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Rodriguez Ruiz A, Van Dam AR. Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains. PeerJ 2023; 11:e16276. [PMID: 38025758 PMCID: PMC10676084 DOI: 10.7717/peerj.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples.
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Affiliation(s)
- Alfredo Rodriguez Ruiz
- Departamento de Biología, Universidad de Puerto Rico Recinto Universitario de Mayagüez, Mayagüez, Puerto Rico, United States of America
| | - Alex R. Van Dam
- Departamento de Biología, Universidad de Puerto Rico Recinto Universitario de Mayagüez, Mayagüez, Puerto Rico, United States of America
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2
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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3
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Cohen T, Medini H, Mordechai C, Eran A, Mishmar D. Human mitochondrial RNA modifications associate with tissue-specific changes in gene expression, and are affected by sunlight and UV exposure. Eur J Hum Genet 2022; 30:1363-1372. [PMID: 35246665 PMCID: PMC9712611 DOI: 10.1038/s41431-022-01072-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/30/2022] [Accepted: 02/10/2022] [Indexed: 11/08/2022] Open
Abstract
RNA-DNA differences (RDD) have previously been identified in the human mitochondrial RNA (mt-RNA) transcripts, yet their functional impact is poorly understood. By analyzing 4928 RNA-seq samples from 23 body sites, we found that mtDNA gene expression negatively correlated with the levels of both m1A 947 16 S rRNA modification (mtDNA position 2617) and the m1A 1812 ND5 mRNA modification (mtDNA position 13,710) in 15 and 14 body sites, respectively. Such correlation was not evident in all tested brain tissues, thus suggesting a tissue-specific impact of these modifications on mtDNA gene expression. To assess the response of the tested modifications to environmental cues, we analyzed pairs of skin samples that were either exposed to the sun or not. We found that the correlations of mtDNA gene expression with both mt-RNA modifications were compromised upon sun exposure. As a first step to explore the underlying mechanism, we analyzed RNA-seq data from keratinocytes that were exposed to increasing doses of UV irradiation. Similar to sun exposure, we found a significant decrease in mtDNA gene expression upon increase in UV dosage. In contrast, there was a significant increase in the m1A 947 16 S rRNA modification levels upon elevation in UV dose. Finally, we identified candidate modulators of such responses. Taken together, our results indicate that mt-RNA modifications functionally correlate with mtDNA gene expression, and responds to environmental cues, hence supporting their physiological importance.
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Affiliation(s)
- Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Chen Mordechai
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Alal Eran
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
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4
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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5
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Biró B, Gál Z, Schiavo G, Ribari A, Joe Utzeri V, Brookman M, Fontanesi L, Hoffmann OI. Nuclear mitochondrial DNA sequences in the rabbit genome. Mitochondrion 2022; 66:1-6. [PMID: 35842180 DOI: 10.1016/j.mito.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 07/10/2022] [Indexed: 10/17/2022]
Abstract
Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.
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Affiliation(s)
- Bálint Biró
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Zoltán Gál
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Giuseppina Schiavo
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribari
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Valerio Joe Utzeri
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Michael Brookman
- Hanze University of Applied Sciences, Department for Biology and Medical Laboratory Research, Zernikeplein 7, 9747 AS Groningen, Netherlands
| | - Luca Fontanesi
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Orsolya Ivett Hoffmann
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary.
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Hazkani-Covo E. A Burst of Numt Insertion in the Dasyuridae Family During Marsupial Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nuclear pseudogenes of mitochondrial origin (numts) are common in all eukaryotes. Our previous scan of numts in sequenced nuclear genomes suggested that the highest numt content currently known in animals is that in the gray short-tailed opossum. The present work sought to determine numt content in marsupials and to compare it to those in placental and monothematic mammals as well as in non-mammalian vertebrates. To achieve this, 70 vertebrate species with available nuclear and mitochondrial genomes were scanned for numt content. An extreme numt content was found in the Dasyuridae, with 3,450 in Sarcophilus harrisii (1,955 kb) and 2,813 in Antechinus flavipes (847 kb). The evolutionarily closest species analyzed, the extinct Thylacinus cynocephalus belonging to the Thylacindae family, had only 435 numts (238 kb). These two Dasyuridae genomes featured the highest numt content identified in animals to date. A phylogenetic analysis of numts longer than 300 bp, using a Diprotodonita mitochondrial tree, indicated a burst of numt insertion that began before the divergence of the Dasyurini and Phascogalini, reaching a peak in the early evolution of the two tribes. No comparable increase was found in the early divergent species T. cynocephalus. Divergence of the Dasyuridae tribes has been previously dated to shortly after the Miocene climate transition, characterized by a rapid temperature decline. Interestingly, deviation from optimal growth temperature is one of the environmental factors reported to increase numt insertions in a laboratory setting.
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Abstract
Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.
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Affiliation(s)
- Piotr K Kopinski
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, Jarvis ED. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol 2021; 22:120. [PMID: 33910595 PMCID: PMC8082918 DOI: 10.1186/s13059-021-02336-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/31/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
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Affiliation(s)
- Giulio Formenti
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA.
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Balacco
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | - Bettina Haase
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | | | - Olivier Fedrigo
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | - Samara Brown
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, State of Qatar
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Iliana Bista
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Shane McCarthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | | | | | | | - Daniel Fordham
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Vania Costa
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Simon Mayes
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, Milan, Italy
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erich D Jarvis
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA.
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA.
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Interference of nuclear mitochondrial DNA segments in mitochondrial DNA testing resembles biparental transmission of mitochondrial DNA in humans. Genet Med 2021; 23:1514-1521. [PMID: 33846581 DOI: 10.1038/s41436-021-01166-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Reports have questioned the dogma of exclusive maternal transmission of human mitochondrial DNA (mtDNA), including the recent report of an admixture of two mtDNA haplogroups in individuals from three multigeneration families. This was interpreted as being consistent with biparental transmission of mtDNA in an autosomal dominant-like mode. The authenticity and frequency of these findings are debated. METHODS We retrospectively analyzed individuals with two mtDNA haplogroups from 2017 to 2019 and selected four families for further study. RESULTS We identified this phenomenon in 104/27,388 (approximately 1/263) unrelated individuals. Further study revealed (1) a male with two mitochondrial haplogroups transmits only one haplogroup to some of his offspring, consistent with nuclear transmission; (2) the heteroplasmy level of paternally transmitted variants is highest in blood, lower in buccal, and absent in muscle or urine of the same individual, indicating it is inversely correlated with mtDNA content; and (3) paternally transmitted apparent large-scale mtDNA deletions/duplications are not associated with a disease phenotype. CONCLUSION These findings strongly suggest that the observed mitochondrial haplogroup of paternal origin resulted from coamplification of rare, concatenated nuclear mtDNA segments with genuine mtDNA during testing. Evaluation of additional specimen types can help clarify the clinical significance of the observed results.
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Mitochondrial gene expression in single cells shape pancreatic beta cells' sub-populations and explain variation in insulin pathway. Sci Rep 2021; 11:466. [PMID: 33432158 PMCID: PMC7801437 DOI: 10.1038/s41598-020-80334-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/21/2020] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial gene expression is pivotal to cell metabolism. Nevertheless, it is unknown whether it diverges within a given cell type. Here, we analysed single-cell RNA-seq experiments from human pancreatic alpha (N = 3471) and beta cells (N = 1989), as well as mouse beta cells (N = 1094). Cluster analysis revealed two distinct human beta cells populations, which diverged by mitochondrial (mtDNA) and nuclear DNA (nDNA)-encoded oxidative phosphorylation (OXPHOS) gene expression in healthy and diabetic individuals, and in newborn but not in adult mice. Insulin gene expression was elevated in beta cells with higher mtDNA gene expression in humans and in young mice. Such human beta cell populations also diverged in mitochondrial RNA mutational repertoire, and in their selective signature, thus implying the existence of two previously overlooked distinct and conserved beta cell populations. While applying our approach to human alpha cells, two sub-populations of cells were identified which diverged in mtDNA gene expression, yet these cellular populations did not consistently diverge in nDNA OXPHOS genes expression, nor did they correlate with the expression of glucagon, the hallmark of alpha cells. Thus, pancreatic beta cells within an individual are divided into distinct groups with unique metabolic-mitochondrial signature.
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Hoser SM, Hoffmann A, Meindl A, Gamper M, Fallmann J, Bernhart SH, Müller L, Ploner M, Misslinger M, Kremser L, Lindner H, Geley S, Schaal H, Stadler PF, Huettenhofer A. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biol 2020; 21:299. [PMID: 33292386 PMCID: PMC7722341 DOI: 10.1186/s13059-020-02199-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/09/2020] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive. RESULTS Employing in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3'-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay. CONCLUSIONS We propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing.
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Affiliation(s)
- Simon M Hoser
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Andreas Meindl
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Maximilian Gamper
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Lisa Müller
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Melanie Ploner
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Matthias Misslinger
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Heiner Schaal
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany
| | - Alexander Huettenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
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12
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Kowal K, Tkaczyk A, Pierzchała M, Bownik A, Ślaska B. Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna. Int J Mol Sci 2020; 21:E8725. [PMID: 33218217 PMCID: PMC7699184 DOI: 10.3390/ijms21228725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
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Affiliation(s)
- Krzysztof Kowal
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Angelika Tkaczyk
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36a Str., 05-552 Jastrzębiec, Poland;
| | - Adam Bownik
- Faculty of Environmental Biology, Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37 Str., 20-262 Lublin, Poland;
| | - Brygida Ślaska
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
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Tracking the Distribution and Burst of Nuclear Mitochondrial DNA Sequences (NUMTs) in Fig Wasp Genomes. INSECTS 2020; 11:insects11100680. [PMID: 33036463 PMCID: PMC7600805 DOI: 10.3390/insects11100680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary Nuclear mitochondrial DNA sequences (NUMTs), which result from the insertion of exogenous mtDNA into the nuclear genome, are widely distributed in eukaryotes. However, how NUMTs are inserted into the nuclear genome and their post-insertion fates remain a mystery. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, which will be helpful to study the biological issues of NUMTs. We here select 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results show that the distributions of NUMTs are species- or lineage-specific. Furthermore, genomic environmental factors such as genome size, the damage-prone regions, and the mode of TE dynamics can determine the insertion and post-insertion fate of NUMTs. Especially because of TEs, the fragmentation and duplication of NUMTs, and thus their burst, are common. This is a relatively comprehensive investigation of the specific distribution of NUMTs and its influencing factors. Our study will help people to understand the evolution of exogenous fragments in the nuclear genome. Abstract Mitochondrial DNA sequences can be transferred into the nuclear genome, giving rise to nuclear mitochondrial DNA sequences (NUMTs). NUMTs have been described in numerous eukaryotes. However, the studies on the distribution of NUMTs and its influencing factors are still inadequate and even controversial. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, in which we selected 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results showed that the contents of NUMTs varied greatly in these species, and bursts of NUMTs existed in some species or lineages. Further detailed analyses showed that the large number of NUMTs might be related to the large genomes; NUMTs tended to be inserted into unstable regions of the genomes; and the inserted NUMTs might also be affected by transposable elements (TEs) in the neighbors, leading to fragmentations and duplications, followed by bursts of NUMTs. In summary, our results suggest that a variety of genomic environmental factors can determine the insertion and post-insertion fate of NUMTs, resulting in their species- or lineage-specific distribution patterns, and that studying the evolution of NUMTs can provide good evidence and theoretical basis for exploring the dynamics of exogenous DNA entering into the nuclear genome.
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Barcia G, Assouline Z, Magen M, Pennisi A, Rötig A, Munnich A, Bonnefont JP, Steffann J. Improving post-natal detection of mitochondrial DNA mutations. Expert Rev Mol Diagn 2020; 20:1003-1008. [PMID: 32902337 DOI: 10.1080/14737159.2020.1820326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Currently, genetic testing of mitochondrial DNA mutations includes screening for single-nucleotide variants, several base pair insertions or deletions, large-scale deletions, or relative depletion of total mitochondrial DNA content. Within the last decade, next-generation sequencing (NGS) has resulted in remarkable advances in the field of mitochondrial diseases (MD) and has become a routine step of the diagnostic workup. AREAS COVERED We aimed to present an overview of current technologies employed in molecular diagnosis of mitochondrial DNA diseases. We report on the recent contributions of NGS testing to the diagnosis and understanding of MD. EXPERT OPINION The progress of NGS technologies allows the simultaneous detection of mutations and quantification of the heteroplasmy level, ensuring sensitivity and specificity requested for the detection of mitochondrial DNA point mutations. NGS protocols enabling the simultaneous analysis of mitochondrial and nuclear DNA are now efficient and cost-saving approaches, and have become the gold-standard technique in diagnostic laboratories.
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Affiliation(s)
- Giulia Barcia
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Zahra Assouline
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Maryse Magen
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Alessandra Pennisi
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Agnès Rötig
- Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Arnold Munnich
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Jean-Paul Bonnefont
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Julie Steffann
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
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15
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Wallace DC. CRISPR-Free Mitochondrial DNA Base Editing. CRISPR J 2020; 3:228-230. [PMID: 32833534 DOI: 10.1089/crispr.2020.29101.dwa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Sreekumar PG, Kannan R. Mechanisms of protection of retinal pigment epithelial cells from oxidant injury by humanin and other mitochondrial-derived peptides: Implications for age-related macular degeneration. Redox Biol 2020; 37:101663. [PMID: 32768357 PMCID: PMC7767738 DOI: 10.1016/j.redox.2020.101663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/18/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023] Open
Abstract
The mitochondrial-derived peptides (MDPs) are a new class of small open reading frame encoded polypeptides with pleiotropic properties. The prominent members are Humanin (HN) and small HN-like peptide (SHLP) 2, which encode 16S rRNA, while mitochondrial open reading frame of the twelve S c (MOTS-c) encodes 12S rRNA of the mitochondrial genome. While the multifunctional properties of HN and its analog 14-HNG have been well documented, their protective role in the retinal pigment epithelium (RPE)/retina has been investigated only recently. In this review, we have summarized the multiple effects of HN and its analogs, SHLP2 and MOTS-c in oxidatively stressed human RPE and the regulatory pathways of signaling, mitochondrial function, senescence, and inter-organelle crosstalk. Emphasis is given to the mitochondrial functions such as biogenesis, bioenergetics, and autophagy in RPE undergoing oxidative stress. Further, the potential use of HN and its analogs in the prevention of age-related macular degeneration (AMD) are also presented. In addition, the role of novel, long-acting HN elastin-like polypeptides in nanotherapy of AMD and other ocular diseases stemming from oxidative damage is discussed. It is expected MDPs will become a promising group of mitochondrial peptides with valuable therapeutic applications in the treatment of retinal diseases.
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Affiliation(s)
- Parameswaran G Sreekumar
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA
| | - Ram Kannan
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA; Stein Eye Institute, Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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17
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Wang D, Xiang H, Ning C, Liu H, Liu JF, Zhao X. Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. Brief Bioinform 2020; 21:1368-1377. [PMID: 31204429 DOI: 10.1093/bib/bbz060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic associations between mitochondrial DNA (mtDNA) and economic traits have been widely reported for pigs, which indicate the importance of mtDNA. However, studies on mtDNA heteroplasmy in pigs are rare. Next generation sequencing (NGS) methodologies have emerged as a promising genomic approach for detection of mitochondrial heteroplasmy. Due to the short reads, flexible bioinformatic analyses and the contamination of nuclear mitochondrial sequences (NUMTs), NGS was expected to increase false-positive detection of heteroplasmy. In this study, Sanger sequencing was performed as a gold standard to detect heteroplasmy with a detection sensitivity of 5% in pigs and then one whole-genome sequencing method (WGS) and two mtDNA enrichment sequencing methods (Capture and LongPCR) were carried out. The aim of this study was to determine whether mitochondrial heteroplasmy identification from NGS data was affected by NUMTs. We find that WGS generated more false intra-individual polymorphisms and less mapping specificity than the two enrichment sequencing methods, suggesting NUMTs indeed led to false-positive mitochondrial heteroplasmies from NGS data. In addition, to accurately detect mitochondrial diversity, three commonly used tools-SAMtools, VarScan and GATK-with different parameter values were compared. VarScan achieved the best specificity and sensitivity when considering the base alignment quality re-computation and the minimum variant frequency of 0.25. It also suggested bioinformatic workflow interfere in the identification of mtDNA SNPs. In conclusion, intra-individual polymorphism in pig mitochondria from NGS data was confused with NUMTs, and mtDNA-specific enrichment is essential before high-throughput sequencing in the detection of mitochondrial genome sequences.
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Affiliation(s)
- Dan Wang
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hai Xiang
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong 528231, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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18
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Morris MJ, Hesson LB, Youngson NA. Non-CpG methylation biases bisulphite PCR towards low or unmethylated mitochondrial DNA: recommendations for the field. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa001. [PMID: 32154030 PMCID: PMC7055202 DOI: 10.1093/eep/dvaa001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 05/04/2023]
Abstract
Mitochondrial DNA (mtDNA) is a circular genome of 16 kb that is present in multiple copies in mitochondria. mtDNA codes for genes that contribute to mitochondrial structure and function. A long-standing question has asked whether mtDNA is epigenetically regulated similarly to the nuclear genome. Recently published data suggest that unlike the nuclear genome where CpG methylation is the norm, mtDNA is methylated predominantly at non-CpG cytosines. This raises important methodological considerations for future investigations. In particular, existing bisulphite PCR techniques may be unsuitable due to primers being biased towards amplification from unmethylated mtDNA. Here, we describe how this may have led to previous studies underestimating the level of mtDNA methylation and reiterate methodological strategies for its accurate assessment.
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Affiliation(s)
| | - Luke B Hesson
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
| | - Neil A Youngson
- School of Medical Sciences, UNSW Sydney, NSW 2052, Australia
- The Institute of Hepatology, Foundation for Liver Research, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Correspondence address. The Institute of Hepatology, Foundation for Liver Research, London, UK. Tel : +44 (0)20 7255 9835; E-mail:
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Strobl C, Churchill Cihlar J, Lagacé R, Wootton S, Roth C, Huber N, Schnaller L, Zimmermann B, Huber G, Lay Hong S, Moura-Neto R, Silva R, Alshamali F, Souto L, Anslinger K, Egyed B, Jankova-Ajanovska R, Casas-Vargas A, Usaquén W, Silva D, Barletta-Carrillo C, Tineo DH, Vullo C, Würzner R, Xavier C, Gusmão L, Niederstätter H, Bodner M, Budowle B, Parson W. Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. Forensic Sci Int Genet 2019; 42:244-251. [PMID: 31382159 DOI: 10.1016/j.fsigen.2019.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/21/2019] [Indexed: 12/24/2022]
Abstract
The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.
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Affiliation(s)
- Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Robert Lagacé
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Seah Lay Hong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Rodrigo Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosane Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Farida Alshamali
- Dubai Police, Gen. Dept. Forensic Science & Criminology, Dubai, United Arab Emirates
| | - Luis Souto
- Laboratorio de Genética Aplicada, Departamento de Biologia, Universidade de Aveiro, Portugal
| | | | - Balazs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Renata Jankova-Ajanovska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Macedonia
| | - Andrea Casas-Vargas
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Wiliam Usaquén
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Dayse Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - Dean Herman Tineo
- Universidad Nacional Mayor de San Marcos, Instituto de Medicina Legal del Perú, Lima, Peru
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology team (EAAF), Córdoba, Argentina
| | - Reinhard Würzner
- Division of Hygiene & Med. Microbiology, Medical University of Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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Misassembly of long reads undermines de novo-assembled ethnicity-specific genomes: validation in a Chinese Han population. Hum Genet 2019; 138:757-769. [DOI: 10.1007/s00439-019-02032-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/21/2019] [Indexed: 01/05/2023]
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21
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Wheeler JH, Young CKJ, Young MJ. Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization. CURRENT PROTOCOLS IN TOXICOLOGY 2019; 80:e75. [PMID: 30982231 PMCID: PMC6581606 DOI: 10.1002/cptx.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joel H. Wheeler
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K. J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Matthew J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
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Marom S, Blumberg A, Kundaje A, Mishmar D. mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis. iScience 2019; 12:141-151. [PMID: 30684873 PMCID: PMC6352746 DOI: 10.1016/j.isci.2018.12.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/08/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023] Open
Abstract
Unlike the nuclear genome, the mammalian mitochondrial genome (mtDNA) is thought to be coated solely by mitochondrial transcription factor A (TFAM), whose binding sequence preferences are debated. Therefore, higher-order mtDNA organization is considered much less regulated than both the bacterial nucleoid and the nuclear chromatin. However, our recently identified conserved DNase footprinting pattern in human mtDNA, which co-localizes with regulatory elements and responds to physiological conditions, likely reflects a structured higher-order mtDNA organization. We hypothesized that this pattern emerges during embryogenesis. To test this hypothesis, we analyzed assay for transposase-accessible chromatin sequencing (ATAC-seq) results collected during the course of mouse and human early embryogenesis. Our results reveal, for the first time, a gradual and dynamic emergence of the adult mtDNA footprinting pattern during embryogenesis of both mammals. Taken together, our findings suggest that the structured adult chromatin-like mtDNA organization is gradually formed during mammalian embryogenesis. Mouse and human mtDNA ATAC-seq footprinting patterns are formed during embryogenesis mtDNA footprinting sites were either occupied in preimplantation or appeared later mtDNA footprinting associates with regulatory elements and protein-binding sites The mtDNA footprinting sites tend to harbor secondary structures
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Affiliation(s)
- Shani Marom
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Amit Blumberg
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Dan Mishmar
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
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Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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Abicht A, Scharf F, Kleinle S, Schön U, Holinski-Feder E, Horvath R, Benet-Pagès A, Diebold I. Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method. Mol Genet Genomic Med 2018; 6:1188-1198. [PMID: 30406974 PMCID: PMC6305657 DOI: 10.1002/mgg3.500] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/21/2023] Open
Abstract
Background The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next‐Generation Sequencing (NGS) technology offers a robust high‐throughput platform for nuclear and mitochondrial DNA (mtDNA) analyses. Method We developed a custom Agilent SureSelect Mitochondrial and Nuclear Disease Panel (Mito‐aND‐Panel) capture kit that allows parallel enrichment for subsequent NGS‐based sequence analysis of nuclear mitochondrial disease‐related genes and the complete mtDNA genome. Sequencing of enriched mtDNA simultaneously with nuclear genes was compared with the separated sequencing of the mitochondrial genome and whole exome sequencing (WES). Results The Mito‐aND‐Panel permits accurate detection of low‐level mtDNA heteroplasmy due to a very high sequencing depth compared to standard diagnostic procedures using Sanger sequencing/SNaPshot and WES which is crucial to identify maternally inherited mitochondrial disorders. Conclusion We established a NGS‐based method with combined sequencing of the complete mtDNA and nuclear genes which enables a more sensitive heteroplasmy detection of mtDNA mutations compared to traditional methods. Because the method promotes the analysis of mtDNA variants in large cohorts, it is cost‐effective and simple to setup, we anticipate this is a highly relevant method for sequence‐based genetic diagnosis in clinical diagnostic applications.
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Affiliation(s)
- Angela Abicht
- Medical Genetic Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | | | | | - Rita Horvath
- Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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Blumberg A, Danko CG, Kundaje A, Mishmar D. A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome Res 2018; 28:1158-1168. [PMID: 30002158 PMCID: PMC6071632 DOI: 10.1101/gr.230409.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/13/2018] [Indexed: 12/16/2022]
Abstract
Human mitochondrial DNA (mtDNA) is believed to lack chromatin and histones. Instead, it is coated solely by the transcription factor TFAM. We asked whether mtDNA packaging is more regulated than once thought. To address this, we analyzed DNase-seq experiments in 324 human cell types and found, for the first time, a pattern of 29 mtDNA Genomic footprinting (mt-DGF) sites shared by ∼90% of the samples. Their syntenic conservation in mouse DNase-seq experiments reflect selective constraints. Colocalization with known mtDNA regulatory elements, with G-quadruplex structures, in TFAM-poor sites (in HeLa cells) and with transcription pausing sites, suggest a functional regulatory role for such mt-DGFs. Altered mt-DGF pattern in interleukin 3-treated CD34+ cells, certain tissue differences, and significant prevalence change in fetal versus nonfetal samples, offer first clues to their physiological importance. Taken together, human mtDNA has a conserved protein-DNA organization, which is likely involved in mtDNA regulation.
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Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105 Israel
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105 Israel
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26
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Barshad G, Blumberg A, Cohen T, Mishmar D. Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes. Genome Res 2018; 28:952-967. [PMID: 29903725 PMCID: PMC6028125 DOI: 10.1101/gr.226324.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/31/2018] [Indexed: 01/04/2023]
Abstract
Oxidative phosphorylation (OXPHOS), a fundamental energy source in all human tissues, requires interactions between mitochondrial (mtDNA)- and nuclear (nDNA)-encoded protein subunits. Although such interactions are fundamental to OXPHOS, bi-genomic coregulation is poorly understood. To address this question, we analyzed ∼8500 RNA-seq experiments from 48 human body sites. Despite well-known variation in mitochondrial activity, quantity, and morphology, we found overall positive mtDNA-nDNA OXPHOS genes' co-expression across human tissues. Nevertheless, negative mtDNA-nDNA gene expression correlation was identified in the hypothalamus, basal ganglia, and amygdala (subcortical brain regions, collectively termed the "primitive" brain). Single-cell RNA-seq analysis of mouse and human brains revealed that this phenomenon is evolutionarily conserved, and both are influenced by brain cell types (involving excitatory/inhibitory neurons and nonneuronal cells) and by their spatial brain location. As the "primitive" brain is highly oxidative, we hypothesized that such negative mtDNA-nDNA co-expression likely controls for the high mtDNA transcript levels, which enforce tight OXPHOS regulation, rather than rewiring toward glycolysis. Accordingly, we found "primitive" brain-specific up-regulation of lactate dehydrogenase B (LDHB), which associates with high OXPHOS activity, at the expense of LDHA, which promotes glycolysis. Analyses of co-expression, DNase-seq, and ChIP-seq experiments revealed candidate RNA-binding proteins and CEBPB as the best regulatory candidates to explain these phenomena. Finally, cross-tissue expression analysis unearthed tissue-dependent splice variants and OXPHOS subunit paralogs and allowed revising the list of canonical OXPHOS transcripts. Taken together, our analysis provides a comprehensive view of mito-nuclear gene co-expression across human tissues and provides overall insights into the bi-genomic regulation of mitochondrial activities.
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Affiliation(s)
- Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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27
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Gidlund EK, von Walden F, Venojärvi M, Risérus U, Heinonen OJ, Norrbom J, Sundberg CJ. Humanin skeletal muscle protein levels increase after resistance training in men with impaired glucose metabolism. Physiol Rep 2018; 4:4/23/e13063. [PMID: 27923980 PMCID: PMC5357820 DOI: 10.14814/phy2.13063] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022] Open
Abstract
Humanin (HN) is a mitochondrially encoded and secreted peptide linked to glucose metabolism and tissue protecting mechanisms. Whether skeletal muscle HN gene or protein expression is influenced by exercise remains unknown. In this intervention study we show, for the first time, that HN protein levels increase in human skeletal muscle following 12 weeks of resistance training in persons with prediabetes. Male subjects (n = 55) with impaired glucose regulation (IGR) were recruited and randomly assigned to resistance training, Nordic walking or a control group. The exercise interventions were performed three times per week for 12 weeks with progressively increased intensity during the intervention period. Biopsies from the vastus lateralis muscle and venous blood samples were taken before and after the intervention. Skeletal muscle and serum protein levels of HN were analyzed as well as skeletal muscle gene expression of the mitochondrially encoded gene MT‐RNR2, containing the open reading frame for HN. To elucidate mitochondrial training adaptation, mtDNA, and nuclear DNA as well as Citrate synthase were measured. Skeletal muscle HN protein levels increased by 35% after 12 weeks of resistance training. No change in humanin protein levels was seen in serum in any of the intervention groups. There was a significant correlation between humanin levels in serum and the improvements in the 2 h glucose loading test in the resistance training group. The increase in HN protein levels in skeletal muscle after regular resistance training in prediabetic males may suggest a role for HN in the regulation of glucose metabolism. Given the preventative effect of exercise on diabetes type 2, the role of HN as a mitochondrially derived peptide and an exercise‐responsive mitokine warrants further investigation.
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Affiliation(s)
- Eva-Karin Gidlund
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinand von Walden
- Neuropediatrics Unit, Department of Women's and Children's Health, Karolinska Institutet and Astrid Lindgren's Pediatric Hospital, Stockholm, Sweden
| | - Mika Venojärvi
- Institute of Biomedicine, Sports and exercise medicine, University of Eastern Finland, Kuopio, Finland
| | - Ulf Risérus
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Olli J Heinonen
- Paavo Nurmi Centre and Departmen of Health & Physical Activity, University of Turku, Turku, Finland
| | - Jessica Norrbom
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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28
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Hazkani-Covo E, Martin WF. Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health. Genome Biol Evol 2017; 9:1190-1203. [PMID: 28444372 PMCID: PMC5570036 DOI: 10.1093/gbe/evx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 12/28/2022] Open
Abstract
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health.
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Affiliation(s)
- Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
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29
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Singh KK, Choudhury AR, Tiwari HK. Numtogenesis as a mechanism for development of cancer. Semin Cancer Biol 2017; 47:101-109. [PMID: 28511886 DOI: 10.1016/j.semcancer.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/20/2017] [Accepted: 10/14/2016] [Indexed: 01/10/2023]
Abstract
Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.
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Affiliation(s)
- Keshav K Singh
- Departments of Genetics, Birmingham, AL, 35294, USA; Departments of Pathology, Birmingham, AL, 35294, USA; Departments of Environmental Health, Center for Free Radical Biology, Birmingham, AL, 35294, USA; Center for Aging, Birmingham, AL, 35294, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, AL, 35294, USA; Birmingham Veterans Affairs Medical Center, AL, 35294, USA.
| | | | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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30
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Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome Res 2017; 27:362-373. [PMID: 28049628 PMCID: PMC5340964 DOI: 10.1101/gr.209924.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA (mtDNA) genes are long known to be cotranscribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end, we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TISs) in the heavy and light strands revealed a novel conserved transcription pausing site near the light-strand TIS. This pausing site correlated with the presence of a bacterial pausing sequence motif, with reduced SNP density, and with a DNase footprinting signal in all tested cells. Its location within conserved sequence block 3 (CSBIII), just upstream of the known transcription–replication transition point, suggests involvement in such transition. Analysis of nonhuman organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (Pan troglodytes, Macaca mulatta, Rattus norvegicus, and Mus musculus) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila melanogaster and Caenorhabditis elegans) profoundly diverged. Our approach paves the path toward in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes.
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Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
| | - Edward J Rice
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
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31
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Seligmann H. Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons. J Theor Biol 2016; 414:76-90. [PMID: 27899286 DOI: 10.1016/j.jtbi.2016.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins. Analyses assuming endoproteinase GluC and elastase digestions (cleavages after residues D, E, and A, L, I, V, respectively) detect additional peptides colocalizing with detected non-canonical RNAs. Analyses detect fewer peptides matching GluC-, elastase- than trypsin-digestions: artificial trypsin-digestion outweighs natural proteolysis. Results suggest occurrences of complete proteins entirely matching non-canonical, superimposed encoding(s). Protein-coding after bijective transformations could explain genetic code symmetries, such as along Rumer's transformation.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, IHU (Institut Hospitalo-Universitaire), Aix-Marseille University, Marseille, France.
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32
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Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns. PLoS Genet 2016; 12:e1006407. [PMID: 27812116 PMCID: PMC5094714 DOI: 10.1371/journal.pgen.1006407] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/06/2016] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial DNA (mtDNA) variants have been traditionally used as markers to trace ancient population migrations. Although experiments relying on model organisms and cytoplasmic hybrids, as well as disease association studies, have served to underline the functionality of certain mtDNA SNPs, only little is known of the regulatory impact of ancient mtDNA variants, especially in terms of gene expression. By analyzing RNA-seq data of 454 lymphoblast cell lines from the 1000 Genomes Project, we found that mtDNA variants defining the most common African genetic background, the L haplogroup, exhibit a distinct overall mtDNA gene expression pattern, which was independent of mtDNA copy numbers. Secondly, intra-population analysis revealed subtle, yet significant, expression differences in four tRNA genes. Strikingly, the more prominent African mtDNA gene expression pattern best correlated with the expression of nuclear DNA-encoded RNA-binding proteins, and with SNPs within the mitochondrial RNA-binding proteins PTCD1 and MRPS7. Our results thus support the concept of an ancient regulatory transition of mtDNA-encoded genes as humans left Africa to populate the rest of the world. The mitochondrion is an organelle found in all cells of our body and plays a significant role in the energy and heat production. This is the only organelle in animal cells harboring its own genome outside of the nucleus. Mitochondrial DNA (mtDNA) variants have been traditionally used as neutral markers to trace ancient population migrations. As a result, the functional impact of human mtDNA population variants on gene regulation is poorly understood. To address this question, we analyzed available data of mtDNA gene expression pattern in a large group of individuals (454) from diverse human populations. Here, we show for the first time that the ancient migration of humans out of Africa correlated with differences in mitochondrial gene expression patterns, and could be explained by the activity of certain RNA-binding proteins. These findings suggest a major mitochondrial regulatory transition, as humans left Africa to populate the rest of the world.
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Khan N. Recent advancements in diagnostic tools in mitochondrial energy metabolism diseases. Adv Med Sci 2016; 61:244-248. [PMID: 26998934 DOI: 10.1016/j.advms.2016.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/27/2015] [Accepted: 02/05/2016] [Indexed: 01/02/2023]
Abstract
The involvement of mitochondrial energy metabolism in human disease ranges from rare monogenic disease to common diseases and aging with a genetic and/or lifestyle/environmental cause. This wide ranging involvement is due to the central role played by mitochondrion in cellular metabolism, its role in cellular perception of threats and its role in effecting responses to these threats. Investigating mitochondrial function/dysfunction or mitochondria-associated cell-biological responses have thus become a common finding where the pathogenic processes are investigated. Although, such investigations are warranted, it is not always clear if mitochondria can indeed be associated with cause or merely playing a responsive role in disease pathology. As this key question is also essential to disease progression and therapy, it should be recognized in investigative design. We herewith, present an overview of the current approaches and technologies used and the practicalities around these technologies.
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Affiliation(s)
- Naazneen Khan
- Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa.
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Payne BAI, Gardner K, Coxhead J, Chinnery PF. Deep resequencing of mitochondrial DNA. Methods Mol Biol 2015; 1264:59-66. [PMID: 25631003 DOI: 10.1007/978-1-4939-2257-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Detecting and quantifying low-level variants in mitochondrial DNA (mtDNA) by deep resequencing can lead to important insights into the biology of mtDNA in health and disease. Massively parallel ("next-generation") sequencing is an attractive tool owing to the great depth and breadth of coverage. However, there are several important challenges to be considered when using this method, in particular: the avoidance of false discovery due to the unintended amplification of nuclear pseudogenes and the approach to delineating signal from noise at very great depths of coverage. Here we present methods for whole mtDNA genome deep sequencing (Illumina MiSeq) and short amplicon deep sequencing (Roche 454 GS-FLX).
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Affiliation(s)
- Brendan A I Payne
- Mitochondrial Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle-upon-Tyne, NE1 3BZ, UK,
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Paharkova V, Alvarez G, Nakamura H, Cohen P, Lee KW. Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production. Mol Cell Endocrinol 2015; 413:96-100. [PMID: 26116236 DOI: 10.1016/j.mce.2015.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
Evidence for the putative mitochondrial origin of the Humanin (HN) peptide has been lacking, although its cytoprotective activity has been demonstrated in a variety of organismal and cellular systems. We sought to establish proof-of-principle for a mitochondria-derived peptide (MDP) in a rat-derived cellular system as the rat HN sequence is predicted to lack nuclear insertions of mitochondrial origin (NUMT). We found that the rat HN (Rattin; rHN) homologue is derived from the mitochondrial genome as evidenced by decreased production in Rho-0 cells, and that peptide translation occurs in the mitochondria as it is unaffected by cycloheximide. Rat HN localizes to the mitochondria in cellular subfractionation and immunohistochemical studies. Addition of a HN analogue to isolated mitochondria from rat INS-1 beta cells reduced hydrogen peroxide production by 55%. In summary, a locally bioactive peptide is derived and translated from an open reading frame (ORF) within rat mitochondrial DNA encoding 16S rRNA.
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Affiliation(s)
- Vladislava Paharkova
- Pediatric Endocrinology, Mattel Children's Hospital UCLA; David Geffen School of Medicine at UCLA, USA
| | - Griselda Alvarez
- Pediatric Endocrinology, Mattel Children's Hospital UCLA; David Geffen School of Medicine at UCLA, USA
| | - Hiromi Nakamura
- Pediatric Endocrinology, Mattel Children's Hospital UCLA; David Geffen School of Medicine at UCLA, USA
| | - Pinchas Cohen
- Davis School of Gerontology, University of Southern California, USA
| | - Kuk-Wha Lee
- Pediatric Endocrinology, Mattel Children's Hospital UCLA; David Geffen School of Medicine at UCLA, USA.
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Truong DM, Hewitt FC, Hanson JH, Cui X, Lambowitz AM. Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation. PLoS Genet 2015; 11:e1005422. [PMID: 26241656 PMCID: PMC4524724 DOI: 10.1371/journal.pgen.1005422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/05/2015] [Indexed: 12/22/2022] Open
Abstract
Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a “ribozyme”) and an intron-encoded reverse transcriptase, which function together to promote intron integration into new DNA sites by a mechanism termed “retrohoming”. Although mobile group II introns splice and retrohome efficiently in bacteria, all examined thus far function inefficiently in eukaryotes, where their ribozyme activity is limited by low Mg2+ concentrations, and intron-containing transcripts are subject to nonsense-mediated decay (NMD) and translational repression. Here, by using RNA polymerase II to express a humanized group II intron reverse transcriptase and T7 RNA polymerase to express intron transcripts resistant to NMD, we find that simply supplementing culture medium with Mg2+ induces the Lactococcus lactis Ll.LtrB intron to retrohome into plasmid and chromosomal sites, the latter at frequencies up to ~0.1%, in viable HEK-293 cells. Surprisingly, under these conditions, the Ll.LtrB intron reverse transcriptase is required for retrohoming but not for RNA splicing as in bacteria. By using a genetic assay for in vivo selections combined with deep sequencing, we identified intron RNA mutations that enhance retrohoming in human cells, but <4-fold and not without added Mg2+. Further, the selected mutations lie outside the ribozyme catalytic core, which appears not readily modified to function efficiently at low Mg2+ concentrations. Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ribozyme core that limit how much group II intron retrohoming in eukaryotes can be enhanced. These findings have implications for group II intron use for gene targeting in eukaryotes and suggest how differences in intracellular Mg2+ concentrations between bacteria and eukarya may have impacted the evolution of introns and gene expression mechanisms. Mobile group II introns are bacterial retrotransposons that are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase, which together promote intron mobility to new DNA sites by a mechanism called retrohoming. Although found in bacteria, archaea and eukaryotic organelles, group II introns are absent from eukaryotic nuclear genomes, where host defenses impede their expression and lower intracellular Mg2+ concentrations limit their ribozyme activity. Here, we developed a mobile group II intron expression system that bypasses expression barriers and show that simply adding Mg2+ to culture medium enables group II intron retrohoming into plasmid and chromosomal target sites in human cells at appreciable frequencies. Genetic selections and deep sequencing identified intron RNA mutations that moderately enhance retrohoming in human cells, but not without added Mg2+. Thus, low Mg2+ concentrations in human cells are a natural barrier to efficient retrohoming that is not readily overcome by mutational variation and selection. Our results have implications for group II intron use for gene targeting in higher organisms and highlight the impact of different intracellular environments on intron evolution and gene expression mechanisms in bacteria and eukarya.
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Affiliation(s)
- David M. Truong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - F. Curtis Hewitt
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Joseph H. Hanson
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Xiaoxia Cui
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alan M. Lambowitz
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MTM, van't Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res 2015; 25:814-24. [PMID: 25963125 PMCID: PMC4448678 DOI: 10.1101/gr.190470.115] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
Abstract
Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.
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Affiliation(s)
- Young Seok Ju
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - William Mifsud
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Beiyuan Fu
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Helen R Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Lucy Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Anthony Fullam
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Moritz Gerstung
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jyoti Nangalia
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Anthony R Green
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Carlos Caldas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Åke Borg
- BioCare, Strategic Cancer Research Program, SE-223 81 Lund, Sweden; CREATE Health, Strategic Centre for Translational Cancer Research, SE-221 00 Lund, Sweden; Department of Oncology and Pathology, Lund University Cancer Center, SE-221 85 Lund, Sweden
| | - Andrew Tutt
- Breakthrough Breast Cancer Research Unit, Research Oncology, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, 230-0045 Yokohama, Japan; National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Laura J van't Veer
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA; Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Benita K T Tan
- Department of General Surgery, Singapore General Hospital, Singapore 169608
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Paul N Span
- Department of Radiation Oncology and Department of Laboratory Medicine, Radboud University Medical Center, 6525 HP Nijmegen, Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Anne Vincent-Salomon
- Institut Curie, INSERM U934 and Department of Tumor Biology, 75248 Paris cédex 05, France
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | | | | | - Adrienne M Flanagan
- Royal National Orthopaedic Hospital, Middlesex HA7 4LP, United Kingdom; UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Christopher Foster
- University of Liverpool and HCA Pathology Laboratories, London WC1E 6JA, United Kingdom
| | - David E Neal
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, United Kingdom; Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Colin Cooper
- Institute of Cancer Research, Sutton, London SM2 5NG, United Kingdom; Department of Biological Sciences and School of Medicine, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton SM2 5NG, United Kingdom; Royal Marsden NHS Foundation Trust, London SW3 6JJ and Sutton SM2 5PT, United Kingdom
| | | | - Sunil R Lakhani
- University of Queensland, School of Medicine, Brisbane, QLD 4006, Australia; Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia; University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD 4029, Australia
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000 Brussels, Belgium
| | - Gilles Thomas
- Université Lyon 1, Institut National du Cancer (INCa)-Synergie, 69008 Lyon, France
| | - Andrea L Richardson
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Colin A Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Alastair M Thompson
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res 2014; 42:12640-9. [PMID: 25348406 PMCID: PMC4227756 DOI: 10.1093/nar/gku1038] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon that has been previously limited to the study of static reference genomes. The recent advancement of high throughput sequencing has enabled an expanded exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) within human populations. We have developed an approach to discover and genotype novel Numt insertions using whole genome, paired-end sequencing data. We have applied this method to a thousand individuals in 20 populations from the 1000 Genomes Project and other datasets and identified 141 new sites of Numt insertions, extending our current knowledge of existing NumtS by almost 20%. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases that differ in some respects from previous studies on older, fixed NumtS in the reference genome. We determined the complete inserted sequence for a subset of these events and have identified a number of nearly full-length mitochondrial genome insertions into nuclear chromosomes. We further define their age and origin of insertion and present an analysis of their potential impact to ongoing studies of mitochondrial heteroplasmy and disease.
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Affiliation(s)
- Gargi Dayama
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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Blumberg A, Sri Sailaja B, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D. Transcription factors bind negatively selected sites within human mtDNA genes. Genome Biol Evol 2014; 6:2634-46. [PMID: 25245407 PMCID: PMC4224337 DOI: 10.1093/gbe/evu210] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcription of mitochondrial DNA (mtDNA)-encoded genes is thought to be regulated by a handful of dedicated transcription factors (TFs), suggesting that mtDNA genes are separately regulated from the nucleus. However, several TFs, with known nuclear activities, were found to bind mtDNA and regulate mitochondrial transcription. Additionally, mtDNA transcriptional regulatory elements, which were proved important in vitro, were harbored by a deletion that normally segregated among healthy individuals. Hence, mtDNA transcriptional regulation is more complex than once thought. Here, by analyzing ENCODE chromatin immunoprecipitation sequencing (ChIP-seq) data, we identified strong binding sites of three bona fide nuclear TFs (c-Jun, Jun-D, and CEBPb) within human mtDNA protein-coding genes. We validated the binding of two TFs by ChIP-quantitative polymerase chain reaction (c-Jun and Jun-D) and showed their mitochondrial localization by electron microscopy and subcellular fractionation. As a step toward investigating the functionality of these TF-binding sites (TFBS), we assessed signatures of selection. By analyzing 9,868 human mtDNA sequences encompassing all major global populations, we recorded genetic variants in tips and nodes of mtDNA phylogeny within the TFBS. We next calculated the effects of variants on binding motif prediction scores. Finally, the mtDNA variation pattern in predicted TFBS, occurring within ChIP-seq negative-binding sites, was compared with ChIP-seq positive-TFBS (CPR). Motifs within CPRs of c-Jun, Jun-D, and CEBPb harbored either only tip variants or their nodal variants retained high motif prediction scores. This reflects negative selection within mtDNA CPRs, thus supporting their functionality. Hence, human mtDNA-coding sequences may have dual roles, namely coding for genes yet possibly also possessing regulatory potential.
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Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Badi Sri Sailaja
- Department of Genetics, The Institute of Life Sciences, and The Edmond Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Israel
| | - Anshul Kundaje
- Department of Genetics, Stanford University Department of Computer Science, Stanford University
| | - Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sara Dadon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Shimrit Shmorak
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Medical School, Ein Karem, Jerusalem, Israel
| | - Eitan Shaulian
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Medical School, Ein Karem, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, The Institute of Life Sciences, and The Edmond Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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López-Gallardo E, Emperador S, Solano A, Llobet L, Martín-Navarro A, López-Pérez MJ, Briones P, Pineda M, Artuch R, Barraquer E, Jericó I, Ruiz-Pesini E, Montoya J. Expanding the clinical phenotypes of MT-ATP6 mutations. Hum Mol Genet 2014; 23:6191-200. [DOI: 10.1093/hmg/ddu339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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41
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Distribution of nuclear mitochondrial pseudogenes in three pollinator fig wasps associated with Ficus pumila. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2014. [DOI: 10.1016/j.actao.2013.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Yen HC, Li SL, Hsu WC, Tang P. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system. PLoS One 2014; 9:e92817. [PMID: 24664244 PMCID: PMC3963942 DOI: 10.1371/journal.pone.0092817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/25/2014] [Indexed: 01/02/2023] Open
Abstract
High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.
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Affiliation(s)
- Hsiu-Chuan Yen
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- * E-mail:
| | - Shiue-Li Li
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Wei-Chien Hsu
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Petrus Tang
- Department of Public Health and Parasitology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
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43
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Song S, Jiang F, Yuan J, Guo W, Miao Y. Exceptionally high cumulative percentage of NUMTs originating from linear mitochondrial DNA molecules in the Hydra magnipapillata genome. BMC Genomics 2013; 14:447. [PMID: 23826818 PMCID: PMC3716686 DOI: 10.1186/1471-2164-14-447] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 07/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background In contrast to most animal genomes, mitochondrial genomes in species belonging to the phylum Cnidaria show distinct variations in genome structure, including the mtDNA structure (linear or circular) and the presence or absence of introns in protein-coding genes. Therefore, the analysis of nuclear insertions of mitochondrial sequences (NUMTs) in cnidarians allows us to compare the NUMT content in animals with different mitochondrial genome structures. Results NUMT identification in the Hydra magnipapillata, Nematostella vectensis and Acropora digitifera genomes showed that the NUMT density in the H. magnipapillata genome clearly exceeds that in other two cnidarians with circular mitochondrial genomes. We found that H. magnipapillata is an exceptional ancestral metazoan with a high NUMT cumulative percentage but a large genome, and its mitochondrial genome linearisation might be responsible for the NUMT enrichment. We also detected the co-transposition of exonic and intronic fragments within NUMTs in N. vectensis and provided direct evidence that mitochondrial sequences can be transposed into the nuclear genome through DNA-mediated fragment transfer. In addition, NUMT expression analyses showed that NUMTs are co-expressed with adjacent protein-coding genes, suggesting the relevance of their biological function. Conclusions Taken together, our results provide valuable information for understanding the impact of mitochondrial genome structure on the interaction of mitochondrial molecules and nuclear genomes.
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Affiliation(s)
- Shen Song
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
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44
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Grechko VV. The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers. Mol Biol 2013. [DOI: 10.1134/s0026893313010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Abstract
It is well known that remnants of partial or whole copies of mitochondrial DNA, known as Nuclear MiTochondrial sequences (NUMTs), are found in nuclear genomes. Since whole genome sequences have become available, many bioinformatics studies have identified putative NUMTs and from those attempted to infer the factors involved in NUMT creation. These studies conclude that NUMTs represent randomly chosen regions of the mitochondrial genome. There is less consensus regarding the nuclear insertion sites of NUMTs - previous studies have discussed the possible role of retrotransposons, but some recent ones have reported no correlation or even anti-correlation between NUMT sites and retrotransposons. These studies have generally defined NUMT sites using BLAST with default parameters. We analyze a redefined set of human NUMTs, computed with a carefully considered protocol. We discover that the inferred insertion points of NUMTs have a strong tendency to have high-predicted DNA curvature, occur in experimentally defined open chromatin regions and often occur immediately adjacent to A + T oligomers. We also show clear evidence that their flanking regions are indeed rich in retrotransposons. Finally we show that parts of the mitochondrial genome D-loop are under-represented as a source of NUMTs in primate evolution.
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Affiliation(s)
- Junko Tsuji
- Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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46
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Rogers HH, Griffiths-Jones S. Mitochondrial pseudogenes in the nuclear genomes of Drosophila. PLoS One 2012; 7:e32593. [PMID: 22412894 PMCID: PMC3296715 DOI: 10.1371/journal.pone.0032593] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 01/30/2012] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species. However, the numt content of different genomes and their properties is not uniform, and study of these differences provides insight into the mechanisms and dynamics of genome evolution in different organisms. In the genus Drosophila, numts have previously only been identified on a genome-wide scale in the melanogaster subgroup. The present study extends the identification to 11 species of the Drosophila genus. We identify a total of 302 numts and show that the numt complement is highly variable in Drosophilids, ranging from just 4 in D. melanogaster to 67 in D. willistoni, broadly correlating with genome size. Many numts have undergone large-scale rearrangements in the nucleus, including interruptions, inversions, deletions and duplications of sequence of variable size. Estimating the age of the numts in the nucleus by phylogenetic tree reconstruction reveals the vast majority of numts to be recent gains, 90% having arisen on terminal branches of the species tree. By identifying paralogs and counting duplications among the extant numts we estimate that 23% of extant numts arose through post-insertion duplications. We estimate genus average rates of insertion of 0.75 per million years, and a duplication rate of 0.010 duplications per numt per million years.
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Affiliation(s)
- Hubert H. Rogers
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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47
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Behura SK. Rarity of TagSNPs across transferred mtDNA inserts in human genome. Mol Biol 2012. [DOI: 10.1134/s0026893312010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Lloyd AH, Rousseau-Gueutin M, Timmis JN, Sheppard AE, Ayliffe MA. Promiscuous Organellar DNA. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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49
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Polymorphic NumtS trace human population relationships. Hum Genet 2011; 131:757-71. [DOI: 10.1007/s00439-011-1125-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/30/2011] [Indexed: 11/26/2022]
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50
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Ramos A, Barbena E, Mateiu L, del Mar González M, Mairal Q, Lima M, Montiel R, Aluja MP, Santos C. Nuclear insertions of mitochondrial origin: Database updating and usefulness in cancer studies. Mitochondrion 2011; 11:946-53. [DOI: 10.1016/j.mito.2011.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/10/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
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