Nature Communications

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  1. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.

    Nature Communications 8:15058 (2017) PMID 28497783

    Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featu...
  2. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.

    Nature Communications 8:15178 (2017) PMID 28474669

    CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and off-target sites, likely due to DNA damage. Here, to test potential solutions to this issue, we design and analyse a CRISPR-Cas9 library ...
  3. Hit and go CAS9 delivered through a lentiviral based self-limiting circuit.

    Nature Communications 8:15334 (2017) PMID 28530235

    In vivo application of the CRISPR-Cas9 technology is still limited by unwanted Cas9 genomic cleavages. Long-term expression of Cas9 increases the number of genomic loci non-specifically cleaved by the nuclease. Here we develop a Self-Limiting Cas9 circuit for Enhanced Safety and specificity (SLiC...
  4. Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC.

    Nature Communications 8:15315 (2017) PMID 28497787

    Efforts to manipulate locus-specific histone acetylation to assess their causal role in gene expression and cellular and behavioural phenotypes have been impeded by a lack of experimental tools. The Cas9 nuclease has been adapted to target epigenomic modifications, but a detailed description of t...
  5. CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum.

    Nature Communications 8:15179 (2017) PMID 28469274

    Corynebacterium glutamicum is an important industrial metabolite producer that is difficult to genetically engineer. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been adapted for genome editing of multiple bacteria, it cannot be introduced into C. glutamicum. Here we report a F...
  6. Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression.

    Nature Communications 8:15403 (2017) PMID 28534478

    CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative app...
  7. Automated multiplex genome-scale engineering in yeast.

    Nature Communications 8:15187 (2017) PMID 28469255

    Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and wide...
  8. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting.

    Nature Communications 8:14958 (2017) PMID 28387220

    Bacterial CRISPR-Cas systems comprise diverse effector endonucleases with different targeting ranges, specificities and enzymatic properties, but many of them are inactive in mammalian cells and are thus precluded from genome-editing applications. Here we show that the type II-B FnCas9 from Franc...
  9. Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

    Nature Communications 8:15013 (2017) PMID 28440293

    Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate human pathogen. Here, we describe an appro...
  10. Disrupted neuronal maturation in Angelman syndrome-derived induced pluripotent stem cells.

    Nature Communications 8:15038 (2017) PMID 28436452

    Angelman syndrome (AS) is a neurogenetic disorder caused by deletion of the maternally inherited UBE3A allele and is characterized by developmental delay, intellectual disability, ataxia, seizures and a happy affect. Here, we explored the underlying pathophysiology using induced pluripotent stem ...
  11. Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice.

    Nature Communications 8:14716 (2017) PMID 28291770

    In retinitis pigmentosa, loss of cone photoreceptors leads to blindness, and preservation of cone function is a major therapeutic goal. However, cone loss is thought to occur as a secondary event resulting from degeneration of rod photoreceptors. Here we report a genome editing approach in which ...
  12. FMNL formins boost lamellipodial force generation.

    Nature Communications 8:14832 (2017) PMID 28327544

    Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucl...
  13. A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue.

    Nature Communications 8:14574 (2017) PMID 28262680

    Benzoxaboroles are effective against bacterial, fungal and protozoan pathogens. We report potent activity of the benzoxaborole AN3661 against Plasmodium falciparum laboratory-adapted strains (mean IC50 32?nM), Ugandan field isolates (mean ex vivo IC50 64?nM), and murine P. berghei and P. falcipar...
  14. Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs.

    Nature Communications 8:14633 (2017) PMID 28256578

    CRISPR-based transcription regulators (CRISPR-TRs) have transformed the current synthetic biology landscape by allowing specific activation or repression of any target gene. Here we report a modular and versatile framework enabling rapid implementation of inducible CRISPR-TRs in mammalian cells. ...
  15. Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9.

    Nature Communications 8:14725 (2017) PMID 28290446

    Imaging chromatin dynamics is crucial to understand genome organization and its role in transcriptional regulation. Recently, the RNA-guidable feature of CRISPR-Cas9 has been utilized for imaging of chromatin within live cells. However, these methods are mostly applicable to highly repetitive reg...
  16. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

    Nature Communications 8:14370 (2017) PMID 28224990

    The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional ...
  17. Microenvironment-derived factors driving metastatic plasticity in melanoma.

    Nature Communications 8:14343 (2017) PMID 28181494

    Cellular plasticity is a state in which cancer cells exist along a reversible phenotypic spectrum, and underlies key traits such as drug resistance and metastasis. Melanoma plasticity is linked to phenotype switching, where the microenvironment induces switches between invasive/MITF(LO) versus pr...
  18. LncRNA AK023948 is a positive regulator of AKT.

    Nature Communications 8:14422 (2017) PMID 28176758

    Despite the overwhelming number of human long non-coding RNAs (lncRNAs) reported so far, little is known about their physiological functions for the majority of them. The present study uses a CRISPR/Cas9-based synergistic activation mediator (SAM) system to identify potential lncRNAs capable of r...
  19. CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis.

    Nature Communications 8:14291 (2017) PMID 28169275

    Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens...
  20. Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy.

    Nature Communications 8:14454 (2017) PMID 28195574

    Gene replacement therapies utilizing adeno-associated viral (AAV) vectors hold great promise for treating Duchenne muscular dystrophy (DMD). A related approach uses AAV vectors to edit specific regions of the DMD gene using CRISPR/Cas9. Here we develop multiple approaches for editing the mutation...