Unravelling Active Galactic Nuclei

A complete flat-spectrum radio-loud sample of AGN includes a significant fraction of Seyfert-like AGN including a NLS1. Analysis of their optical spectra suggests that the reddest continuum colours are either associated with AGN in nearby resolved galaxies, or distant quasars showing relatively narrow permitted emission lines.Comment: Poster contribution presented at the Joint MPE,AIP,ESO workshop on NLS1s, Bad Honnef, Dec. 1999, to appear in New Astronomy Reviews; also available at http://wave.xray.mpe.mpg.de/conferences/nls1-worksho

Black Hole Mass Estimates of Radio Selected Quasars

The black hole (BH) mass in the centre of AGN has been estimated for a sample of radio-selected flat-spectrum quasars to investigate the relationship between BH mass and radio properties of quasars. We have used the virial assumption with measurements of the H$\beta$ FWHM and luminosity to estimate the central BH mass. In contrast to previous studies we find no correlation between BH mass and radio power in these AGN. We find a range in BH mass similar to that seen in radio-quiet quasars from previous studies. We believe the reason that the low BH mass radio-loud quasars have not been measured in previous studies is due to optical selection effects which tend to miss the less optically luminous radio-loud sources.Comment: 22 pages, 7 figures, accepted for publication in Ap

A Very Radio-Loud Narrow-Line Seyfert 1: PKS 2004-447

We have discovered a very radio-loud Narrow-Line Seyfert 1 candidate: PKS 2004-447. This Seyfert is consistent with the formal definition for NLS1s, although it does not have quite the same spectral features as some typical members of this subclass. Only ROSAT survey data is available at X-ray wavelengths, so it has not been possible to compare this source with other NLS1s at these wavelengths. A full comparison of this source with other members of the subclass will improve our physical understanding of NLS1s. In addition, using standard calculations, we estimate the central black hole to have a mass of $\sim 5 \times 10^6 M_{\odot}$. This does not agree with predictions in the literature, that radio-loud AGN host very massive black holes.Comment: 15 pages, 4 figures, accepted for publication in ApJ, minor typos change

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

BACKGROUND: Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. RESULTS: Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. CONCLUSIONS: These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02728-5

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

BACKGROUND Birds have a ZZ male: ZW female sex chromosome system and while the Z-linked DMRT1 gene is necessary for testis development, the exact mechanism of sex determination in birds remains unsolved. This is partly due to the poor annotation of the W chromosome, which is speculated to carry a female determinant. Few genes have been mapped to the W and little is known of their expression. RESULTS We used RNA-seq to produce a comprehensive profile of gene expression in chicken blastoderms and embryonic gonads prior to sexual differentiation. We found robust sexually dimorphic gene expression in both tissues pre-dating gonadogenesis, including sex-linked and autosomal genes. This supports the hypothesis that sexual differentiation at the molecular level is at least partly cell autonomous in birds. Different sets of genes were sexually dimorphic in the two tissues, indicating that molecular sexual differentiation is tissue specific. Further analyses allowed the assembly of full-length transcripts for 26 W chromosome genes, providing a view of the W transcriptome in embryonic tissues. This is the first extensive analysis of W-linked genes and their expression profiles in early avian embryos. CONCLUSION Sexual differentiation at the molecular level is established in chicken early in embryogenesis, before gonadal sex differentiation. We find that the W chromosome is more transcriptionally active than previously thought, expand the number of known genes to 26 and present complete coding sequences for these W genes. This includes two novel W-linked sequences and three small RNAs reassigned to the W from the Un_Random chromosome.Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack and Craig A Smit

FIRST-based survey of Compact Steep Spectrum sources, II. MERLIN and VLA observations of Medium-sized Symmetric Objects

A new sample of candidate Compact Steep Spectrum (CSS) sources that are much weaker than the CSS source prototypes has been selected from the VLA FIRST catalogue. MERLIN `snapshot' observations of the sources at 5 GHz indicate that six of them have an FR II-like morphology, but are not edge-brightened as is normal for Medium-sized Symmetric Objects (MSOs) and FR IIs. Further observations of these six sources with the VLA at 4.9 GHz and MERLIN at 1.7 GHz, as well as subsequent full-track observations with MERLIN at 5 GHz of what appeared to be the two sources of greatest interest are presented. The results are discussed with reference to the established evolutionary model of CSS sources being young but in which not all of them evolve to become old objects with extended radio structures. A lack of stable fuelling in some of them may result in an early transition to a so-called coasting phase so that they fade away instead of growing to become large-scale objects. It is possible that one of the six sources (1542+323) could be labelled as a prematurely `dying' MSO or a `fader'.Comment: 13 pages, matches the version printed in Astronomy & Astrophysic

The spectral energy distribution of PKS 2004-447: a compact steep-spectrum source and possible radio-loud narrow-line Seyfert 1 galaxy

(abridged) The spectral energy distribution (SED) of the compact steep spectrum (CSS) source and possible radio-loud narrow-line Seyfert 1 galaxy (NLS1), PKS2004-447, is presented. Five out of six well studied RL NLS1 share this dual classification (optically defined as a NLS1 with radio definition of a CSS or giga-hertz peaked spectrum (GPS) source). The SED is created from simultaneous observations at radio (ATCA), optical/NIR (Siding Spring) and UV/X-ray (XMM-Newton) wavelengths. The X-ray data show evidence of short-term variability, a possible soft excess, and negligible absorption. Together with the rest of the SED, the X-ray emission is excessive in comparison to synchrotron plus synchrotron self-Compton (SSC) models. The SED can be described with a two component model consisting of extended synchrotron/SSC emission with Comptonisation in the X-rays, though SSC models with a very high electron-to-magnetic energy density ratio cannot be excluded either. The peak emission in the SED appears to be in the near infrared, which can be attributed to thermal emission from a dusty torus. Analysis of a non-contemporaneous, low resolution optical spectrum suggests that the narrow-line region (NLR) is much more reddened than the X-ray emitting region suggesting that the gas-to-dust ratio in PKS2004-447 may be very different then in our own Galaxy. Long-term radio monitoring of PKS2004-447 shows a rather constant light curve over nearly a six month period with the exception of one outburst when the 6.65GHz flux increased by ~35% over 19 days. In comparison to general samples of GPS sources, which appear to be X-ray weak, NLS1-CSS/GPS sources possess stronger X-ray emission relative to radio, and lower intrinsic absorption than GPS sources of similar X-ray luminosity.Comment: 10 pages, 8 figures. Accepted for publication in MNRA

MGMR: leveraging RNA-Seq population data to optimize expression estimation

<p>Abstract</p> <p>Background</p> <p>RNA-Seq is a technique that uses Next Generation Sequencing to identify transcripts and estimate transcription levels. When applying this technique for quantification, one must contend with reads that align to multiple positions in the genome (multireads). Previous efforts to resolve multireads have shown that RNA-Seq expression estimation can be improved using probabilistic allocation of reads to genes. These methods use a probabilistic generative model for data generation and resolve ambiguity using likelihood-based approaches. In many instances, RNA-seq experiments are performed in the context of a population. The generative models of current methods do not take into account such population information, and it is an open question whether this information can improve quantification of the individual samples</p> <p>Results</p> <p>In order to explore the contribution of population level information in RNA-seq quantification, we apply a hierarchical probabilistic generative model, which assumes that expression levels of different individuals are sampled from a Dirichlet distribution with parameters specific to the population, and reads are sampled from the distribution of expression levels. We introduce an optimization procedure for the estimation of the model parameters, and use HapMap data and simulated data to demonstrate that the model yields a significant improvement in the accuracy of expression levels of paralogous genes.</p> <p>Conclusions</p> <p>We provide a proof of principal of the benefit of drawing on population commonalities to estimate expression. The results of our experiments demonstrate this approach can be beneficial, primarily for estimation at the gene level.</p