A Review of Online Resources to Explore Mitochondrial Genomics
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“Mitochondrial toolbox” - A review of online resources to explore mitochondrial genomics Cappa, R., de Campos, C., Maxwell, P., & McKnight, A. J. (2020). “Mitochondrial toolbox” - A review of online resources to explore mitochondrial genomics. Frontiers in Genetics, 11, [439]. https://doi.org/10.3389/fgene.2020.00439 Published in: Frontiers in Genetics Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright © 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. 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Sep. 2021 fgene-11-00439 May 6, 2020 Time: 19:47 # 1 REVIEW published: 08 May 2020 doi: 10.3389/fgene.2020.00439 “Mitochondrial Toolbox” – A Review of Online Resources to Explore Mitochondrial Genomics Ruaidhri Cappa1*, Cassio de Campos2, Alexander P. Maxwell1 and Amy J. McKnight1 1 Centre for Public Health, Institute of Clinical Sciences B, Queen’s University Belfast, Royal Victoria Hospital, Belfast, United Kingdom, 2 School of Electronics, Electrical Engineering and Computer Science, Queen’s University Belfast, Belfast, United Kingdom Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This ‘mitochondrial Edited by: toolbox’ summary resource will enable researchers to rapidly identify the resource(s) Isidore Rigoutsos, most suitable for their needs. These resources fulfil a variety of functions, with some Thomas Jefferson University, United States being highly specialised. No single tool will provide all users with the resources they Reviewed by: require; therefore, the most suitable tool will vary between users depending on the Constantinos Stathopoulos, nature of the work they aim to carry out. Genetics resources are well established for University of Patras, Greece Adam Scheid, phylogeny and DNA sequence changes, but further epigenetic and gene expression University of Kansas Medical Center, resources need to be developed for mitochondrial genomics. United States Keywords: association, genome, methylation, mitochondria, resource, SNP, toolbox *Correspondence: Ruaidhri Cappa [email protected] INTRODUCTION Specialty section: This article was submitted to In this review, we discuss the role of the mitochondria in relation to disease, with a focus on Bioinformatics and Computational mitochondrial genomics, and review the bioinformatic tools currently available for the analysis of Biology, the mitochondrial genome. This brief overview highlights the importance of the mitochondrial a section of the journal genome from a scientific and clinical perspective, and also provides readers with signposts to Frontiers in Genetics the bioinformatics tools currently available. We discuss and compare the capabilities offered by Received: 24 October 2019 a variety of bioinformatics software (Figures 1, 2), helping readers to make an informed choice Accepted: 09 April 2020 as to which tools would best suit their needs. We also discuss challenges relating to the field of Published: 08 May 2020 mitochondrial genomics and discuss bioinformatics capabilities which are currently lacking. This Citation: may provide perspective for researchers seeking to develop new bioinformatics tools by informing Cappa R, de Campos C, them of the current gaps in the market, and therefore may provide inspiration for the development Maxwell AP and McKnight AJ (2020) of new tools which would enable researchers to investigate the mitochondrial genome further. This “Mitochondrial Toolbox” – A Review of Online Resources to Explore review extends a mini-review previous published by Bris et al.(2018). Mitochondrial Genomics. Mitochondrial diseases affect more than 10 per 100,000 individuals (including mitochondrial Front. Genet. 11:439. disorders caused by mutations in either the mitochondrial or nuclear genomes) (Gorman doi: 10.3389/fgene.2020.00439 et al., 2015). Developing and implementing effective treatments and preventative strategies Frontiers in Genetics| www.frontiersin.org 1 May 2020| Volume 11| Article 439 fgene-11-00439 May 6, 2020 Time: 19:47 # 2 Cappa et al. Mitochondrial Toolbox for mitochondrial disease may improve the health of a substantial would serve if imported. While certain studies suggested that portion of the population (Gorman et al., 2015). RNAs imported into the mitochondria may serve functions such Identifying pathogenic mutations in mitochondrial DNA as mitochondrial RNA processing (Chang and Clayton, 1987; (mtDNA) may also provide more effective diagnostic tools in Rosenblad et al., 2006), this was contradicted by other studies addition to aiding disease prevalence studies, which can be (Kiss and Filipowicz, 1992; Jacobson et al., 1995; Wanrooij et al., used to inform healthcare budgets and public health strategies 2010). It has been suggested that mammalian mitochondria could (Gorman et al., 2015). Correctly diagnosing severe pathogenic function normally without the need for endogenous RNA import mutations in mtDNA is also necessary when considering (Gammage et al., 2018) although it has been shown that a techniques such as in vitro fertilisation to prevent such mutations range of RNAs can be artificially targeted to the mitochondria being passed on to future generations (Gorman et al., 2015). (Wang et al., 2012). This has been demonstrated in proof of concept studies, which A major limitation of current genetic engineering techniques have used an approach of transplanting pronuclei soon before the in relation to modifying the mitochondrial genome is the first mitotic division occurred; however, it has been found that inability of these tools to introduce the desired modifications normally fertilised zygotes are unable to satisfactorily tolerate this in a homoplasmic manner (Verechshagina et al., 2019). approach (Hyslop et al., 2016). An alternative method has been Current tools shift the mtDNA heteroplasmy level toward a developed in which pronuclei are transplanted just after meiosis more desirable state (Verechshagina et al., 2019). Changes has been completed prior to the first mitotic division. This in mitochondrial heteroplasmy may have transcriptomic, method did appear to be successful as development continued epigenomic, and metabolomic consequences, such as altered successfully to blastocyst stage (Hyslop et al., 2016). Using this histone modifications and changes to the redox state (Kopinski method, mtDNA carryover was reduced to less than 2% in 79% et al., 2019). Therefore, it is possible that the use of existing of pronuclear transplantation (PNT) blastocysts (Hyslop et al., genetic engineering techniques to modify the mitochondrial 2016). This avoided the progressive increase in heteroplasmy genome in a heteroplasmic manner may have unintended which has been observed when mtDNA carryover levels are at and possibly negative consequences. In order for a tool to be 4% or higher (Hyslop et al., 2016). The PNT method could reduce considered a reliable means of modifying the mitochondria the likelihood of mitochondrial disease occurring, however, there genome it would be required to induce the desired alterations in is no guarantee that disease would not occur (Hyslop et al., 2016). a specific and homoplasmic manner (Verechshagina et al., 2019). Another method of avoiding transmission of mtDNA disease Therefore it is generally accepted that there are no reliable to offspring is the replacement of oocyte maternal mtDNA. methods for modifying the human mitochondrial genome at The mother’s oocytes mutant mtDNA can be replaced using a present (Klucnika and Ma, 2020). spindle transfer method, resulting in the development of embryos Alternative approaches have achieved some success, such as which contained over 99% donor mtDNA (which lacked harmful approaches which utilise mitochondrially targeted zinc finger- mutations) (Kang et al., 2016). Embryonic stem cells derived nucleases. Such systems are engineered