Transcriptional and epigenetic mechanisms of the first cell fate decision and reprogramming

The placenta is a transient but vital organ mediating a myriad of interactions between maternal and embryonic tissues. The cells in the trophectoderm (TE) lineage are responsible for proper implantation, placentation, and immunological functions of the placenta. However, our understanding of molecular mechanisms underlying placentation and TE development is still rudimentary. Deciphering the mechanisms by which key TE-specific transcription factors (TFs) control the first cell fate decision, as well as the maintenance and differentiation of TE, is a prerequisite for understanding early embryonic development and ultimately improving healthy pregnancy. First, using a combination of functional genomics, bioinformatics, and mouse genetics, I revealed that Arid3a is a critical regulator for controlling the first cell fate decision and placental development. Ectopically expressed Arid3a induces TE-like gene expression programs in embryonic stem (ES) cells. Moreover, Arid3a is not only essential for maintaining self-renewing TS cells, but also for promoting further differentiation of trophoblastic lineages. Consistently, Arid3a-/- mice suffer from severely impaired post-implantation development, resulting in early embryonic lethality. I further showed that Arid3a directly activates TE-specific genes while repressing pluripotency genes by recruiting HDAC1. Second, I studied the mechanisms underlying TF-mediated conversion of ES to trophoblast stem (TS)-like cells. Upon overexpression of TS cell-specific TFs, Cdx2, Arid3a, and Gata3 (CAG factors) in ES cells, I performed time–course profiling of chromatin accessibility, transcriptomes, and occupancy of these reprogramming factors during reprogramming. Using an integrative analysis, I discovered that CAG factors orchestrate the conversion via a sequential two-step regulation in a timely, ordered manner, with repression of pluripotency genes by decommissioning active enhancers, followed by activation of TS cell-specific genes as pioneer factors that can access closed chromatin. Taken together, my studies unveiled that Arid3a functions as a pivotal regulator of TE and placental development by regulating the commitment to the first cell fate, as well as by executing TE lineage differentiation. I advanced our understanding of the mechanisms underlying TF-mediated reprogramming of ES to TS-like cells, in particular Arid3a-mediated transcriptional and epigenetic regulation. Thus, my studies will be beneficial for enhancing clinical applications such as disease modeling, drug screening, and regenerative therapies.Cellular and Molecular Biolog

Tgif1 Counterbalances The Activity Of Core Pluripotency Factors In Mouse Embryonic Stem Cells

Core pluripotency factors, such as Oct4, Sox2, and Nanog, play important roles in maintaining embryonic stem cell (ESC) identity by autoregulatory feedforward loops. Nevertheless, the mechanism that provides precise control of the levels of the ESC core factors without indefinite amplification has remained elusive. Here, we report the direct repression of core pluripotency factors by Tgif1, a previously known terminal repressor of TGF beta/activin/nodal signaling. Overexpression of Tgif1 reduces the levels of ESC core factors, whereas its depletion leads to the induction of the pluripotency factors. We confirm the existence of physical associations between Tgif1 and Oct4, Nanog, and HDAC1/2 and further show the level of Tgif1 is not significantly altered by treatment with an activator/inhibitor of the TGF beta/activin/nodal signaling. Collectively, our findings establish Tgif1 as an integral member of the core regulatory circuitry of mouse ESCs that counterbalances the levels of the core pluripotency factors in a TGF beta/activin/nodal-independent manner.Cancer Prevention Research Institute of Texas (CPRIT) R1106Molecular Bioscience

The Wide Field Spectrograph (WiFeS): Performance and Data Reduction

This paper describes the on-telescope performance of the Wide Field Spectrograph (WiFeS). The design characteristics of this instrument, at the Research School of Astronomy and Astrophysics (RSAA) of the Australian National University (ANU) and mounted on the ANU 2.3m telescope at the Siding Spring Observatory has been already described in an earlier paper (Dopita et al. 2007). Here we describe the throughput, resolution and stability of the instrument, and describe some minor issues which have been encountered. We also give a description of the data reduction pipeline, and show some preliminary results.Comment: Accepted for publication in Astrophysics & Space Science, 15pp, 11 figure

The Perils of Recreational Marijuana Use: Relationships With Mental Health Among Emergency Department Patients

Abstract Introduction Marijuana is a commonly used drug in the United States. Many states have legalized the recreational use of marijuana. The effects of marijuana on mental health are unknown. Methods In this prospective survey study, eligible participants included ED patients age 18 and older, who had ever used recreational marijuana. A survey instrument was developed, piloted, and revised. Data collected included reasons for marijuana use, marijuana\u27s perceived effectiveness, and history of mental health conditions, including depression, anxiety, and suicidal thoughts. Results Among 303 participants (86% response rate), the median age of first marijuana use was 16 ([IQR 14, 19], range 6–65). The most commonly cited reasons for marijuana use included recreational use (70%; n = 211), to treat anxiety (30%; n = 89), to treat pain (25%; n = 74), and to treat depression (17%; n = 51). Mental health issues were common in the study population. A majority of patients reported anxiety in the last 30 days (59%; n = 176), and a significant minority of patients reported serious depression in the last 30 days (46%; n = 137). Some patients reported suicidal thoughts in the last 30 days (9%; n = 29). Participants who used marijuana more frequently reported more days of anxiety (median 15.5, compared to 1; P = 0.001). Among participants with mental health conditions, most began using marijuana before the onset of the mental health conditions (77%, n = 167). Earlier age of starting to use marijuana was correlated with higher number of years of anxiety or tension in lifetime (r = −0.11, P = 0.05, n = 301). Perceived effects of marijuana use on mental health were variable. Most participants stated that marijuana improved their mental health (62%; n = 163), and some reported that marijuana did not improve their mental health (37%; n = 98). Conclusions Many ED patients have used marijuana, either currently or in the past. Mental health conditions are also common, including anxiety, depression, and suicidal thoughts. Most participants reported marijuana use starting at an age under 18. Marijuana use preceded the onset of mental health conditions in the majority of participants

Congenital Atrophoderma of Pasini and Pierini

Idiopathic atrophoderma of Pasini and Pierini is a form of dermal atrophy of unknown etiology, usually affecting women during their adolescence and young adulthood. A 2-yr-old girl was presented with erythematous atrophic lesion on the right shoulder, which appeared from birth. The histologic findings were consistent with atrophoderma. This patient, to the best of our knowledge, is the first case of atrophoderma with an onset since birth

HDAC9 is implicated in atherosclerotic aortic calcification and affects vascular smooth muscle cell phenotype.

Aortic calcification is an important independent predictor of future cardiovascular events. We performed a genome-wide association meta-analysis to determine SNPs associated with the extent of abdominal aortic calcification (n = 9,417) or descending thoracic aortic calcification (n = 8,422). Two genetic loci, HDAC9 and RAP1GAP, were associated with abdominal aortic calcification at a genome-wide level (P < 5.0 × 10-8). No SNPs were associated with thoracic aortic calcification at the genome-wide threshold. Increased expression of HDAC9 in human aortic smooth muscle cells promoted calcification and reduced contractility, while inhibition of HDAC9 in human aortic smooth muscle cells inhibited calcification and enhanced cell contractility. In matrix Gla protein-deficient mice, a model of human vascular calcification, mice lacking HDAC9 had a 40% reduction in aortic calcification and improved survival. This translational genomic study identifies the first genetic risk locus associated with calcification of the abdominal aorta and describes a previously unknown role for HDAC9 in the development of vascular calcification

Telomerase Efficiently Elongates Highly Transcribing Telomeres in Human Cancer Cells

RNA polymerase II transcribes the physical ends of linear eukaryotic chromosomes into a variety of long non-coding RNA molecules including telomeric repeat-containing RNA (TERRA). Since TERRA discovery, advances have been made in the characterization of TERRA biogenesis and regulation; on the contrary its associated functions remain elusive. Most of the biological roles so far proposed for TERRA are indeed based on in vitro experiments carried out using short TERRA-like RNA oligonucleotides. In particular, it has been suggested that TERRA inhibits telomerase activity. We have exploited two alternative cellular systems to test whether TERRA and/or telomere transcription influence telomerase-mediated telomere elongation in human cancer cells. In cells lacking the two DNA methyltransferases DNMT1 and DNMT3b, TERRA transcription and steady-state levels are greatly increased while telomerase is able to elongate telomeres normally. Similarly, telomerase can efficiently elongate transgenic inducible telomeres whose transcription has been experimentally augmented. Our data challenge the current hypothesis that TERRA functions as a general inhibitor of telomerase and suggest that telomere length homeostasis is maintained independently of TERRA and telomere transcription

Means to an End: An Assessment of the Status-blind Approach to Protecting Undocumented Worker Rights

This article applies the tenets of bureaucratic incorporation theory to an investigation of bureaucratic decision making in labor standards enforcement agencies (LSEAs), as they relate to undocumented workers. Drawing on 25 semistructured interviews with high-level officials in San Jose and Houston, I find that bureaucrats in both cities routinely evade the issue of immigration status during the claims-making process, and directly challenge employers’ attempts to use the undocumented status of their workers to deflect liability. Respondents offer three institutionalized narratives for this approach: (1) to deter employer demand for undocumented labor, (2) the conviction that the protection of undocumented workers is essential to the agency’s ability to regulate industry standards for all workers, and (3) to clearly demarcate the agency’s jurisdictional boundaries to preserve institutional autonomy and scarce resources. Within this context, enforcing the rights of undocumented workers becomes simply an institutional means to an end

Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator

The putative methyltransferase LaeA is a global regulator that affects the expression of multiple secondary metabolite gene clusters in several fungi, and it can modify heterochromatin structure in Aspergillus nidulans. We have recently shown that the LaeA ortholog of Trichoderma reesei (LAE1), a fungus that is an industrial producer of cellulase and hemicellulase enzymes, regulates the expression of cellulases and polysaccharide hydrolases. To learn more about the function of LAE1 in T. reesei, we assessed the effect of deletion and overexpression of lae1 on genome-wide gene expression. We found that in addition to positively regulating 7 of 17 polyketide or nonribosomal peptide synthases, genes encoding ankyrin-proteins, iron uptake, heterokaryon incompatibility proteins, PTH11-receptors, and oxidases/monoxygenases are major gene categories also regulated by LAE1. chromatin immunoprecipitation sequencing with antibodies against histone modifications known to be associated with transcriptionally active (H3K4me2 and -me3) or silent (H3K9me3) chromatin detected 4089 genes bearing one or more of these methylation marks, of which 75 exhibited a correlation between either H3K4me2 or H3K4me3 and regulation by LAE1. Transformation of a laeA-null mutant of A. nidulans with the T. reesei lae1 gene did not rescue sterigmatocystin formation and further impaired sexual development. LAE1 did not interact with A. nidulans VeA in yeast two-hybrid assays, whereas it interacted with the T. reesei VeA ortholog, VEL1. LAE1 was shown to be required for the expression of vel1, whereas the orthologs of velB and VosA are unaffected by lae1 deletion. Our data show that the biological roles of A. nidulans LaeA and T. reesei LAE1 are much less conserved than hitherto thought. In T. reesei, LAE1 appears predominantly to regulate genes increasing relative fitness in its environment.Keywords: Flavus, Secondary metabolism, Aspergillus nidulans, Gene expression, Hypocrea jecorina, DNA methylation, Histone H3, Protein kinase, Neurospora crassa, Penicillin biosynthesi

Nucleoside Reverse Transcriptase Inhibitor Resistance Mutations Associated with First-Line Stavudine-Containing Antiretroviral Therapy: Programmatic Implications for Countries Phasing Out Stavudine

Background The World Health Organization Antiretroviral Treatment Guidelines recommend phasing-out stavudine because of its risk of long-term toxicity. There are two mutational pathways of stavudine resistance with different implications for zidovudine and tenofovir cross-resistance, the primary candidates for replacing stavudine. However, because resistance testing is rarely available in resource-limited settings, it is critical to identify the cross-resistance patterns associated with first-line stavudine failure. Methods We analyzed HIV-1 resistance mutations following first-line stavudine failure from 35 publications comprising 1,825 individuals. We also assessed the influence of concomitant nevirapine vs. efavirenz, therapy duration, and HIV-1 subtype on the proportions of mutations associated with zidovudine vs. tenofovir cross-resistance. Results Mutations with preferential zidovudine activity, K65R or K70E, occurred in 5.3% of individuals. Mutations with preferential tenofovir activity, ≥two thymidine analog mutations (TAMs) or Q151M, occurred in 22% of individuals. Nevirapine increased the risk of TAMs, K65R, and Q151M. Longer therapy increased the risk of TAMs and Q151M but not K65R. Subtype C and CRF01_AE increased the risk of K65R, but only CRF01_AE increased the risk of K65R without Q151M. Conclusions Regardless of concomitant nevirapine vs. efavirenz, therapy duration, or subtype, tenofovir was more likely than zidovudine to retain antiviral activity following first-line d4T therap