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

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

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

ХАРАКТЕРИСТИКИ САМОПОДОБИЯ СЕЙСМИЧНОСТИ И РАЗЛОМНОЙ СЕТИ СИХОТЭ‐АЛИНЬСКОГО ОРОГЕННОГО ПОЯСА И ПРИЛЕГАЮЩИХ ТЕРРИТОРИЙ

We performed a comprehensive analysis of the characteristics of self‐similarity of seismicity and the fault network within the Sikhote Alin orogenic belt and the adjacent areas. It has been established that the main features of seismicity are controlled by the crustal earthquakes. Differentiation of the study area according to the density of earthquake epicenters and the fractal dimension of the epicentral field of earthquakes (De) shows that the most active crustal areas are linked to the Kharpi‐Kur‐Priamurye zone, the northern Bureya massif and the Mongol‐Okhotsk folded system. The analysis of the earthquake recurrence plot slope values reveals that the highest b‐values correlate with the areas of the highest seismic activity of the northern part of the Bureya massif and, to a less extent, of the Mongol‐Okhotsk folded system. The increased fractal dimension values for the fault network (Df) correlate with the folded systems (Sikhote Alin and Mongol‐Okhotsk), while the decreased values conform to the depressions and troughs (Middle Amur, Uda and Torom). A comparison of the fractal analysis results for the fault network with the recent stress‐strain data gives evidence of their general confineness to the contemporary areas of intense compression. The correspondence between the field of the parameter b‐value for the upper crustal earthquakes and the fractal dimension value for the fault network (Df) suggests a general consistency between the self‐similar earthquake magnitude (energy) distribution and the fractal distribution of the fault sizes. The analysis results demonstrate that the selfsimilarity parameters provide an important quantitative characteristic in seismotectonics and can be used for the neotectonic and geodynamic analyses.Проведен комплексный анализ характеристик самоподобия сейсмичности и сети разломов в пределах Сихотэ‐Алиньского орогенного пояса и прилегающих территорий. Установлено, что основные осо‐ бенности сейсмичности определяются коровыми землетрясениями. Дифференциация исследуемой территории по плотности эпицентров и величине фрактальной размерности поля эпицентров (De) показывает, что наиболее активные участки земной коры связаны с Харпийско‐Курско‐Приамурской зоной, с северной частью Буреинского массива и Монголо‐Охотской складчатой системой. Анализ значений наклона графика повторяемости землетрясений (b) показывает, что наибольшие его величины соответствует районам наибольшей сейсмической активности: северной части Буреинского массива и, в меньшей степени, – Монголо‐Охотской системе. Повышенные значения фрактальной размерности разломной сети (Df) соответствуют складчатым системам (Сихотэ‐Алиньской и Монголо‐Охотской), а пониженные – впадинам и прогибам (Среднеамурская, Удский и Торомский). Сопоставление результатов фрактального анализа сети разломов с данными по современному напряженно‐деформированному состоянию показывает их общую приуроченность к областям интенсивного современного сжатия. Соответствие поля параметра b для верхнекоровых землетрясений и поля размерности сети разломов Df указывает на общую согласованность самоподобного распределения магнитуды (энергии) землетрясений и фрактального распределения размеров разрывных нарушений. Полученные результаты показывают, что параметры самоподобия являются важной количественной характеристикой в сейсмотектонике и могут использоваться при неотектоническом и геодинамическом анализе

2D Spectroscopy of Candidate Polar-Ring Galaxies: I. The Pair of Galaxies UGC 5600/09

Observations of the pair of galaxies VV 330 with the SCORPIO multimode instrument on the 6-m Special Astrophysical Observatory telescope are presented. Large-scale velocity fields of the ionized gas in H-alfa and brightness distributions in continuum and H-alfa have been constructed for both galaxies with the help of a scanning Fabry Perot interferometer. Long-slit spectroscopy is used to study the stellar kinematics. Analysis of the data obtained has revealed a complex structure in each of the pair components. Three kinematic subsystems have been identified in UGC 5600: a stellar disk, an inner gas ring turned with respect to the disk through ~80degrees, and an outer gas disk. The stellar and outer gas disks are noncoplanar. Possible scenarios for the formation of the observed multicomponent kinematic galactic structure are considered, including the case where the large-scale velocity field of the gas is represented by the kinematic model of a disk with a warp. The velocity field in the second galaxy of the pair, UGC 5609, is more regular. A joint analysis of the data on the photometric structure and the velocity field has shown that this is probably a late-type spiral galaxy whose shape is distorted by the gravitational interaction, possibly, with UGC 5600.Comment: 18 pages, 6 figure

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&

A dust-parallax distance of 19 megaparsecs to the supermassive black hole in NGC 4151

The active galaxy NGC 4151 has a crucial role as one of only two active galactic nuclei for which black hole mass measurements based on emission line reverberation mapping can be calibrated against other dynamical methods. Unfortunately, effective calibration requires an accurate distance to NGC 4151, which is currently not available. Recently reported distances range from 4 to 29 megaparsecs (Mpc). Strong peculiar motions make a redshift-based distance very uncertain, and the geometry of the galaxy and its nucleus prohibit accurate measurements using other techniques. Here we report a dust-parallax distance to NGC 4151 of $D_A = 19.0^{+2.4}_{-2.6}$ Mpc. The measurement is based on an adaptation of a geometric method proposed previously using the emission line regions of active galaxies. Since this region is too small for current imaging capabilities, we use instead the ratio of the physical-to-angular sizes of the more extended hot dust emission as determined from time-delays and infrared interferometry. This new distance leads to an approximately 1.4-fold increase in the dynamical black hole mass, implying a corresponding correction to emission line reverberation masses of black holes if they are calibrated against the two objects with additional dynamical masses.Comment: Authors' version of a letter published in Nature (27 November 2014); 8 pages, 5 figures, 1 tabl

Epigenetic «probes» for lung cancer monitoring: LINE-1 methylation pattern in blood- circulating DNA

Malignant cell transformation is accompanied by two processes of DNA methylation changes: promoter hypermethylation of specific genes and hypomethylation of retrotransposons. The composition of circulating DNA (cirDNA) from plasma and cell-surface-bound circulating DNA (csb- cirDNA) was shown earlier to be altered in the blood of cancer patients due to accumulation of tumor- specific aberrantly methylated DNA fragments, which are currently considered valuable cancer markers. The present study compares LINE-1 retrotransposon methylation patterns in plasma cirDNA and csb- cirDNA from 21 untreated lung cancer patients (LC) and 23 healthy donors. Concentrations of methylated LINE-1 region 1 copies (LINE-1met) were assayed by real-time methylation-specific PCR. In order to normalize the LINE-1 methylation level, the LINE-1 region 2 concentration was evaluated, which was independent of the methylation status (LINE-1Ind). The LINE-1met concentration in csb-cirDNA tended to decrease (by a factor of 1.4) in blood from LC patients in comparison to healthy donors (Mann- Whitney test, P=0.16). The LINE-1Ind concentration in csb-cirDNA (methylation-independent) was found to be threefold lower in LC patients and fourfold lower in patients with adenocarcinoma than in healthy donors. That is why, along with the expected decrease in LINE-1met concentration in csb-cirDNA, we recorded an unexpected statistically significant increase of the LINE-1 methylation index determined as (LINE-1met/LINE-1Ind) due to the profound LINE-1Ind decrease. Plasma cirDNA demonstrated no difference in the LINE-1 methylation index (LINE-1met/LINE-1Ind) between LC patients and healthy donors (Mann-Whitney test, P = 0.40). The data obtained agree with our earlier results, which showed that csb-cirDNA was a highly informative material for lung cancer diagnostics