High-throughput assessment of context-dependent effects of chromatin proteins

Background: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mo

CANOES: detecting rare copy number variants from whole exome sequencing data

We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and specificity is comparable to that of XHMM. Moreover, the method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data

Review: The Journal of Dramaturgy, volume 20, 2009/2010

Contents include: Recognizing Toward a Dramaturgical Sensibility, Geoff Proehl, recipient of the 2009 ATHE Outstanding Book Award; Geoff Proehl\u27s Acceptance Speech, Association for Theatre in Higher Education Awards Ceremony August 10, 2009; Millennial Dramaturgy, A conversation about the new book Dramaturgy and Performance; Creating Sub/Text, Dramaturging the ReStaged Festival; Dramaturgy and Interdisciplinary Learning, A Case Study of Russian Theatre and Politics; Thinking about Theatre Photography; Theatre / Photography. Issue editors: D.J. Hopkins, Sydney Cheek O\u27Donnell, Lauren Beckhttps://soundideas.pugetsound.edu/lmdareview/1040/thumbnail.jp

Local rewiring of genome-nuclear lamina interactions by transcription

Transcriptionally inactive genes are often positioned at the nuclear lamina (NL), as part of large lamina-associated domains (LADs). Activation of such genes is often accompanied by repositioning toward the nuclear interior. How this process works and how it impacts flanking chromosomal regions are poorly understood. We addressed these questions by systematic activation or inactivation of individual genes, followed by detailed genome-wide analysis of NL interactions, replication timing, and transcription patterns. Gene activation inside LADs typically causes NL detachment of the entire transcription unit, but rarely more than 50-100 kb of flanking DNA, even when multiple neighboring genes are activated. The degree of detachment depends on the expression level and the length of the activated gene. Loss of NL interactions coincides with a switch from late to early replication timing, but the latter can involve longer stretches of DNA. Inactivation of active genes can lead to increased NL contacts. These extensive datasets are a resource for the analysis of LAD rewiring by transcription and reveal a remarkable flexibility of interphase chromosomes

De novo mutations in histone modifying genes in congenital heart disease

Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births1. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. By analysis of exome sequencing of parent-offspring trios, we compared the incidence of de novo mutations in 362 severe CHD cases and 264 controls. CHD cases showed a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging mutations. Similar odds ratios were seen across major classes of severe CHD. We found a marked excess of de novo mutations in genes involved in production, removal or reading of H3K4 methylation (H3K4me), or ubiquitination of H2BK120, which is required for H3K4 methylation2–4. There were also two de novo mutations in SMAD2; SMAD2 signaling in the embryonic left-right organizer induces demethylation of H3K27me5. H3K4me and H3K27me mark `poised' promoters and enhancers that regulate expression of key developmental genes6. These findings implicate de novo point mutations in several hundred genes that collectively contribute to ~10% of severe CHD

Low Frequency Vibrations Disrupt Left-Right Patterning in the Xenopus Embryo

The development of consistent left-right (LR) asymmetry across phyla is a fascinating question in biology. While many pharmacological and molecular approaches have been used to explore molecular mechanisms, it has proven difficult to exert precise temporal control over functional perturbations. Here, we took advantage of acoustical vibration to disrupt LR patterning in Xenopus embryos during tightly-circumscribed periods of development. Exposure to several low frequencies induced specific randomization of three internal organs (heterotaxia). Investigating one frequency (7 Hz), we found two discrete periods of sensitivity to vibration; during the first period, vibration affected the same LR pathway as nocodazole, while during the second period, vibration affected the integrity of the epithelial barrier; both are required for normal LR patterning. Our results indicate that low frequency vibrations disrupt two steps in the early LR pathway: the orientation of the LR axis with the other two axes, and the amplification/restriction of downstream LR signals to asymmetric organs

The Master of Ceremonies : Dramaturgies of Power

This dissertation argues that the theatrical master of ceremonies, an entity seen in many genres of popular theatre across centuries, exists in every instance as the expression of specific understandings of (and anxieties about) coercive social power. By examining key dramaturgical components of this entity, and comparing them to attributes of several modes of real power, I will show how the MC adapts the presentational techniques of power for the stage, producing a phenomenon I call "synthetic authority," and how his appearance, dramaturgical position in the show, and use of space and of speech always refer to sources of coercive power beyond the theatre's walls. This study argues that there are three chief dramaturgical attributes of a theatrical MC. The first is his dramaturgical singularity, which describes both his uniqueness as a figure on the stage and his central-yet-outside position with respect to the rest of the show, especially as it manifests in his practice of interstitial framing. The second is his high onstage status, the result of many visual, sexual, spatial, interpersonal signals and behaviors that serve to align him with economic and other power elites. The third important dramaturgical attribute of the MC as a type is his capacity for direct address. The MC, through his ability to speak directly to a crowd, wields enormous power, literally sculpting with his words the theatrical reality in which the audience participates. This is also his most direct route to the synthetic power that allows him to run the stage: his ability to appropriate the discourses of power elites of many kinds and present them as his own in the course of a performance. Theatrical MCs tend to perform their control of the theatrical environment in one of two main registers: one warm, stable, and paternalistic; one cold, complex, and dominating. While "warm" MCs function conservatively, to reassure audiences and reaffirm existing power relations, the different power of the "cold" MC challenges the audience, making room for critique of the uses and sources of power. Overall, I hope to demonstrate that MCs perform discourses of coercive power originating from sources outside the theatre by appropriating their gestural, vocal, and visual signals, and that out of them, he creates a synthetic authority by virtue of which he controls his areas on the stage, the stage itself; and the theatricalized combination of stage and audience seating area I call the "world of the room." The ultimate goal of this study is to contribute to the dramaturgical (versus historical or theoretical) study of contemporary unscripted American variety theatre, especially by exposing the complexity of its dramaturgies, and developing useful critical language specific to the forms and goals of variety theatre that may be useful as scholars continue to build work on this topi

MOESM3 of High-throughput assessment of context-dependent effects of chromatin proteins

Additional file 3: Figure S3. GFP expression and transfection rate (measured via mCherry) of TRIP pool as quantified by FACS by days 2, 4 and 6 after transfection