The ARID1A subunit of SWI/SNF chromatin remodeling complexes is a potent tumor suppressor. Here, a degron is applied to detect rapid loss of chromatin accessibility at thousands of loci where ARID1A ...acts to generate accessible minidomains of nucleosomes. Loss of ARID1A also results in the redistribution of the coactivator EP300. Co-incident EP300 dissociation and lost chromatin accessibility at enhancer elements are highly enriched adjacent to rapidly downregulated genes. In contrast, sites of gained EP300 occupancy are linked to genes that are transcriptionally upregulated. These chromatin changes are associated with a small number of genes that are differentially expressed in the first hours following loss of ARID1A. Indirect or adaptive changes dominate the transcriptome following growth for days after loss of ARID1A and result in strong engagement with cancer pathways. The identification of this hierarchy suggests sites for intervention in ARID1A-driven diseases.
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•Degradation of ARID1A disrupts nucleosomes flanking pluripotency transcription factors•EP300 is rapidly redistributed with increased occupancy adjacent to upregulated genes•These changes are associated with misregulation of a few hundred genes within 2 h•During subsequent days, widespread indirect changes mimic a premalignant state
Blümli et al. show that degradation of ARID1A reorganizes nucleosomes flanking pluripotency transcription factors and causes redistribution of the coactivator EP300. Lost EP300 at enhancers is associated with downregulation of transcription and gained EP300 with upregulation. Few genes are directly affected, but widespread indirect effects accumulate slowly to phenocopy premalignancy.
GRS 1915+105: the brightest Galactic black hole Done, Chris; Wardziński, Grzegorz; Gierliński, Marek
Monthly notices of the Royal Astronomical Society,
April 2004, Letnik:
349, Številka:
2
Journal Article
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Odprti dostop
We compare the evolution of spectral shape with luminosity in GRS 1915+105 with that of ‘normal’ black holes. The pathological variability of GRS 1915+105, which probably indicates a disc ...instability, does not require that GRS 1915+105 belongs in a different class to all the other objects. At comparable fractions of Eddington luminosity its spectra and (more importantly) apparent disc stability are both similar to that seen in the ‘normal’ black holes. Its unique limit-cycle variability only appears when it radiates at uniquely high (super-Eddington) luminosities.
Proper chromosome segregation in mitosis relies on correct kinetochore interaction with spindle microtubules. In early mitosis, each kinetochore usually interacts with the lateral side of each ...microtubule and is subsequently tethered at the microtubule end. However, since eukaryotic cells carry multiple chromosomes, multiple kinetochores could occasionally interact with a single microtubule. The consequence of this is unknown. Here, we find that, although two kinetochores (two pairs of sister kinetochores) can interact with the lateral side of one microtubule, only one kinetochore can form a sustained attachment to the microtubule end in budding yeast (
). This leads to detachment of the other kinetochore from the microtubule end (or a location in its proximity). Intriguingly, in this context, kinetochore sliding along a microtubule towards a spindle pole delays and diminishes discernible kinetochore detachment. This effect expedites collection of the entire set of kinetochores to a spindle pole. We propose that cells are equipped with the kinetochore-sliding mechanism to mitigate problems associated with multiple kinetochores on one microtubule in early mitosis.
RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed to ensure valid biological ...interpretation of the results or which statistical tools are best for analyzing the data. An RNA-seq experiment with 48 biological replicates in each of two conditions was performed to answer these questions and provide guidelines for experimental design. With three biological replicates, nine of the 11 tools evaluated found only 20%-40% of the significantly differentially expressed (SDE) genes identified with the full set of 42 clean replicates. This rises to >85% for the subset of SDE genes changing in expression by more than fourfold. To achieve >85% for all SDE genes regardless of fold change requires more than 20 biological replicates. The same nine tools successfully control their false discovery rate at ≲5% for all numbers of replicates, while the remaining two tools fail to control their FDR adequately, particularly for low numbers of replicates. For future RNA-seq experiments, these results suggest that at least six biological replicates should be used, rising to at least 12 when it is important to identify SDE genes for all fold changes. If fewer than 12 replicates are used, a superior combination of true positive and false positive performances makes edgeR and DESeq2 the leading tools. For higher replicate numbers, minimizing false positives is more important and DESeq marginally outperforms the other tools.
We review how the recent increase in X-ray and radio data from black hole and neutron star binaries can be merged together with theoretical advances to give a coherent picture of the physics of the ...accretion flow in strong gravity. Both long term X-ray light curves, X-ray spectra, the rapid X-ray variability and the radio jet behaviour are consistent with a model where a standard outer accretion disc is truncated at low luminosities, being replaced by a hot, inner flow which also acts as the launching site of the jet. Decreasing the disc truncation radius leads to softer spectra, as well as higher frequencies (including quasi periodic oscillations, QPOs) in the power spectra, and a faster jet. The collapse of the hot flow when the disc reaches the last stable orbit triggers the dramatic decrease in radio flux, as well as giving a qualitative (and often quantitative) explanation for the major hard-soft spectral transition seen in black holes. The neutron stars are also consistent with the same models, but with an additional component due to their surface, giving implicit evidence for the event horizon in black holes. We review claims of observational data which conflict with this picture, but show that these can also be consistent with the truncated disc model. We also review suggested alternative models for the accretion flow which do not involve a truncated disc. The most successful of these converge on a similar geometry, where there is a transition at some radius larger than the last stable orbit between a standard disc and an inner, jet dominated region, with the X-ray source associated with a mildly relativistic outflow, beamed away from the disc. However, the observed uniformity of properties between black holes at different inclinations suggests that even weak beaming of the X-ray emission may be constrained by the data. After collapse of the hot inner flow, the spectrum in black hole systems can be dominated by the disc emission. Its behaviour is consistent with the existence of a last stable orbit, and such data can be used to estimate the black hole spin. By contrast, these systems can also show very different spectra at these high luminosities, in which the disc spectrum (and probably structure) is strongly distorted by Comptonization. The structure of the accretion flow becomes increasingly uncertain as the luminosity approaches (and exceeds) the Eddington luminosity, though there is growing evidence that winds may play an important role. We stress that these high Eddington fraction flows are key to understanding many disparate and currently very active fields such as ULX, Narrow Line Seyfert 1's, and the growth of the first black holes in the Early Universe. PUBLICATION ABSTRACT
Background
: It has been known for many years that in metazoan cells, replication origins are organised into clusters where origins within each cluster fire near-synchronously. Despite clusters being ...a fundamental organising principle of metazoan DNA replication, the location of origin clusters on the genome has not been documented.
Methods
: We synchronised human U2OS by thymidine block and release followed by a brief block with L-mimosine to create a population of cells progressing into S phase with a high degree of synchrony. At different times after release into S phase, cells were pulsed with EdU; the EdU-labelled DNA was then pulled down, sequenced and mapped back onto the human genome.
Results
: The early replicating DNA showed features at a range of scales. Wavelet analysis showed that the major feature of the early replicating DNA was at a size of 500 kb, consistent with clusters of replication origins. Over the first two hours of S phase, these Replicon Cluster Domains broadened in width, consistent with their being enlarged by the progression of replication forks at their outer boundaries. The total replication signal associated with each Replicon Cluster Domain varied considerably, and this variation was reproducible and conserved over time. We provide evidence that this variability in replication signal was at least in part caused by Replicon Cluster Domains being activated at different times in different cells in the population. We also provide evidence that adjacent clusters were preferentially activated in sequence across a group, consistent with the ‘domino’ model of replication focus activation observed by microscopy.
Conclusions
: We show that early replicating DNA is organised into Replicon Cluster Domains that behave as expected of replicon clusters observed by DNA fibre analysis. The coordinated activation of different Replicon Cluster Domains can generate the replication timing programme by which the genome is duplicated.
Abstract
We systematically analyse all publicly available XMM-Newton spectra of radio-quiet PG quasars. The soft X-ray excess in these objects is well modelled by an additional, cool, Compton ...scattering region. However, the remarkably constant temperature derived for this component over the whole sample requires a puzzling fine tuning of the parameters. Instead, we propose that the soft excess is an artifact of strong, relativistically smeared, partially ionized absorption. The strong jump in opacity at ∼0.7 keV from O vii, O viii and iron can lead to an apparent soft excess below this energy, which is trivially constant since it depends on atomic processes. This can have a dramatic effect on the derived spectrum, which has implications for fitting the relativistic smearing of the reflected iron line emission from the disc.
ABSTRACT
We have obtained new solutions and methods for the process of thermal Comptonization. We modify the solution to the kinetic equation of Sunyaev and Titarchuk to allow its application up to ...mildly relativistic electron temperatures and optical depths $\gtrsim {1}$. The solution can be used for spectral fitting of X-ray spectra from astrophysical sources. We also have developed an accurate Monte Carlo method for calculating spectra and timing properties of thermal Comptonization sources. The accuracy of our kinetic equation solution is verified by comparison with the Monte Carlo results. We also compare our results with those of other publicly available methods. Furthermore, based on our Monte Carlo code, we present distributions of the photon emission times and the evolution of the average photon energy for both up and down scattering.
Robust protocols for directed differentiation of human pluripotent cells are required to determine whether mechanisms operating in model organisms are relevant to our own development. Recent work in ...vertebrate embryos has identified neuromesodermal progenitors as a bipotent cell population that contributes to paraxial mesoderm and spinal cord. However, precise protocols for
differentiation of human spinal cord progenitors are lacking. Informed by signalling in amniote embryos, we show here that transient dual-SMAD inhibition, together with retinoic acid (dSMADi-RA), provides rapid and reproducible induction of human spinal cord progenitors from neuromesodermal progenitor-like cells. Using CRISPR-Cas9 to engineer human embryonic stem cells with a GFP-reporter for neuromesodermal progenitor-associated gene
we facilitate selection of this cell population. RNA-sequencing was then used to identify human and conserved neuromesodermal progenitor transcriptional signatures, to validate this differentiation protocol and to reveal new pathways/processes in human neural differentiation. This optimised protocol, novel reporter line and transcriptomic data are useful resources with which to dissect molecular mechanisms regulating human spinal cord generation and allow the scaling-up of distinct cell populations for global analyses, including proteomic, biochemical and chromatin interrogation.
We build a simple model of the optical/ultraviolet (UV) emission from irradiation of the outer disc by the inner disc and coronal emission in black hole binaries. We apply this to the broad-band ...Swift data from the outburst of the black hole binary XTE J1817−330 to confirm previous results that the optical/UV emission in the soft state is consistent with a reprocessing a constant fraction of the bolometric X-ray luminosity. However, this is very surprising as the disc temperature drops by more than a factor of 3 in the soft state, which should produce a marked change in the reprocessing efficiency. The easiest way to match the observed constant reprocessed fraction is for the disc skin to be highly ionized (as suggested 30 yr ago by van Paradijs), so that the bulk of the disc flux is reflected and only the hardest X-rays heat the disc. The constant reprocessed fraction also favours direct illumination of the disc over a scattering origin as the optical depth/solid angle of any scattering material (wind/corona) over the disc should decrease as the source luminosity declines. By contrast, the reprocessed fraction increases very significantly (by a factor of ∼6) as the source enters the hard state. This dramatic change is not evident from X-ray/UV flux correlations as it is masked by bandpass effects. However, it does not necessarily signal a change in emission, for example, the emergence of the jet dominating the optical/UV flux as the reflection albedo must change with the dramatic change in spectral shape.
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