Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases

The development of customizable sequence-specific nucleases such as TALENs, ZFNs and the powerful CRISPR/Cas9 system has revolutionized the field of genome editing. The CRISPR/Cas9 system is particularly versatile and has been applied in numerous species representing all branches of life. Regardless of the target organism, all researchers using sequence-specific nucleases face similar challenges: confirmation of the desired on-target mutation and the detection of off-target events. Here, we evaluate the most widely-used methods for the detection of on-target and off-target mutations in terms of workflow, sensitivity, strengths and weaknesses

Overcoming low yields of plant-made antibodies by a protein engineering approach

The commercial development of plant-based antibody production platforms is often limited by low and variable yields, but little is known about the factors that affect antibody accumulation during and after translation. Here, we present a strategy to identify yield-limiting regions in the transcript and protein. We exchanged variable heavy chain (VH) domain sequences between two human antibodies at structurally conserved positions, thus creating ten chimeric VH domains containing sequences from M12 (similar to 1000 mu g/g leaf fresh weight [FW]) and 4E10 (similar to 100 mu g/g FW). After transient expression in Nicotiana benthamiana leaves, we measured mRNA and protein levels by quantitative real-time PCR and surface plasmon resonance spectroscopy, respectively. Transcript levels were similar for all constructs, but antibody levels ranged from similar to 250 mu g/g to over 2000 mu g/g FW. Analysis of the expression levels showed that: (i) 4E10 yields were only marginally increased by suppression of post-transcriptional gene silencing; (ii) the complementarity determining region 3 (CDR3) of 4E10 contains a protease site; and (iii) a bipartite, yield-limiting region exists in the CDR2/CDR3. Our findings highlight the strong impact of cotranslational and posttranslational events on antibody yields and show that protein engineering is a powerful tool that can be used to overcome the remaining limitations affecting antibody production in plants

Response to Comment on “Type I CD20 Antibodies Recruit the B Cell Receptor for Complement-Dependent Lysis of Malignant B Cells”

Transplantation and autoimmunit

Diverse migration strategies in hoopoes (Upupa epops) lead to weak spatial but strong temporal connectivity

The annual cycle of migrating birds is shaped by their seasonal movements between breeding and non-breeding sites. Studying how migratory populations are linked throughout the annual cycle—migratory connectivity, is crucial to understanding the population dynamics of migrating bird species. This requires the consideration not only of spatial scales as has been the main focus to date but also of temporal scales: only when both aspects are taken into account, the degree of migratory connectivity can be properly defined. We investigated the migration behaviour of hoopoes (Upupa epops) from four breeding populations across Europe and characterised migration routes to and from the breeding grounds, location of non-breeding sites and the timing of key migration events. Migration behaviour was found to vary both within and amongst populations, and even though the spatial migratory connectivity amongst the populations was weak, temporal connectivity was strong with differences in timing amongst populations, but consistent timing within populations. The combination of diverse migration routes within populations and co- occurrence on the non-breeding grounds between populations might promote exchange between breeding populations. As a result, it might make hoopoes and other migrating bird species with similar strategies more resilient to future habitat or climatic changes and stabilise population trends

CRISPR-Cas-mediated gene knockout in tomato

Loss-of-function mutants are crucial for plant functional genomics studies. With the advent of CRISPR-Cas genome editing, generating null alleles for one or multiple specific gene(s) has become feasible for many plant species including tomato (Solanum lycopersicum). An easily programmable RNA-guided Cas endonuclease efficiently creates DNA double-strand breaks (DSBs) at targeted genomic sites that can be repaired by nonhomologous end joining (NHEJ) typically leading to small insertions or deletions that can produce null mutations. Here, we describe how to utilize CRISPR-Cas genome editing to obtain stable tomato gene knockout lines

Patterns of CRISPR/Cas9 activity in plants, animals and microbes

The CRISPR/Cas9 system and related RNA-guided endonucleases can introduce double-strand breaks (DSBs) at specific sites in the genome, allowing the generation of targeted mutations in one or more genes as well as more complex genomic rearrangements. Modifications of the canonical CRISPR/Cas9 system from Streptococcus pyogenes and the introduction of related systems from other bacteria have increased the diversity of genomic sites that can be targeted, providing greater control over the resolution of DSBs, the targeting efficiency (frequency of on-target mutations), the targeting accuracy (likelihood of off-target mutations) and the type of mutations that are induced. Although much is now known about the principles of CRISPR/Cas9 genome editing, the likelihood of different outcomes is species-dependent and there have been few comparative studies looking at the basis of such diversity