CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization.

Programmable control of spatial genome organization is a powerful approach for studying how nuclear structure affects gene regulation and cellular function. Here, we develop a versatile CRISPR-genome organization (CRISPR-GO) system that can efficiently control the spatial positioning of genomic loci relative to specific nuclear compartments, including the nuclear periphery, Cajal bodies, and promyelocytic leukemia (PML) bodies. CRISPR-GO is chemically inducible and reversible, enabling interrogation of real-time dynamics of chromatin interactions with nuclear compartments in living cells. Inducible repositioning of genomic loci to the nuclear periphery allows for dissection of mitosis-dependent and -independent relocalization events and also for interrogation of the relationship between gene position and gene expression. CRISPR-GO mediates rapid de novo formation of Cajal bodies at desired chromatin loci and causes significant repression of endogenous gene expression over long distances (30-600 kb). The CRISPR-GO system offers a programmable platform to investigate large-scale spatial genome organization and function.

Predicting the molecular complexity of sequencing libraries.

Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing.

Modeling genome coverage in single-cell sequencing.

MOTIVATION: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. RESULTS: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. AVAILABILITY AND IMPLEMENTATION: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. CONTACT: andrewds@usc.edu SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

A prospective study of treatments for adult-onset divergence insufficiency-type esotropia.

PURPOSE: To describe 10-week and 12-month outcomes following treatment for divergence insufficiency-type esotropia in adults. METHODS: In this prospective observational study, 110 adults with divergence insufficiency-type esotropia, with a distance esodeviation measuring 2Δ to 30Δ and at least 25% larger at distance than near, and binocular diplopia present at least "sometimes" at distance, were enrolled at 28 sites when initiating new treatment. Surgery, prism, or divergence exercises/therapy were chosen at the investigator's discretion. Diplopia was assessed at enrollment and at 10-week and 12-month outcome examinations using a standardized diplopia questionnaire (DQ). Success was defined as DQ responses of "rarely" or "never" when looking straight ahead in the distance, with no alternative treatment initiated. RESULTS: Of the 110 participants, 32 (29%) were prescribed base-out prism; none had received prior treatment for esotropia. Success criteria were met by 22 of 30 at 10 weeks (73%; 95% CI, 54%-88%) and by 16 of 26 at 12 months (62%; 95% CI, 41%-80%). For the 76 (68%) who underwent strabismus surgery (82% of whom had been previously treated with prism), success criteria were met by 69 of 74 at 10 weeks (93%; 95% CI, 85%-98%) and by 57 of 72 at 12 months (79%; 95% CI, 68%-88%). CONCLUSIONS: In this study cohort, both base-out prism as initial therapy and strabismus surgery (usually following prism) were successful in treating diplopia for most adults with divergence insufficiency-type esotropia when assessed during the first year of follow-up.

2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP-dependent metabolic regulation of chromatin structure.

Temporal lobe epilepsy is a common form of drug-resistant epilepsy that sometimes responds to dietary manipulation such as the 'ketogenic diet'. Here we have investigated the effects of the glycolytic inhibitor 2-deoxy-D-glucose (2DG) in the rat kindling model of temporal lobe epilepsy. We show that 2DG potently reduces the progression of kindling and blocks seizure-induced increases in the expression of brain-derived neurotrophic factor and its receptor, TrkB. This reduced expression is mediated by the transcription factor NRSF, which recruits the NADH-binding co-repressor CtBP to generate a repressive chromatin environment around the BDNF promoter. Our results show that 2DG has anticonvulsant and antiepileptic properties, suggesting that anti-glycolytic compounds may represent a new class of drugs for treating epilepsy. The metabolic regulation of neuronal genes by CtBP will open avenues of therapy for neurological disorders and cancer.

A benchmark of algorithms for the analysis of pooled CRISPR screens.

Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments.

For many types of high-throughput sequencing experiments, success in downstream analysis depends on attaining sufficient coverage for individual positions in the genome. For example, when identifying single-nucleotide variants de novo, the number of reads supporting a particular variant call determines our confidence in that variant call. If sequenced reads are distributed uniformly along the genome, the coverage of a nucleotide position is easily approximated by a Poisson distribution, with rate equal to average sequencing depth. Unfortunately, as has become well known, high-throughput sequencing data are never uniform. The numerous factors contributing to variation in coverage have resisted attempts at direct modeling and change along with minor adjustments in the underlying technology. We propose a new nonparametric method to predict the portion of a genome that will attain some specified minimum coverage, as a function of sequencing effort, using information from a shallow sequencing experiment from the same library. Simulations show our approach performs well under an array of distributional assumptions that deviate from uniformity. We applied this approach to estimate coverage at varying depths in single-cell whole-genome sequencing data from multiple protocols. These resulted in highly accurate predictions, demonstrating the effectiveness of our approach in analyzing complexity of sequencing libraries and optimizing design of sequencing experiments.

GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.

Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approach (GEMINI) that jointly analyzes all samples and reagents to identify genetic interactions in pairwise knockout screens. The improved accuracy and scalability of GEMINI enables the systematic analysis of combinatorial CRISPR knockout screens, regardless of design and dimension. GEMINI is available as an open source R package on GitHub at https://github.com/sellerslab/gemini .

CRISPR-mediated live imaging of genome editing and transcription.

We report a robust, versatile approach called CRISPR live-cell fluorescent in situ hybridization (LiveFISH) using fluorescent oligonucleotides for genome tracking in a broad range of cell types, including primary cells. An intrinsic stability switch of CRISPR guide RNAs enables LiveFISH to accurately detect chromosomal disorders such as Patau syndrome in prenatal amniotic fluid cells and track multiple loci in human T lymphocytes. In addition, LiveFISH tracks the real-time movement of DNA double-strand breaks induced by CRISPR-Cas9-mediated editing and consequent chromosome translocations. Finally, by combining Cas9 and Cas13 systems, LiveFISH allows for simultaneous visualization of genomic DNA and RNA transcripts in living cells. The LiveFISH approach enables real-time live imaging of DNA and RNA during genome editing, transcription, and rearrangements in single cells.

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.

Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects. We present a method, CRISPhieRmix, that resolves these issues by using a hierarchical mixture model with a broad-tailed null distribution. We show that CRISPhieRmix allows for more accurate and powerful inferences in large-scale pooled CRISPRi/a screens. We discuss key issues in the analysis and design of screens, particularly the number of guides needed for faithful full discovery.

Unsupervised clustering and epigenetic classification of single cells.

Characterizing epigenetic heterogeneity at the cellular level is a critical problem in the modern genomics era. Assays such as single cell ATAC-seq (scATAC-seq) offer an opportunity to interrogate cellular level epigenetic heterogeneity through patterns of variability in open chromatin. However, these assays exhibit technical variability that complicates clear classification and cell type identification in heterogeneous populations. We present scABC, an R package for the unsupervised clustering of single-cell epigenetic data, to classify scATAC-seq data and discover regions of open chromatin specific to cell identity.

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming.

Comprehensive identification of factors that can specify neuronal fate could provide valuable insights into lineage specification and reprogramming, but systematic interrogation of transcription factors, and their interactions with each other, has proven technically challenging. We developed a CRISPR activation (CRISPRa) approach to systematically identify regulators of neuronal-fate specification. We activated expression of all endogenous transcription factors and other regulators via a pooled CRISPRa screen in embryonic stem cells, revealing genes including epigenetic regulators such as Ezh2 that can induce neuronal fate. Systematic CRISPR-based activation of factor pairs allowed us to generate a genetic interaction map for neuronal differentiation, with confirmation of top individual and combinatorial hits as bona fide inducers of neuronal fate. Several factor pairs could directly reprogram fibroblasts into neurons, which shared similar transcriptional programs with endogenous neurons. This study provides an unbiased discovery approach for systematic identification of genes that drive cell-fate acquisition.

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki .

Applications of species accumulation curves in large-scale biological data analysis.

The species accumulation curve, or collector's curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45-63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Patience is a virtue: an argument for delayed surgical intervention in fulminant Clostridium difficile colitis.

Recently, the incidence and severity of Clostridium difficile infection (CDI) has increased. In cases of fulminant infection, surgery is a viable therapeutic option but associated with high mortality. We sought to examine factors associated with mortality in a large sample of patients with severe CDI that underwent surgery. A retrospective study was conducted in patients with severe CDI undergoing colectomy. Demographics, risk factors, comorbidities, clinical and laboratory data, and time between admission/diagnosis of CDI and colectomy were collected. Conventional markers of severity were evaluated as predictors of mortality. Sixty-four cases were included for analysis. The overall observed mortality rate was 45.3 per cent. Few conventional markers of severity were significantly associated with mortality. Risk factors that correlated with postsurgical mortality were vasopressor use (odds ratio, 3.08; 95% confidence interval, 1.00 to 9.92) and shorter time between diagnosis and surgery (median time, 2 vs 3 days, P = 0.009). This study suggests that a delay in surgery after diagnosis of severe CDI may improve overall outcomes. The finding regarding timing of surgery is contrary to traditional teaching and may be the result of improved medical treatment and stabilization before surgery. Consideration should be given to the importance of timing of colectomy in fulminant CDI, whereas prospective studies should be conducted to elucidate causal relationships.

Sexual selection targets cetacean pelvic bones.

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis that seems to serve no other function except to anchor muscles that maneuver the penis. Here, we create a novel morphometric pipeline to analyze the size and shape evolution of pelvic bones from 130 individuals (29 species) in the context of inferred mating system. We present two main findings: (1) males from species with relatively intense sexual selection (inferred by relative testes size) tend to evolve larger penises and pelvic bones compared to their body length, and (2) pelvic bone shape has diverged more in species pairs that have diverged in inferred mating system. Neither pattern was observed in the anterior-most pair of vertebral ribs, which served as a negative control. This study provides evidence that sexual selection can affect internal anatomy that controls male genitalia. These important functions may explain why cetacean pelvic bones have not been lost through evolutionary time.

Resolution of hypertropia with correction of intermittent exotropia.

PURPOSE: We describe the spontaneous resolution of hypertropia in a subset of patients with preoperative exotropia and hypertropia, who underwent surgery for intermittent exotropia alone. DESIGN: This was a retrospective case series. METHODS: The charts were reviewed of 17 patients who underwent surgical correction for an intermittent exotropia, who additionally were noted on preoperative exam to have greater than 5 prism dioptres of vertical deviation in primary position. Patients were excluded if they had prior strabismus surgery, dissociated vertical deviation, and paretic or restrictive deviations. RESULTS: All patients were documented to have complete resolution of any vertical deviation in any field of gaze. This effect was noted to persist. CONCLUSIONS: We propose that the measured distance hypertropia, which is coincident with intermittent exotropia, even with the appearance of superior oblique dysfunction or inferior oblique overaction, is not created by a true vertical or cyclovertical muscle imbalance. Further, that the reduction of the hypertropia at near fixation predicts its resolution with horizontal muscle surgery. Therefore, vertical surgery should not be performed to address the coincident vertical deviation in these patients.

Fulminant Clostridium difficile infection: An association with prior appendectomy?

AIM: To examine if fulminant Clostridium difficile infections (CDI) resulting in colectomy was associated with a prior appendectomy and whether any association affected the severity of the disease. METHODS: A retrospective chart review was performed on patients who underwent colectomy for CDI between 2001 and 2011. The appendectomy rate was calculated based on the absence of an appendix on the surgical pathology report. This was compared to an established lifetime risk of appendectomy in the general population. A chart review was performed for mortality and traditional markers of CDI disease severity. Fisher's exact test was used to calculate the likelihood of association between prior appendectomy, mortality, and clinical markers of severity of infection. RESULTS: Fifty-five specimens were identified with pseudomembranous colitis consistent with CDI. All patients had a clinical history consistent with CDI and 45 of 55 (81.8%) specimens also had microbiological confirmation of CDI. Appendectomy was observed in 24 of 55 specimens (0.436, 99%CI: 0.280-0.606). This was compared to the lifetime incidence of appendectomy of 17.6%. The rate of appendectomy in our sample was significantly higher than would be expected in the general population (43.6% vs 17.6%, P < 0.01). Disease severity did not differ based on presence or absence of an appendix and no association was detected between prior appendectomy and mortality (OR = 0.588, 95%CI: 0.174-1.970). CONCLUSION: The rate of appendectomy in the patients whose CDI led to colectomy, was significantly higher than the calculated lifetime risk, suggesting an association of appendectomy and severe CDI resulting in colectomy. Larger prospective studies are needed to assess any potential causal relationships affecting fulminant CDI.

Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes.

Negative regulation of transcription is an important strategy in establishing and maintaining cell-specific gene expression patterns. Many neuronal genes are subject to active transcriptional repression outside the nervous system to establish neuronal specificity. NRSF/REST has been demonstrated to regulate at least 30 genes and contribute to their neuronal targeting by repressing transcription outside the nervous system. Further, human genome database searches reveal that over 800 genes contain an NRSE. Here we report that NRSF recruits the histone methylase G9a to silence NRSF target genes in nonneuronal cells. We show that G9a generates a highly localized domain of dimethylated histone H3-K9 around NRSEs, but H3-K27 remains unmethylated. The NRSEs are also associated with HP1. Finally, we demonstrate that dominant-negative G9a abrogates silencing of chromosomal neuronal genes. These findings implicate a role for histone methylation in targeting neuronal gene expression to the nervous system.