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      Mitochondrial Genome Engineering: The Revolution May Not Be CRISPR-Ized

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          Abstract

          In recent years mitochondrial DNA (mtDNA) has transitioned to greater prominence across diverse areas of biology and medicine. The recognition of mitochondria as a major biochemical hub, contributions of mitochondrial dysfunction to various diseases, and several high-profile attempts to prevent hereditary mtDNA disease through mitochondrial replacement therapy have roused interest in the organellar genome. Subsequently, attempts to manipulate mtDNA have been galvanized, although with few robust advances and much controversy. Re-engineered protein-only nucleases such as mtZFN and mitoTALEN function effectively in mammalian mitochondria, although efficient delivery of nucleic acids into the organelle remains elusive. Such an achievement, in concert with a mitochondria-adapted CRISPR/Cas9 platform, could prompt a revolution in mitochondrial genome engineering and biological understanding. However, the existence of an endogenous mechanism for nucleic acid import into mammalian mitochondria, a prerequisite for mitochondrial CRISPR/Cas9 gene editing, remains controversial.

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          Engineering of mammalian mtDNA has been hampered by an inability to import nucleic acids into mitochondria.

          A limited toolkit exists for manipulation of mammalian mtDNA, relying on protein-only nucleolysis and heteroplasmy-shifting approaches.

          Although present in lower metazoans, the weight of evidence against an efficient endogenous RNA import mechanism in mammalian mitochondria is considerable.

          Controversially, the application of CRISPR/Cas9 for manipulation of mammalian mtDNA in human cells has been reported.

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          Most cited references87

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          A TALE nuclease architecture for efficient genome editing.

          Nucleases that cleave unique genomic sequences in living cells can be used for targeted gene editing and mutagenesis. Here we develop a strategy for generating such reagents based on transcription activator-like effector (TALE) proteins from Xanthomonas. We identify TALE truncation variants that efficiently cleave DNA when linked to the catalytic domain of FokI and use these nucleases to generate discrete edits or small deletions within endogenous human NTF3 and CCR5 genes at efficiencies of up to 25%. We further show that designed TALEs can regulate endogenous mammalian genes. These studies demonstrate the effective application of designed TALE transcription factors and nucleases for the targeted regulation and modification of endogenous genes.
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            Maintenance and Expression of Mammalian Mitochondrial DNA.

            Mammalian mitochondrial DNA (mtDNA) encodes 13 proteins that are essential for the function of the oxidative phosphorylation system, which is composed of four respiratory-chain complexes and adenosine triphosphate (ATP) synthase. Remarkably, the maintenance and expression of mtDNA depend on the mitochondrial import of hundreds of nuclear-encoded proteins that control genome maintenance, replication, transcription, RNA maturation, and mitochondrial translation. The importance of this complex regulatory system is underscored by the identification of numerous mutations of nuclear genes that impair mtDNA maintenance and expression at different levels, causing human mitochondrial diseases with pleiotropic clinical manifestations. The basic scientific understanding of the mechanisms controlling mtDNA function has progressed considerably during the past few years, thanks to advances in biochemistry, genetics, and structural biology. The challenges for the future will be to understand how mtDNA maintenance and expression are regulated and to what extent direct intramitochondrial cross talk between different processes, such as transcription and translation, is important.
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              Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases.

              Mitochondria are eukaryotic organelles that generate most of the energy in the cell by oxidative phosphorylation (OXPHOS). Each mitochondrion contains multiple copies of a closed circular double-stranded DNA genome (mtDNA). Human (mammalian) mtDNA encodes 13 essential subunits of the inner membrane complex responsible for OXPHOS. These mRNAs are translated by the mitochondrial protein synthesis machinery, which uses the 22 species of mitochondrial tRNAs (mt tRNAs) encoded by mtDNA. The unique structural features of mt tRNAs distinguish them from cytoplasmic tRNAs bearing the canonical cloverleaf structure. The genes encoding mt tRNAs are highly susceptible to point mutations, which are a primary cause of mitochondrial dysfunction and are associated with a wide range of pathologies. A large number of nuclear factors involved in the biogenesis and function of mt tRNAs have been identified and characterized, including processing endonucleases, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases. These nuclear factors are also targets of pathogenic mutations linked to various diseases, indicating the functional importance of mt tRNAs for mitochondrial activity.
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                Author and article information

                Contributors
                Journal
                Trends Genet
                Trends Genet
                Trends in Genetics
                Elsevier Trends Journals
                0168-9525
                1 February 2018
                February 2018
                : 34
                : 2
                : 101-110
                Affiliations
                [1 ]Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
                [2 ]Miller School of Medicine, University of Miami, Miami, FL, USA
                Author notes
                Article
                S0168-9525(17)30191-9
                10.1016/j.tig.2017.11.001
                5783712
                29179920
                f22f8ba5-9b51-42e7-ac4e-370b22164285
                © 2017 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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                Categories
                Article

                Genetics
                mitochondria,mtdna,crispr/cas9,mtzfn,mitotalen,rna import
                Genetics
                mitochondria, mtdna, crispr/cas9, mtzfn, mitotalen, rna import

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