Next-generation mammalian genetics toward organism-level systems biology

Abstract

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

The Mouse as a Model Organism for Assessing Anesthetic Sensitivity

“…In this chapter, we highlight the uses of mice as a model organism for assessing the effects of anesthetic drugs with the ultimate goal of determining both molecular and neuronal sites of sedation and hypnosis. Given the explosive technical advances in recent years (Bucan & Abel, 2002; Rossant & McMahon, 1999; Singh, Schimenti, & Bolcun-Filas, 2015; Susaki, Ukai, & Ueda, 2017) and new found ability to manipulate the activity of discrete populations of neurons with optogenetic and chemogenetic approaches (Ressler, 2017), it is increasingly likely that anesthetic mechanisms research in mice will continue to provide novel insights into drug action.…”

Paternal knockout of Slc38a4 /SNAT4 causes placental hypoplasia associated with intrauterine growth restriction in mice

“…Triple-Target CRISPR. Triple-target CRISPR was performed as described elsewhere (20,21). Briefly, 3 sgRNAs targeting distinct exons of each target gene were designed using the MIT CRISPR Designer (currently closed).…”

“…Transporter in Placental Development. To determine whether any of the SNAT genes play a critical role in placental development in mice, we performed a triple-target CRISPR screen, a technique that allows the production of whole-body homozygous KO founder mice directly from zygotes at a very high efficiency (20,21). We designed 3 single-guide RNAs (sgRNAs) targeting distinct protein-coding exons for each gene.…”

Neuronal Mechanisms for Sleep/Wake Regulation and Modulatory Drive

“…Dreamless mutants, that have a mutation in the sodium leak channel NALCN, show a decrease in REM sleep amount and episode duration (Funato et al, 2016). Although the precise mechanisms by which these mutations modulate sleep need are still unclear, the use of unbiased forward-genetic screens in mammals will likely lead to major insights into the pathways and mechanisms of sleep regulation, as it did for circadian biology (Allada et al, 2001;Susaki et al, 2017;Vitaterna et al, 1994).…”