SILICONE ON ITS STRUCTURE AND MECHANICAL PROPERTIES

Исследованы микроструктура и механические свойства литых дисков автомобильных колес из силумина марки АК7 после раскатки обода. В результате деформации и последующей термической обработки достигнуто повышение механических свойств.The microstructure and mechanical properties of cast wheel discs from silumin brand AK7 after rolling the rim. As a result, deformation and subsequent heat treatment achieved improvement in the mechanical properties