Chromosome looping at the human alpha-globin locus is mediated via the major upstream regulatory element (HS-40)

Previous studies in the mouse have shown that high levels of alpha-globin gene expression in late erythropoiesis depend on long-range, physical interactions between remote upstream regulatory elements and the globin promoters. Using quantitative chromosome conformation capture (q3C), we have now analyzed all interactions between 4 such elements lying 10 to 50 kb upstream of the human alpha cluster and their interactions with the alpha-globin promoter. All of these elements interact with the alpha-globin gene in an erythroid-specific manner. These results were confirmed in a mouse model of human alpha globin expression in which the human cluster replaces the mouse cluster in situ (humanized mouse). We have also shown that expression and all of the long-range interactions depend largely on just one of these elements; removal of the previously characterized major regulatory element (called HS -40) results in loss of all the interactions and alpha-globin expression. Reinsertion of this element at an ectopic location restores both expression and the intralocus interactions. In contrast to other more complex systems involving multiple upstream elements and promoters, analysis of the human alpha-globin cluster during erythropoiesis provides a simple and tractable model to understand the mechanisms underlying long-range gene regulation.</p

Spitzer IRAC observations of newly-discovered planetary nebulae from the Macquarie-AAO-Strasbourg H-alpha Planetary Nebula Project

We compare H-alpha, radio continuum, and Spitzer Space Telescope (SST) images of 58 planetary nebulae (PNe) recently discovered by the Macquarie-AAO-Strasbo- urg H-alpha PN Project (MASH) of the SuperCOSMOS H-alpha Survey. Using InfraRed Array Camera (IRAC) data we define the IR colors of PNe and demonstrate good isolation between these colors and those of many other types of astronomical object. The only substantive contamination of PNe in the color-color plane we illustrate is due to YSOs. However, this ambiguity is readily resolved by the unique optical characteristics of PNe and their environs. We also examine the relationships between optical and MIR morphologies from 3.6 to 8.0um and explore the ratio of mid-infrared (MIR) to radio nebular fluxes, which is a valuable discriminant between thermal and nonthermal emission. MASH emphasizes late evolutionary stages of PNe compared with previous catalogs, enabling study of the changes in MIR and radio flux that attend the aging process. Spatially integrated MIR energy distributions were constructed for all MASH PNe observed by the GLIMPSE Legacy Project, using the H-alpha morphologies to establish the dimensions for the calculations of the Midcourse Space Experiment (MSX), IRAC, and radio continuum (from the Molonglo Observatory Synthesis Telescope and the Very Large Array) flux densities. The ratio of IRAC 8.0-um to MSX 8.3-um flux densities provides a measure of the absolute diffuse calibration of IRAC at 8.0 um. We independently confirm the aperture correction factor to be applied to IRAC at 8.0um to align it with the diffuse calibration of MSX. The result agrees with the recommendations of the Spitzer Science Center and with results from a parallel study of HII regions. These PNe probe the diffuse calibration of IRAC on a spatial scale of 9-77 arcsec.Comment: 48 pages, LaTeX (aastex), incl. 18 PostScript (eps) figures and 3 tables. Accepted by Astrophysical Journa

The chromatin remodeller ATRX: a repeat offender in human disease.

The regulation of chromatin structure is of paramount importance for a variety of fundamental nuclear processes, including gene expression, DNA repair, replication, and recombination. The ATP-dependent chromatin-remodelling factor ATRX (α thalassaemia/mental retardation X-linked) has emerged as a key player in each of these processes. Exciting recent developments suggest that ATRX plays a variety of key roles at tandem repeat sequences within the genome, including the deposition of a histone variant, prevention of replication fork stalling, and the suppression of a homologous recombination-based pathway of telomere maintenance. Here, we provide a mechanistic overview of the role of ATRX in each of these processes, and propose how they may be connected to give rise to seemingly disparate human diseases

A search for steep spectrum radio relics and halos with the GMRT

Context: Diffuse radio emission, in the form of radio halos and relics, traces regions in clusters with shocks or turbulence, probably produced by cluster mergers. Some models of diffuse radio emission in clusters indicate that virtually all clusters should contain diffuse radio sources with a steep spectrum. External accretion shocks associated with filamentary structures of galaxies could also accelerate electrons to relativistic energies and hence produce diffuse synchrotron emitting regions. Here we report on Giant Metrewave Radio Telescope (GMRT) observations of a sample of steep spectrum sources from the 74 MHz VLSS survey. These sources are diffuse and not associated with nearby galaxies. Aims: The main aim of the observations is to search for diffuse radio emission associated with galaxy clusters or the cosmic web. Methods: We carried out GMRT 610 MHz continuum observations of unidentified diffuse steep spectrum sources. Results: We have constructed a sample of diffuse steep spectrum sources, selected from the 74 MHz VLSS survey. We identified eight diffuse radio sources probably all located in clusters. We found five radio relics, one cluster with a giant radio halo and a radio relic, and one radio mini-halo. By complementing our observations with measurements from the literature we find correlations between the physical size of relics and the spectral index, in the sense that smaller relics have steeper spectra. Furthermore, larger relics are mostly located in the outskirts of clusters while smaller relics are located closer to the cluster center.Comment: 20 pages, 26 figures, accepted for publication in A&A on October 7, 200

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment

Genes on different chromosomes can be spatially associated in the nucleus in several transcriptional and regulatory situations; however, the functional significance of such associations remains unclear. Using human erythropoiesis as a model, we show that five cotranscribed genes, which are found on four different chromosomes, associate with each other at significant but variable frequencies. Those genes most frequently in association lie in decondensed stretches of chromatin. By replacing the mouse alpha-globin gene cluster in situ with its human counterpart, we demonstrate a direct effect of the regional chromatin environment on the frequency of association, whereas nascent transcription from the human alpha-globin gene appears unaffected. We see no evidence that cotranscribed erythroid genes associate at shared transcription foci, but we do see stochastic clustering of active genes around common nuclear SC35-enriched speckles (hence the apparent non-random association between genes). Thus, association between active genes may result from their location on decondensed chromatin that enables clustering around common nuclear speckles.</p

Disordered eating behaviour is associated with blunted cortisol and cardiovascular reactions to acute psychological stress

Research suggests a potential dysregulation of the stress response in individuals with bulimia nervosa. This study measured both cardiovascular and cortisol reactions to a standardised laboratory stress task in individuals identified as showing disordered eating behaviour to determine whether dysregulation of the stress response is characteristic of the two branches of the stress response system. Female students (N = 455) were screened using two validated eating disorder questionnaires. Twelve women with disordered eating, including self-induced vomiting, and 12 healthy controls were selected for laboratory stress testing. Salivary cortisol and cardiovascular activity, via Doppler imaging and semi-automatic blood pressure monitoring, were measured at resting baseline and during and after exposure to a 10-min mental arithmetic stress task. Compared to controls the disordered eating group showed blunted cortisol, cardiac output, heart rate, and stroke volume reactions to the acute stress, as well as an attenuated vasodilatory reaction. These effects could not be accounted for in terms of group differences in stress task performance, subjective task impact/engagement, age, BMI, neuroticism, cardiorespiratory fitness, or co-morbid exercise dependence. Our findings suggest that disordered eating is characterised by a dysregulation of the autonomic stress-response system. As such, they add further weight to the general contention that blunted stress reactivity is characteristic of a number of maladaptive behaviours and states

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations

Functional significance of mutations in the Snf2 domain of ATRX.

ATRX is a member of the Snf2 family of chromatin-remodelling proteins and is mutated in an X-linked mental retardation syndrome associated with alpha-thalassaemia (ATR-X syndrome). We have carried out an analysis of 21 disease-causing mutations within the Snf2 domain of ATRX by quantifying the expression of the ATRX protein and placing all missense mutations in their structural context by homology modelling. While demonstrating the importance of protein dosage to the development of ATR-X syndrome, we also identified three mutations which primarily affect function rather than protein structure. We show that all three of these mutant proteins are defective in translocating along DNA while one mutant, uniquely for a human disease-causing mutation, partially uncouples adenosine triphosphate (ATP) hydrolysis from DNA binding. Our results highlight important mechanistic aspects in the development of ATR-X syndrome and identify crucial functional residues within the Snf2 domain of ATRX. These findings are important for furthering our understanding of how ATP hydrolysis is harnessed as useful work in chromatin remodelling proteins and the wider family of nucleic acid translocating motors