H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells

Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell selfrenewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells

Non-precessional spin-orbit effects on gravitational waves from inspiraling compact binaries to second post-Newtonian order

We derive all second post-Newtonian (2PN), non-precessional effects of spin- orbit coupling on the gravitational wave forms emitted by an inspiraling binary composed of spinning, compact bodies in a quasicircular orbit. Previous post- Newtonian calculations of spin-orbit effects (at 1.5PN order) relied on a fluid description of the spinning bodies. We simplify the calculations by introducing into post-Newtonian theory a delta-function description of the influence of the spins on the bodies' energy-momentum tensor. This description was recently used by Mino, Shibata, and Tanaka (MST) in Teukolsky-formalism analyses of particles orbiting massive black holes, and is based on prior work by Dixon. We compute the 2PN contributions to the wave forms by combining the MST energy-momentum tensor with the formalism of Blanchet, Damour, and Iyer for evaluating the binary's radiative multipoles, and with the well-known 1.5PN order equations of motion for the binary. Our results contribute at 2PN order only to the amplitudes of the wave forms. The secular evolution of the wave forms' phase, the quantity most accurately measurable by LIGO, is not affected by our results until 2.5PN order, at which point other spin-orbit effects also come into play. We plan to evaluate the entire 2.5PN spin-orbit contribution to the secular phase evolution in a future paper, using the techniques of this paper.Comment: 11 pages, submitted to Phys. Rev.

Wolf 1130: A Nearby Triple System Containing a Cool, Ultramassive White Dwarf

Following the discovery of the T8 subdwarf WISEJ200520.38+542433.9 (Wolf 1130C), with common proper motion to a binary (Wolf 1130AB) consisting of an M subdwarf and a white dwarf, we set out to learn more about the old binary in the system. We find that the A and B components of Wolf 1130 are tidally locked, which is revealed by the coherence of more than a year of V band photometry phase folded to the derived orbital period of 0.4967 days. Forty new high-resolution, near-infrared spectra obtained with the Immersion Grating Infrared Spectrometer (IGRINS) provide radial velocities and a projected rotational velocity (v sin i) of 14.7 +/- 0.7 km/s for the M subdwarf. In tandem with a Gaia parallax-derived radius and verified tidal-locking, we calculate an inclination of i=29 +/- 2 degrees. From the single-lined orbital solution and the inclination we derive an absolute mass for the unseen primary (1.24+0.19-0.15 Msun). Its non-detection between 0.2 and 2.5 microns implies that it is an old (>3.7 Gyr) and cool (Teff<7000K) ONe white dwarf. This is the first ultramassive white dwarf within 25pc. The evolution of Wolf 1130AB into a cataclysmic variable is inevitable, making it a potential Type Ia supernova progenitor. The formation of a triple system with a primary mass >100 times the tertiary mass and the survival of the system through the common-envelope phase, where ~80% of the system mass was lost, is remarkable. Our analysis of Wolf 1130 allows us to infer its formation and evolutionary history, which has unique implications for understanding low-mass star and brown dwarf formation around intermediate mass stars.Comment: 37 pages, 9 Figures, 5 Table

HDAC1 regulates pluripotency and lineage specific transcriptional networks in embryonic and trophoblast stem cells

Epigenetic regulation of gene expression is important in maintaining self-renewal of embryonic stem (ES) and trophoblast stem (TS) cells. Histone deacetylases (HDACs) negatively control histone acetylation by removing covalent acetylation marks from histone tails. Because histone acetylation is a known mark for active transcription, HDACs presumably associate with inactive genes. Here, we used genome-wide chromatin immunoprecipitation to investigate targets of HDAC1 in ES and TS cells. Through evaluation of genes associated with acetylated histone H3 marks, and global expression analysis of Hdac1 knockout ES and trichostatin A-treated ES and TS cells, we found that HDAC1 occupies mainly active genes, including important regulators of ES and TS cells self-renewal. We also observed occupancy of methyl-CpG binding domain protein 3 (MBD3), a subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex, at a subset of HDAC1-occupied sequences in ES cells, including the pluripotency regulators Oct4, Nanog and Kfl4. By mapping HDAC1 targets on a global scale, our results describe further insight into epigenetic mechanisms of ES and TS cells self-renewal

Gravitational field and equations of motion of spinning compact binaries to 2.5 post-Newtonian order

We derive spin-orbit coupling effects on the gravitational field and equations of motion of compact binaries in the 2.5 post-Newtonian approximation to general relativity, one PN order beyond where spin effects first appear. Our method is based on that of Blanchet, Faye, and Ponsot, who use a post-Newtonian metric valid for general (continuous) fluids and represent pointlike compact objects with a delta-function stress-energy tensor, regularizing divergent terms by taking the Hadamard finite part. To obtain post-Newtonian spin effects, we use a different delta-function stress-energy tensor introduced by Bailey and Israel. In a future paper we will use the 2.5PN equations of motion for spinning bodies to derive the gravitational-wave luminosity and phase evolution of binary inspirals, which will be useful in constructing matched filters for signal analysis. The gravitational field derived here may help in posing initial data for numerical evolutions of binary black hole mergers.Comment: 18 pages, no figur

Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity

Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells

Strategy for tumor selective disruption of androgen receptor function in the spectrum of prostate cancer

Purpose: Testosterone suppression in prostate cancer (PC) is limited by serious side effects and resistance via restoration of androgen receptor (AR) functionality. ELK1 is required for ARdependent growth in various hormone-dependent and castration resistant PC models. The amino terminal domain of AR docks at two sites on ELK1 to co-activate essential growth genes. This study explores the ability of small molecules to disrupt the ELK1-AR interaction in the spectrum of PC, inhibiting AR activity in a manner that would predict functional tumor selectivity. Experimental design: Small molecule drug discovery and extensive biological characterization of a lead compound. Results: We have discovered a lead molecule (KCI807) that selectively disrupts ELK1-dependent promoter activation by wild-type and variant ARs without interfering with ELK1 activation by ERK. KCI807 has an obligatory flavone scaffold and functional hydroxyl groups on C5 and C3'. KCI807 binds to AR, blocking ELK1 binding, and selectively blocks recruitment of AR to chromatin by ELK1. KCI807 primarily affects a subset of AR target growth genes selectively suppressing AR-dependent growth of PC cell lines with a better inhibitory profile than enzalutamide. KCI807 also inhibits in vivo growth of castration/enzalutamide-resistant cell line-derived and patient-derived tumor xenografts. In the rodent model, KCI807 has a plasma half-life of 6h and maintenance of its antitumor effect is limited by self-induced metabolism at its 3'-hydroxyl. Conclusions: The results offer a mechanism-based therapeutic paradigm for disrupting the AR growth-promoting axis in the spectrum of prostate tumors while reducing global suppression of testosterone actions. KCI807 offers a good lead molecule for drug development

Identification of actionable targets for breast cancer intervention using a diversity outbred mouse model

HER2-targeted therapy has improved breast cancer survival, but treatment resistance and disease prevention remain major challenges. Genes that enable HER2/Neu oncogenesis are the next intervention targets. A bioinformatics discovery platform of HER2/Neu-expressing Diversity Outbred (DO) F1 Mice was established to identify cancer-enabling genes. Quantitative Trait Loci (QTL) associated with onset ages and growth rates of spontaneous mammary tumors were sought. Twenty-six genes in 3 QTL contain sequence variations unique to the genetic backgrounds that are linked to aggressive tumors and 21 genes are associated with human breast cancer survival. Concurrent identification of TSC22D3, a transcription factor, and its target gene LILRB4, a myeloid cell checkpoint receptor, suggests an immune axis for regulation, or intervention, of disease. We also investigated TIEG1 gene that impedes tumor immunity but suppresses tumor growth. Although not an actionable target, TIEG1 study revealed genetic regulation of tumor progression, forming the basis of the genetics-based discovery platform

Wolf 1130: A Nearby Triple System Containing a Cool, Ultramassive White Dwarf

Following the discovery of the T8 subdwarf WISE J200520.38+542433.9 (Wolf 1130C), which has a proper motion in common with a binary (Wolf 1130AB) consisting of an M subdwarf and a white dwarf, we set out to learn more about the old binary in the system. We find that the A and B components of Wolf 1130 are tidally locked, which is revealed by the coherence of more than a year of V-band photometry phase-folded to the derived orbital period of 0.4967 days. Forty new high-resolution, near-infrared spectra obtained with the Immersion Grating Infrared Spectrometer provide radial velocities and a projected rotational velocity (v sin i) of 14.7 ± 0.7 km s^(-1) for the M subdwarf. In tandem with a Gaia parallax-derived radius and verified tidal locking, we calculate an inclination of i = 29° ± 2°. From the single-lined orbital solution and the inclination we derive an absolute mass for the unseen primary (1.24^(+0.19)_(-0.15) M ⊙). Its non-detection between 0.2 and 2.5 μm implies that it is an old (>3.7 Gyr) and cool (T_(eff) 100 times the tertiary mass and the survival of the system through the common-envelope phase, where ~80% of the system mass was lost, is remarkable. Our analysis of Wolf 1130 allows us to infer its formation and evolutionary history, which has unique implications for understanding low-mass star and brown dwarf formation around intermediate-mass stars

Testing gravitational-wave searches with numerical relativity waveforms: Results from the first Numerical INJection Analysis (NINJA) project

The Numerical INJection Analysis (NINJA) project is a collaborative effort between members of the numerical relativity and gravitational-wave data analysis communities. The purpose of NINJA is to study the sensitivity of existing gravitational-wave search algorithms using numerically generated waveforms and to foster closer collaboration between the numerical relativity and data analysis communities. We describe the results of the first NINJA analysis which focused on gravitational waveforms from binary black hole coalescence. Ten numerical relativity groups contributed numerical data which were used to generate a set of gravitational-wave signals. These signals were injected into a simulated data set, designed to mimic the response of the Initial LIGO and Virgo gravitational-wave detectors. Nine groups analysed this data using search and parameter-estimation pipelines. Matched filter algorithms, un-modelled-burst searches and Bayesian parameter-estimation and model-selection algorithms were applied to the data. We report the efficiency of these search methods in detecting the numerical waveforms and measuring their parameters. We describe preliminary comparisons between the different search methods and suggest improvements for future NINJA analyses.Comment: 56 pages, 25 figures; various clarifications; accepted to CQ