No abstract

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.

Retroviruses integrate into the host genome in patterns specific to each virus. Understanding the causes of these patterns can provide insight into viral integration mechanisms, pathology and genome evolution, and is critical to the development of safe gene therapy vectors. We generated murine leukemia virus integrations in human HepG2 and K562 cells and subjected them to second-generation sequencing, using a DNA barcoding technique that allowed us to quantify independent integration events. We characterized >3 700 000 unique integration events in two ENCODE-characterized cell lines. We find that integrations were most highly enriched in a subset of strong enhancers and active promoters. In both cell types, approximately half the integrations were found in <2% of the genome, demonstrating genomic influences even narrower than previously believed. The integration pattern of murine leukemia virus appears to be largely driven by regions that have high enrichment for multiple marks of active chromatin; the combination of histone marks present was sufficient to explain why some strong enhancers were more prone to integration than others. The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors.

Determining the mechanism of gene function is greatly enhanced using conditional mutagenesis. However, generating engineered conditional alleles is inefficient and has only been widely used in mice. Importantly, multiplex conditional mutagenesis requires extensive breeding. Here we demonstrate a system for one-generation multiplex conditional mutagenesis in zebrafish (Danio rerio) using transgenic expression of both cas9 and multiple single guide RNAs (sgRNAs). We describe five distinct zebrafish U6 promoters for sgRNA expression and demonstrate efficient multiplex biallelic inactivation of tyrosinase and insulin receptor a and b, resulting in defects in pigmentation and glucose homeostasis. Furthermore, we demonstrate temporal and tissue-specific mutagenesis using transgenic expression of Cas9. Heat-shock-inducible expression of cas9 allows temporal control of tyr mutagenesis. Liver-specific expression of cas9 disrupts insulin receptor a and b, causing fasting hypoglycemia and postprandial hyperglycemia. We also show that delivery of sgRNAs targeting ascl1a into the eye leads to impaired damage-induced photoreceptor regeneration. Our findings suggest that CRISPR/Cas9-based conditional mutagenesis in zebrafish is not only feasible but rapid and straightforward.KEYWORDS CRISPR/Cas9; conditional mutagenesis; glucose homeostasis; retinal regeneration; zebrafish C ONDITIONAL gene inactivation is necessary for determining physiological functions of genes whose conventional mutation causes embryonic lethality or multiorgan defects. It has been widely used in mice because of the availability of embryonic stem (ES) cells and large collections of both ES cell lines and animals that carry conditional alleles. The conditional alleles usually contain strategically placed Cre or Flp target sites in introns that permit deletion of the intervening exon(s) (Gu et al. 1994). Some conditional alleles harbor a Cre and/or Flp invertible gene trap in an intron that allows an on/off switch of transcription (Schnutgen et al. 2005;Ni et al. 2012). The function or expression of these alleles is "switched" off in the presence of Cre or Flp activity. In Drosophila, conditional gene inactivation can be achieved using RNA interference (RNAi), and genome-wide libraries of RNAi transgenes are available (Dietzl et al. 2007;Ni et al. 2008). For the increasingly popular zebrafish model, however, only limited conditional alleles generated from invertible gene trapping are available (Ni et al. 2012). The lack of ES cells and the inefficiency of RNAi in zebrafish necessitate new approaches for targeted conditional gene inactivation.CRISPR/Cas9 mutagenesis has been applied to many model systems from cultured cells to whole organisms (Doudna and Charpentier 2014;Hsu et al. 2014). The system only requires a two-component RNA-protein complex (RNP): a single guide RNA (sgRNA) that identifies the target through base pairing and the Cas9 endonuclease that generates double-strand breaks (DSBs) at the target site upon sgRNA-target base pairing. CRI...