151
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Prada-Luengo I, Krogh A, Maretty L, Regenberg B. Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. BMC Bioinformatics 2019; 20:663. [PMID: 31830908 PMCID: PMC6909605 DOI: 10.1186/s12859-019-3160-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/14/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data. RESULTS Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision. CONCLUSION Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at https://github.com/iprada/Circle-Map.
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Affiliation(s)
- Iñigo Prada-Luengo
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.
| | - Anders Krogh
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.,Department of Computer Science, University of Copenhagen, Universitetsparken 1, DK-2100, København Ø, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
| | - Birgitte Regenberg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.
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152
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Hull RM, King M, Pizza G, Krueger F, Vergara X, Houseley J. Transcription-induced formation of extrachromosomal DNA during yeast ageing. PLoS Biol 2019; 17:e3000471. [PMID: 31794573 PMCID: PMC6890164 DOI: 10.1371/journal.pbio.3000471] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper-resistance gene CUP1. Transcription of the tandemly repeated CUP1 gene causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2, Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant, we find that CUP1 eccDNA does not replicate efficiently, and high-copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment. Transcription can cause the de novo formation of protein-coding extrachromosomal DNA that accumulates in ageing yeast cells; these extrachromosomal circular DNA molecules form frequently by a DNA double strand break repair mechanism.
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Affiliation(s)
- Ryan M. Hull
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Michelle King
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Grazia Pizza
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Felix Krueger
- Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom
| | - Xabier Vergara
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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153
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Yerlici VT, Lu MW, Hoge CR, Miller RV, Neme R, Khurana JS, Bracht JR, Landweber LF. Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Res 2019; 47:9741-9760. [PMID: 31504770 PMCID: PMC6765146 DOI: 10.1093/nar/gkz725] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/02/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
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Affiliation(s)
- V Talya Yerlici
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael W Lu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Carla R Hoge
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Richard V Miller
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rafik Neme
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jaspreet S Khurana
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - John R Bracht
- Department of Biology, American University, Washington, DC 20016, USA
| | - Laura F Landweber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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154
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Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 2019; 575:699-703. [PMID: 31748743 PMCID: PMC7094777 DOI: 10.1038/s41586-019-1763-5] [Citation(s) in RCA: 362] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 09/26/2019] [Indexed: 01/01/2023]
Abstract
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.
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Affiliation(s)
- Sihan Wu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Nam Nguyen
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Marcella Erb
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jennifer Santini
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Yarui Diao
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cell Biology, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Wenjing Zhang
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Nathan Jameson
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jack Houston
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California at San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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155
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Iparraguirre L, Prada-Luengo I, Regenberg B, Otaegui D. To Be or Not to Be: Circular RNAs or mRNAs From Circular DNAs? Front Genet 2019; 10:940. [PMID: 31681407 PMCID: PMC6797608 DOI: 10.3389/fgene.2019.00940] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
In recent years, there has been a growing interest in circular RNAs (circRNAs) since they are involved in a wide spectrum of cellular functions that might have a large impact on phenotype and disease. CircRNAs are mainly recorded by RNA-Seq and computational methods focused on the detection of back-splicing junction sequences considered the diagnostic feature of circRNAs. While some protocols remove linear RNA prior to sequencing, many have characterized circRNAs by sorting through total RNA sequencing data without excluding the possibility that some linear RNA can provide the same signal as a circRNA. Recent studies have revealed that circular DNAs of chromosomal origin are common in eukaryotic genomes and that they can be transcribed. Transcription events across the junction of circular DNAs would result in a transcript with a junction similar to those present in circRNAs. Therefore, in this report, we want to draw attention to transcripts from such circular DNAs both as an interesting new player in the transcriptome and also as a confounding factor that must be taken into account when studying circRNAs.
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Affiliation(s)
- Leire Iparraguirre
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | | | | | - David Otaegui
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
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156
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Jacky Lam WK, Dennis Lo YM. Circular RNAs as Urinary Biomarkers. Clin Chem 2019; 65:1196-1198. [PMID: 31409599 DOI: 10.1373/clinchem.2019.309773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/16/2023]
Affiliation(s)
- W K Jacky Lam
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; .,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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157
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Denoth-Lippuner A, Jessberger S. Mechanisms of cellular rejuvenation. FEBS Lett 2019; 593:3381-3392. [PMID: 31197818 DOI: 10.1002/1873-3468.13483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 01/15/2023]
Abstract
Aging leads to changes on an organismal but also cellular level. However, the exact mechanisms of cellular aging in mammals remain poorly understood and the identity and functional role of aging factors, some of which have previously been defined in model organisms such as Saccharomyces cerevisiae, remain elusive. Remarkably, during cellular reprogramming most if not all aging hallmarks are erased, offering a novel entry point to study aging and rejuvenation on a cellular level. On the other hand, direct reprogramming of old cells into cells of a different fate preserves many aging signs. Therefore, investigating the process of reprogramming and comparing it to direct reprogramming may yield novel insights about the clearing of aging factors, which is the basis of rejuvenation. Here, we discuss how reprogramming might lead to rejuvenation of a cell, an organ, or even the whole organism.
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Affiliation(s)
- Annina Denoth-Lippuner
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Switzerland
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Switzerland
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158
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Tandon I, Pal R, Pal JK, Sharma NK. Extrachromosomal circular DNAs: an extra piece of evidence to depict tumor heterogeneity. Future Sci OA 2019; 5:FSO390. [PMID: 31285839 PMCID: PMC6609892 DOI: 10.2144/fsoa-2019-0024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/06/2023] Open
Abstract
The tumor microenvironment (TME) comprises a heterogeneous number and type of cellular and noncellular components that vary in the context of molecular, genomic and epigenomic levels. The genotypic diversity and plasticity within cancer cells are known to be affected by genomic instability and genome alterations. Besides genomic instability within the chromosomal linear DNA, an extra factor appears in the form of extrachromosomal circular DNAs (eccDNAs; 2-20 kbp) and microDNAs (200-400 bp). This extra heterogeneity within cancer cells in the form of an abundance of eccDNAs adds another dimension to the expression of procancer players, such as oncoproteins, acting as a driver for cancer cell survival and proliferation. This article reviews research into eccDNAs centering around cancer plasticity and hallmarks, and discusses these facts in light of therapeutics and biomarker development.
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Affiliation(s)
- Ishita Tandon
- Cancer & Translational Research Lab, Dr DY Patil Biotechnology & Bioinformatics Institute, Dr DY Patil Vidyapeeth, Pune, Maharashtra 411033, India
| | - Roshni Pal
- Cancer & Translational Research Lab, Dr DY Patil Biotechnology & Bioinformatics Institute, Dr DY Patil Vidyapeeth, Pune, Maharashtra 411033, India
| | - Jayanta K Pal
- Cancer & Translational Research Lab, Dr DY Patil Biotechnology & Bioinformatics Institute, Dr DY Patil Vidyapeeth, Pune, Maharashtra 411033, India
| | - Nilesh K Sharma
- Cancer & Translational Research Lab, Dr DY Patil Biotechnology & Bioinformatics Institute, Dr DY Patil Vidyapeeth, Pune, Maharashtra 411033, India
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159
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Paulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. Nucleic Acids Res 2019; 47:4586-4596. [PMID: 30828735 PMCID: PMC6511871 DOI: 10.1093/nar/gkz155] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 01/17/2023] Open
Abstract
Interest in extrachromosomal circular DNA (eccDNA) molecules has increased recently because of their widespread presence in normal cells across every species ranging from yeast to humans, their increased levels in cancer cells and their overlap with oncogenic and drug-resistant genes. However, the majority of eccDNA (microDNA) in mammalian tissues and cell lines are too small to carry protein coding genes. We have tested functional capabilities of microDNA by creating artificial microDNA molecules mimicking known microDNA sequences and have discovered that they express functional small regulatory RNA including microRNA and novel si-like RNA. MicroDNA are transcribed in vitro and in vivo independent of a canonical promoter sequence. MicroDNA that carry miRNA genes form transcripts that are processed by the endogenous RNA-interference pathway into mature miRNA molecules, which repress a luciferase reporter gene as well as endogenous mRNA targets of the miRNA. Further, microDNA that contain sequences of exons repress the endogenous gene from which the microDNA were derived through the formation of novel si-like RNA. We also show that endogenous microDNA associate with RNA polymerases subunits, POLR2H and POLR3F. Together, these results suggest that microDNA may modulate gene expression through the production of both known and novel regulatory small RNA.
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Affiliation(s)
- Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Laura Dillon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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160
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Abstract
Recent reports have demonstrated that oncogene amplification on extrachromosomal DNA (ecDNA) is a frequent event in cancer, providing new momentum to explore a phenomenon first discovered several decades ago. The direct consequence of ecDNA gains in these cases is an increase in DNA copy number of the oncogenes residing on the extrachromosomal element. A secondary effect, perhaps even more important, is that the unequal segregation of ecDNA from a parental tumour cell to offspring cells rapidly increases tumour heterogeneity, thus providing the tumour with an additional array of responses to microenvironment-induced and therapy-induced stress factors and perhaps providing an evolutionary advantage. This Perspectives article discusses the current knowledge and potential implications of oncogene amplification on ecDNA in cancer.
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Affiliation(s)
- Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Vineet Bafna
- Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, San Diego, La Jolla, CA, USA.
- UCSD School of Medicine, La Jolla, CA, USA.
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161
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Sau S, Ghosh SK, Liu YT, Ma CH, Jayaram M. Hitchhiking on chromosomes: A persistence strategy shared by diverse selfish DNA elements. Plasmid 2019; 102:19-28. [PMID: 30726706 DOI: 10.1016/j.plasmid.2019.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
An underlying theme in the segregation of low-copy bacterial plasmids is the assembly of a 'segrosome' by DNA-protein and protein-protein interactions, followed by energy-driven directed movement. Analogous partitioning mechanisms drive the segregation of host chromosomes as well. Eukaryotic extra-chromosomal elements, exemplified by budding yeast plasmids and episomes of certain mammalian viruses, harbor partitioning systems that promote their physical association with chromosomes. In doing so, they indirectly take advantage of the spindle force that directs chromosome movement to opposite cell poles. Molecular-genetic, biochemical and cell biological studies have revealed several unsuspected aspects of 'chromosome hitchhiking' by the yeast 2-micron plasmid, including the ability of plasmid sisters to associate symmetrically with sister chromatids. As a result, the plasmid overcomes the 'mother bias' experienced by plasmids lacking a partitioning system, and elevates itself to near chromosome status in equal segregation. Chromosome association for stable propagation, without direct energy expenditure, may also be utilized by a small minority of bacterial plasmids-at least one case has been reported. Given the near perfect accuracy of chromosome segregation, it is not surprising that elements residing in evolutionarily distant host organisms have converged upon the common strategy of gaining passage to daughter cells as passengers on chromosomes.
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Affiliation(s)
- Soumitra Sau
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Yen-Ting Liu
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA.
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162
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Sun T, Wang K, Liu C, Wang Y, Wang J, Li P. Identification of Extrachromosomal Linear microDNAs Interacted with microRNAs in the Cell Nuclei. Cells 2019; 8:cells8020111. [PMID: 30717295 PMCID: PMC6406244 DOI: 10.3390/cells8020111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/17/2019] [Accepted: 01/31/2019] [Indexed: 01/20/2023] Open
Abstract
Extrachromosomal DNA exists in two forms: Covalently closed circular and linear. While diverse types of circular extrachromosomal DNA have been identified with validated in vivo functions, little is known about linear extrachromosomal DNA. In this study, we identified small, single-stranded linear extrachromosomal DNAs (SSLmicroDNAs) in the nuclei of mouse hearts, mouse brains, HEK293, and HeLa cells. We used a pull-down system based on the single-stranded DNA binding protein RecAf. We found that SSLmicroDNAs aligned predominantly to intergenic and intragenic regions of the genome, owned a variety of single nucleotide polymorphism sites, and strongly associated with H3K27Ac marks. The regions were tens to hundreds of nucleotides long, periodically separated by AT, TT, or AA dinucleotides. It has been demonstrated that SSLmicroDNAs in the nuclei of normal cells target microRNAs, which regulate biological processes. In summary, our present work identified a new form of extrachromosomal DNAs, which function inside nuclei and interact with microRNAs. This finding provides a possible research field into the function of extrachromosomal DNA.
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Affiliation(s)
- Teng Sun
- Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan 030001, China.
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China.
| | - Kun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Cuiyun Liu
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Yin Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Jianxun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
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163
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Zhu J, Chen S, Zhang F, Wang L. Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy? Mol Diagn Ther 2019; 22:515-522. [PMID: 29959693 DOI: 10.1007/s40291-018-0348-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are circular DNAs that are originated from chromosomes, but are independent from chromosomal DNA. The eccDNAs are commonly found in various tissues and cell types, and in both normal and diseased conditions. Due to their highly heterogeneous origins and being widely spread in nearly all eukaryotes, the eccDNAs are believed to reflect the genome's plasticity and instability. With the assistance of next-generation sequencing, more eccDNAs have been characterized at the molecular level. Recently, eccDNAs have been reported as cell-free DNAs in the circulation system. Importantly, these circulating eccDNAs have shown some evidence with disease associations, suggesting their potential utility as a new type of biomarker for disease detection, treatment assessment and progress surveillance. However, many challenges need to be addressed before implementing the eccDNAs as a new source of genetic material for liquid biopsy.
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Affiliation(s)
- Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang, China.
| | - Siyu Chen
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, Heilongjiang, China
| | - Fan Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, Heilongjiang, China
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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164
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Nishioka M, Bundo M, Iwamoto K, Kato T. Somatic mutations in the human brain: implications for psychiatric research. Mol Psychiatry 2019; 24:839-856. [PMID: 30087451 PMCID: PMC6756205 DOI: 10.1038/s41380-018-0129-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/27/2018] [Accepted: 05/25/2018] [Indexed: 01/18/2023]
Abstract
Psychiatric disorders such as schizophrenia and bipolar disorder are caused by complex gene-environment interactions. While recent advances in genomic technologies have enabled the identification of several risk variants for psychiatric conditions, including single-nucleotide variants and copy-number variations, these factors can explain only a portion of the liability to these disorders. Although non-inherited factors had previously been attributed to environmental causes, recent genomic analyses have demonstrated that de novo mutations are among the main non-inherited risk factors for several psychiatric conditions. Somatic mutations in the brain may also explain how stochastic developmental events and environmental insults confer risk for a psychiatric disorder following fertilization. Here, we review evidence regarding somatic mutations in the brains of individuals with and without neuropsychiatric diseases. We further discuss the potential biological mechanisms underlying somatic mutations in the brain as well as the technical issues associated with the detection of somatic mutations in psychiatric research.
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Affiliation(s)
- Masaki Nishioka
- 0000 0001 2151 536Xgrid.26999.3dDivision for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- 0000 0001 0660 6749grid.274841.cDepartment of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan ,0000 0004 1754 9200grid.419082.6PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan.
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165
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Abstract
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.
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166
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Xu K, Ding L, Chang TC, Shao Y, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol 2019; 137:123-137. [PMID: 30267146 PMCID: PMC6338707 DOI: 10.1007/s00401-018-1912-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/15/2018] [Accepted: 09/16/2018] [Indexed: 11/28/2022]
Abstract
Double minute chromosomes are extrachromosomal circular DNA fragments frequently found in brain tumors. To understand their evolution, we characterized the double minutes in paired diagnosis and relapse tumors from a pediatric high-grade glioma and four adult glioblastoma patients. We determined the full structures of the major double minutes using a novel approach combining multiple types of supporting genomic evidence. Among the double minutes identified in the pediatric patient, only one carrying EGFR was maintained at high abundance in both samples, whereas two others were present in only trace amounts at diagnosis but abundant at relapse, and the rest were found either in the relapse sample only or in the diagnosis sample only. For the EGFR-carrying double minutes, we found a secondary somatic deletion in all copies at relapse, after erlotinib treatment. However, the somatic mutation was present at very low frequency at diagnosis, suggesting potential resistance to the EGFR inhibitor. This mutation caused an in-frame RNA transcript to skip exon 16, a novel transcript isoform absent in EST database, as well as about 700 RNA-seq of normal brains that we reviewed. We observed similar patterns involving longitudinal copy number shift of double minutes in another four pairs (diagnosis/relapse) of adult glioblastoma. Overall, in three of five paired tumor samples, we found that although the same oncogenes were amplified at diagnosis and relapse, they were amplified on different double minutes. Our results suggest that double minutes readily evolve, increasing tumor heterogeneity rapidly. Understanding patterns of double minute evolution can shed light on future therapeutic solutions to brain tumors carrying such variants.
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Affiliation(s)
- Ke Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jason Chiang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tim I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Laura Hover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Clay McLeod
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - James Dalton
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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167
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Møller HD, Lin L, Xiang X, Petersen TS, Huang J, Yang L, Kjeldsen E, Jensen UB, Zhang X, Liu X, Xu X, Wang J, Yang H, Church GM, Bolund L, Regenberg B, Luo Y. CRISPR-C: circularization of genes and chromosome by CRISPR in human cells. Nucleic Acids Res 2018; 46:e131. [PMID: 30551175 PMCID: PMC6294522 DOI: 10.1093/nar/gky767] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/28/2018] [Accepted: 08/20/2018] [Indexed: 12/18/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) and ring chromosomes are genetic alterations found in humans with genetic disorders. However, there is a lack of genetic engineering tools to recapitulate and study the biogenesis of eccDNAs. Here, we created a dual-fluorescence biosensor cassette, which upon the delivery of pairs of CRISPR/Cas9 guide RNAs, CRISPR-C, allows us to study the biogenesis of a specific fluorophore expressing eccDNA in human cells. We show that CRISPR-C can generate functional eccDNA, using the novel eccDNA biosensor system. We further reveal that CRISPR-C also can generate eccDNAs from intergenic and genic loci in human embryonic kidney 293T cells and human mammary fibroblasts. EccDNAs mainly forms by end-joining mediated DNA-repair and we show that CRISPR-C is able to generate endogenous eccDNAs in sizes from a few hundred base pairs and ranging up to 207 kb. Even a 47.4 megabase-sized ring chromosome 18 can be created by CRISPR-C. Our study creates a new territory for CRISPR gene editing and highlights CRISPR-C as a useful tool for studying the cellular impact, persistence and function of eccDNAs.
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MESH Headings
- Base Sequence
- Biosensing Techniques
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Cell Line
- Chromosomes, Human, Pair 18/chemistry
- Chromosomes, Human, Pair 18/metabolism
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA End-Joining Repair
- DNA, Circular/genetics
- DNA, Circular/metabolism
- Fibroblasts
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Gene Editing/methods
- Genes, Reporter
- Genetic Loci
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Genome, Human
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HEK293 Cells
- Humans
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Denmark
| | - Xi Xiang
- Department of Biomedicine, Aarhus University, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Qingdao, Qingdao 266555, China
| | | | - Jinrong Huang
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Luhan Yang
- eGenesis, Inc., Cambridge, MA 02139, USA
| | - Eigil Kjeldsen
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Uffe Birk Jensen
- Department of Biomedicine, Aarhus University, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xun Xu
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jian Wang
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Huanming Yang
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - George M Church
- eGenesis, Inc., Cambridge, MA 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Birgitte Regenberg
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
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168
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Abstract
Stress conditions such as UV irradiation, exposure to genotoxic agents, stalled DNA replication, and even tumors trigger the release of cytosolic genomic DNA (cgDNA). Classically, cgDNA induces interferon response via its binding to proteins such as STING. In this study, we found previously reported cgDNA (cg721) exists in the cytosol of the mouse cell lines, cultured under no stress conditions. The overexpression of cg721 suppressed the complementary RNA expression using strand selection and knockdown of DNA/RNA hybrid R-loop removing enzyme RNase H and three prime repair exonuclease 1 TREX1 increased the expression levels of cg721 and thus, inhibited the target Naa40 transcript, as well as protein expression, with a phenotypic effect. In addition, cgDNA was incorporated into extracellular vesicles (EVs), and the EV-derived cg721 inhibited gene expression of the acceptor cells. Thus, our findings suggest that cg721 functions as a natural antisense DNA and play a role in cell-to-cell gene regulation once it secreted outside the cell as EVs.
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169
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Dennin RH. Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing. Malays J Med Sci 2018; 25:20-26. [PMID: 30918452 PMCID: PMC6422590 DOI: 10.21315/mjms2018.25.2.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/05/2018] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal (ec) DNA in eukaryotic cells has been known for decades. The structures described range from linear double stranded (ds) DNA to circular dsDNA, distinct from mitochondrial (mt) DNA. The sizes of circular forms are described from some hundred base pairs (bp) up to more than 150 kbp. The number of molecules per cell ranges from several hundred to a thousand. Semi-quantitative determinations of circular dsDNA show proportions as high as several percentages of the total DNA per cell. These ecDNA fractions harbor sequences that are known to be present in chromosomal DNA (chrDNA) too. Sequencing projects on, for example the human genome, have to take into account the ecDNA sequences which are simultaneously ascertained; corrections cannot be performed retrospectively. Concerning the results of sequencings derived from extracted whole DNA: if the ecDNA fractions contained therein are not taken into account, erroneous conclusions at the chromosomal level may result.
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Affiliation(s)
- Reinhard H Dennin
- Department of Infectious Diseases and Microbiology, University of Luebeck, UKSH, Campus Luebeck, D-23538 Luebeck, Germany
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170
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Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet 2018; 34:270-278. [PMID: 29329720 PMCID: PMC5881399 DOI: 10.1016/j.tig.2017.12.010] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/24/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA, plasmids in yeasts, and double minutes (DMs) in cancer cells where the DNA is present in extrachromosomal circles. In addition, specialized extrachromosomal circles of DNA (eccDNA) have been noted to arise from repetitive genomic sequences like telomeric DNA or rDNA. Recently eccDNA arising from unique (nonrepetitive) DNA have been discovered in normal and malignant cells, raising interesting questions about their biogenesis, function and clinical utility. Here, we review recent results and future directions of inquiry on these new forms of eccDNA.
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MESH Headings
- Animals
- Chromosomes, Human/chemistry
- Chromosomes, Human/metabolism
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Chloroplast/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Kinetoplast/chemistry
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Humans
- Kinetoplastida/genetics
- Kinetoplastida/metabolism
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplastic Cells, Circulating/chemistry
- Neoplastic Cells, Circulating/metabolism
- Plants/genetics
- Plants/metabolism
- Plasmids/chemistry
- Plasmids/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Telomere/chemistry
- Telomere/metabolism
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Affiliation(s)
- Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - M Murat Koseoglu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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171
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Abstract
The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal cells as a result of mutations. Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting ~100,000 unique eccDNA types from 16 million nuclei. Half of these structures carry genes or gene fragments and the majority are smaller than 25 kb. Transcription from eccDNAs suggests that eccDNAs reside in nuclei and recurrence of certain eccDNAs in several individuals implies DNA circularization hotspots. Gene-rich chromosomes contribute to more eccDNAs per megabase and the most transcribed protein-coding gene in muscle, TTN (titin), provides the most eccDNAs per gene. Thus, somatic genomes are rich in chromosome-derived eccDNAs that may influence phenotypes through altered gene copy numbers and transcription of full-length or truncated genes. Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences.
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172
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Sutthibutpong T, Noy A, Harris S. Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis. Methods Mol Biol 2017; 1431:195-219. [PMID: 27283311 DOI: 10.1007/978-1-4939-3631-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA.
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Affiliation(s)
- Thana Sutthibutpong
- Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, 10140, Thailand.
| | - Agnes Noy
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah Harris
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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173
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Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. G3-GENES GENOMES GENETICS 2017; 7:3295-3303. [PMID: 28801508 PMCID: PMC5633380 DOI: 10.1534/g3.117.300141] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.
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174
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Zhu J, Zhang F, Du M, Zhang P, Fu S, Wang L. Molecular characterization of cell-free eccDNAs in human plasma. Sci Rep 2017; 7:10968. [PMID: 28887493 PMCID: PMC5591271 DOI: 10.1038/s41598-017-11368-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have been reported in most eukaryotes. However, little is known about the cell-free eccDNA profiles in circulating system such as blood. To characterize plasma cell-free eccDNAs, we performed sequencing analysis in 26 libraries from three blood donors and negative controls. We identified thousands of unique plasma eccDNAs in the three subjects. We observed proportional eccDNA increase with initial DNA input. The detected eccDNAs were also associated with circular DNA enrichment efficiency. Increasing the sequencing depth in an additional sample identified many more eccDNAs with highly heterogenous molecular structure. Size distribution of eccDNAs varied significantly from 31 bp to 19,989 bp. We found significantly higher GC content in smaller eccDNAs (<500 bp) than the larger ones (>500 bp) (p < 0.01). We also found an enrichment of eccDNAs at exons and 3′UTR (enrichment folds from 1.36 to 3.1) as well as the DNase hypersensitive sites (1.58–2.42 fold), H3K4Me1 (1.23–1.42 fold) and H3K27Ac (1.33–1.62 fold) marks. Junction sequence analysis suggested fundamental role of nonhomologous end joining mechanism during eccDNA formation. Further characterization of the extracellular eccDNAs in peripheral blood will facilitate understanding of their molecular mechanisms and potential clinical utilities.
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Affiliation(s)
- Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, 150081, China.,Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Fan Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China
| | - Meijun Du
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Peng Zhang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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175
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Mehanna P, Gagné V, Lajoie M, Spinella JF, St-Onge P, Sinnett D, Brukner I, Krajinovic M. Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines. PLoS One 2017; 12:e0184365. [PMID: 28877255 PMCID: PMC5587290 DOI: 10.1371/journal.pone.0184365] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified. They are on average 100 to 400 bp long and are derived from unique non-repetitive genomic regions with high gene density. MicroDNAs are thought to arise from DNA breaks associated with RNA metabolism or replication slippage. Given the paucity of information on this entirely novel phenomenon, we aimed to get an additional insight into microDNA features by performing the microDNA analysis in 20 independent human lymphoblastoid cell lines (LCLs) prior and after treatment with chemotherapeutic drugs. The results showed non-random genesis of microDNA clusters from the active regions of the genome. The size periodicity of 190 bp was observed, which matches DNA fragmentation typical for apoptotic cells. The chemotherapeutic drug-induced apoptosis of LCLs increased both number and size of clusters further suggesting that part of microDNAs could result from the programmed cell death. Interestingly, proportion of identified microDNA sequences has common loci of origin when compared between cell line experiments. While compatible with the original observation that microDNAs originate from a normal physiological process, obtained results imply complementary source of its production. Furthermore, non-random genesis of microDNAs depicted by redundancy between samples makes these entities possible candidates for new biomarker generation.
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Affiliation(s)
- Pamela Mehanna
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Vincent Gagné
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Mathieu Lajoie
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | | | - Pascal St-Onge
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
| | - Ivan Brukner
- Molecular Diagnostics Laboratory, Jewish General Hospital, McGill University, Montreal, Montreal, Qc, Canada
| | - Maja Krajinovic
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- * E-mail:
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176
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Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Mol Cancer Res 2017; 15:1197-1205. [PMID: 28550083 DOI: 10.1158/1541-7786.mcr-17-0095] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/03/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023]
Abstract
Cell-free circulating linear DNA is being explored for noninvasive diagnosis and management of tumors and fetuses, the so-called liquid biopsy. Previously, we observed the presence of small extrachromosomal circular DNA (eccDNA), called microDNA, in the nuclei of mammalian tissues and cell lines. Now, we demonstrate that cell-free microDNA derived from uniquely mapping regions of the genome is detectable in plasma and serum from both mice and humans and that they are significantly longer (30%-60% >250 bases) than cell-free circulating linear DNA (∼150 bases). Tumor-derived human microDNA is detected in the mouse circulation in a mouse xenograft model of human ovarian cancer. Comparing the microDNA from paired tumor and normal lung tissue specimens reveals that the tumors contain longer microDNA. Consistent with human cancers releasing microDNA into the circulation, serum and plasma samples (12 lung and 11 ovarian cancer) collected prior to surgery are enriched for longer cell-free microDNA compared with samples from the same patient obtained several weeks after surgical resection of the tumor. Thus, circular DNA in the circulation is a previously unexplored pool of nucleic acids that could complement miRNAs and linear DNA for diagnosis and for intercellular communication.Implications: eccDNA derived from chromosomal genomic sequence, first discovered in the nuclei of cells, are detected in the circulation, are longer than linear cell-free DNA, and are released from normal tissue and tumors into the circulation. Mol Cancer Res; 15(9); 1197-205. ©2017 AACR.
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Affiliation(s)
- Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Laura W Dillon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Amir A Jazaeri
- Department of Gynecological Oncology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - David R Jones
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.
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177
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Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
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178
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Charney E. Genes, behavior, and behavior genetics. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2016; 8. [PMID: 27906529 DOI: 10.1002/wcs.1405] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/27/2022]
Abstract
According to the 'first law' of behavior genetics, 'All human behavioral traits are heritable.' Accepting the validity of this first law and employing statistical methods, researchers within psychology, sociology, political science, economics, and business claim to have demonstrated that all the behaviors studied by their disciplines are heritable-no matter how culturally specific these behaviors appear to be. Further, in many cases they claim to have identified specific genes that play a role in those behaviors. The validity of behavior genetics as a discipline depends upon the validity of the research methods used to justify such claims. It also depends, foundationally, upon certain key assumptions concerning the relationship between genotype (one's specific DNA sequences) and phenotype (any and all observable traits or characteristics). In this article, I examine-and find serious flaws with-both the methodologies of behavior genetics and the underlying assumptions concerning the genotype-phenotype relationship. WIREs Cogn Sci 2017, 8:e1405. doi: 10.1002/wcs.1405 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Evan Charney
- Sanford School of Public Policy, Duke Center for Brain Sciences, Duke University, Durham, NC, USA
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179
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Cai J, Wu G, Jose PA, Zeng C. Functional transferred DNA within extracellular vesicles. Exp Cell Res 2016; 349:179-183. [DOI: 10.1016/j.yexcr.2016.10.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 02/07/2023]
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180
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Liu YT, Chang KM, Ma CH, Jayaram M. Replication-dependent and independent mechanisms for the chromosome-coupled persistence of a selfish genome. Nucleic Acids Res 2016; 44:8302-23. [PMID: 27492289 PMCID: PMC5041486 DOI: 10.1093/nar/gkw694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
The yeast 2-micron plasmid epitomizes the evolutionary optimization of selfish extra-chromosomal genomes for stable persistence without jeopardizing their hosts' fitness. Analyses of fluorescence-tagged single-copy reporter plasmids and/or the plasmid partitioning proteins in native and non-native hosts reveal chromosome-hitchhiking as the likely means for plasmid segregation. The contribution of the partitioning system to equal segregation is bipartite- replication-independent and replication-dependent. The former nearly eliminates 'mother bias' (preferential plasmid retention in the mother cell) according to binomial distribution, thus limiting equal segregation of a plasmid pair to 50%. The latter enhances equal segregation of plasmid sisters beyond this level, elevating the plasmid close to chromosome status. Host factors involved in plasmid partitioning can be functionally separated by their participation in the replication-independent and/or replication-dependent steps. In the hitchhiking model, random tethering of a pair of plasmids to chromosomes signifies the replication-independent component of segregation; the symmetric tethering of plasmid sisters to sister chromatids embodies the replication-dependent component. The 2-micron circle broadly resembles the episomes of certain mammalian viruses in its chromosome-associated propagation. This unifying feature among otherwise widely differing selfish genomes suggests their evolutionary convergence to the common logic of exploiting, albeit via distinct molecular mechanisms, host chromosome segregation machineries for self-preservation.
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Affiliation(s)
- Yen-Ting Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Keng-Ming Chang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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181
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Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, K Doye JP, Louis AA, Harris SA. Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res 2016; 44:9121-9130. [PMID: 27664220 PMCID: PMC5100592 DOI: 10.1093/nar/gkw815] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/03/2016] [Indexed: 12/14/2022] Open
Abstract
It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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Affiliation(s)
- Thana Sutthibutpong
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Craig Benham
- UC Davis Genome Centre, Health Sciences Drive, Davis, CA 95616, USA
| | - Gabriel G Slade
- Department of Physics, São Paulo State University, Rua Cristovão, São José do Rio Preto, SP 15054-000, Brazil
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK .,Astbury Centre for Structural and Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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182
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Legéndy CR. Synaptic and extrasynaptic traces of long-term memory: the ID molecule theory. Rev Neurosci 2016; 27:575-98. [PMID: 27206318 DOI: 10.1515/revneuro-2016-0015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 04/20/2016] [Indexed: 12/19/2022]
Abstract
It is generally assumed at the time of this writing that memories are stored in the form of synaptic weights. However, it is now also clear that the synapses are not permanent; in fact, synaptic patterns undergo significant change in a matter of hours. This means that to implement the long survival of distant memories (for several decades in humans), the brain must possess a molecular backup mechanism in some form, complete with provisions for the storage and retrieval of information. It is found below that the memory-supporting molecules need not contain a detailed description of mental entities, as had been envisioned in the 'memory molecule papers' from 50 years ago, they only need to contain unique identifiers of various entities, and that this can be achieved using relatively small molecules, using a random code ('ID molecules'). In this paper, the logistics of information flow are followed through the steps of storage and retrieval, and the conclusion reached is that the ID molecules, by carrying a sufficient amount of information (entropy), can effectively control the recreation of complex multineuronal patterns. In illustrations, it is described how ID molecules can be made to revive a selected cell assembly by waking up its synapses and how they cause a selected cell assembly to ignite by sending slow inward currents into its cells. The arrangement involves producing multiple copies of the ID molecules and distributing them at strategic locations at selected sets of synapses, then reaching them through small noncoding RNA molecules. This requires the quick creation of entropy-rich messengers and matching receptors, and it suggests that these are created from each other by small-scale transcription and reverse transcription.
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183
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184
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Bracht JR, Wang X, Shetty K, Chen X, Uttarotai GJ, Callihan EC, McCloud SS, Clay DM, Wang J, Nowacki M, Landweber LF. Chromosome fusions triggered by noncoding RNA. RNA Biol 2016; 14:620-631. [PMID: 27267579 PMCID: PMC5449082 DOI: 10.1080/15476286.2016.1195940] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Chromosomal fusions are common in normal and cancer cells and can produce aberrant gene products that promote transformation. The mechanisms driving these fusions are poorly understood, but recurrent fusions are widespread. This suggests an underlying mechanism, and some authors have proposed a possible role for RNA in this process. The unicellular eukaryote Oxytricha trifallax displays an exorbitant capacity for natural genome editing, when it rewrites its germline genome to form a somatic epigenome. This developmental process provides a powerful model system to directly test the influence of small noncoding RNAs on chromosome fusion events during somatic differentiation. Here we show that small RNAs are capable of inducing chromosome fusions in 4 distinct cases (out of 4 tested), including one fusion of 3 chromosomes. We further show that these RNA-mediated chromosome fusions are heritable over multiple sexual generations and that transmission of the acquired fusion is associated with endogenous production of novel piRNA molecules that target the fused junction. We also demonstrate the capacity of a long noncoding RNA (lncRNA) to induce chromosome fusion of 2 distal germline loci. These results underscore the ability of short-lived, aberrant RNAs to act as drivers of chromosome fusion events that can be stably transmitted to future generations.
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Affiliation(s)
- John R Bracht
- a Department of Biology , American University , Washington, DC , USA
| | - Xing Wang
- b Department of Chemistry & Chemical Biology , Rensselaer Polytechnic Institute Troy , NY , USA
| | - Keerthi Shetty
- c Department of Molecular Biology , Princeton University , Princeton , NJ , USA.,d Department of Immunobiology , Yale University , New Haven , CT , USA
| | - Xiao Chen
- c Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Grace J Uttarotai
- a Department of Biology , American University , Washington, DC , USA
| | - Evan C Callihan
- a Department of Biology , American University , Washington, DC , USA
| | - Sierra S McCloud
- c Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Derek M Clay
- c Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Jingmei Wang
- e Department of Ecology & Evolutionary Biology , Princeton University , NJ , USA
| | - Mariusz Nowacki
- f Institute of Cell Biology, University of Bern , Switzerland
| | - Laura F Landweber
- e Department of Ecology & Evolutionary Biology , Princeton University , NJ , USA.,g Departments of Biochemistry & Molecular Biophysics and Biological Sciences , Columbia University , NY , USA
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185
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Diaz-Lara A, Gent DH, Martin RR. Identification of Extrachromosomal Circular DNA in Hop via Rolling Circle Amplification. Cytogenet Genome Res 2016; 148:237-40. [PMID: 27160259 DOI: 10.1159/000445849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
During a survey for new viruses affecting hop plants, a circular DNA molecule was identified via rolling circle amplification (RCA) and later characterized. A small region of the 5.7-kb long molecule aligned with a microsatellite region in the Humulus lupulus genome, and no coding sequence was identified. Sequence analysis and literature review suggest that the small DNA molecule is an extranuclear DNA element, specifically, an extrachromosomal circular DNA (eccDNA), and its presence was confirmed by electron microscopy. This work is the first report of eccDNAs in the family Cannabaceae. Additionally, this work highlights the advantages of using RCA to study extrachromosomal DNA in higher plants.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oreg., USA
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186
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Møller HD, Bojsen RK, Tachibana C, Parsons L, Botstein D, Regenberg B. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells. J Vis Exp 2016:e54239 |. [PMID: 27077531 DOI: 10.3791/54239] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
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Affiliation(s)
| | - Rasmus K Bojsen
- National Veterinary Institute, Technical University of Denmark
| | | | - Lance Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
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187
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Ndunguru J, De León L, Doyle CD, Sseruwagi P, Plata G, Legg JP, Thompson G, Tohme J, Aveling T, Ascencio-Ibáñez JT, Hanley-Bowdoin L. Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease. J Virol 2016; 90:4160-4173. [PMID: 26865712 PMCID: PMC4810563 DOI: 10.1128/jvi.02834-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies. IMPORTANCE Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.
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Affiliation(s)
- Joseph Ndunguru
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Catherine D Doyle
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - German Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - James P Legg
- International Institute of Tropical Agriculture-Tanzania, Dar es Salaam, Tanzania
| | - Graham Thompson
- ARC-Institute for Industrial Crops, Rusternburg, South Africa
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Theresa Aveling
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa
| | - Jose T Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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188
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Reon BJ, Dutta A. Biological Processes Discovered by High-Throughput Sequencing. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:722-32. [PMID: 26828742 PMCID: PMC5807928 DOI: 10.1016/j.ajpath.2015.10.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/16/2015] [Accepted: 10/30/2015] [Indexed: 11/20/2022]
Abstract
Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible technology that allows scientists to sequence an entire transcriptome or genome in a timely and cost-effective manner. Application of HTS techniques has led to many key discoveries, including the identification of long noncoding RNAs, microDNAs, a family of small extrachromosomal circular DNA species, and tRNA-derived fragments, which are a group of small non-miRNAs that are derived from tRNAs. Furthermore, public sequencing repositories provide unique opportunities for laboratories to parse large sequencing databases to identify proteins and noncoding RNAs at a scale that was not possible a decade ago. Herein, we review how HTS has led to the discovery of novel nucleic acid species and uncovered new biological processes during the course.
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Affiliation(s)
- Brian J Reon
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Anindya Dutta
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.
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189
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Abstract
By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function. DNA supercoiling strongly affects its metabolism. By electron cryo-tomography, biochemical assays and molecular dynamics simulations, here the authors show that supercoiled DNA minicircles adopt unique and wide distributions of three-dimensional conformations, many with disrupted base pairs.
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190
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Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell Rep 2015; 11:1749-59. [PMID: 26051933 DOI: 10.1016/j.celrep.2015.05.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/11/2015] [Indexed: 12/15/2022] Open
Abstract
MicroDNAs are <400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5'-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair.
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Affiliation(s)
- Laura W Dillon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Shunichi Takeda
- CREST Research Project, Japan Science and Technology Corporation, Radiation Genetics, Faculty of Medicine, Kyoto University, Konoe Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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191
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Abstract
Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs in the Saccharomyces cerevisiae genome using Circle-Seq, a highly sensitive eccDNA purification method. Yeast eccDNAs ranged from an arbitrary lower limit of 1 kb up to 38 kb and covered 23% of the genome, representing thousands of genes. EccDNA arose both from genomic regions with repetitive sequences ≥ 15 bases long and from regions with short or no repetitive sequences. Some eccDNAs were identified in several yeast populations. These eccDNAs contained ribosomal genes, transposon remnants, and tandemly repeated genes (HXT6/7, ENA1/2/5, and CUP1-1/-2) that were generally enriched on eccDNAs. EccDNAs seemed to be replicated and 80% contained consensus sequences for autonomous replication origins that could explain their maintenance. Our data suggest that eccDNAs are common in S. cerevisiae, where they might contribute substantially to genetic variation and evolution.
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192
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Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HYK, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun 2015; 6:7256. [PMID: 26028266 PMCID: PMC4451611 DOI: 10.1038/ncomms8256] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/21/2015] [Indexed: 02/07/2023] Open
Abstract
Investigating genomic structural variants at basepair resolution is crucial for understanding their formation mechanisms. We identify and analyze 8,943 deletion breakpoints in 1,092 samples from the 1000 Genomes Project. We find breakpoints have more nearby SNPs and indels than the genomic average, likely a consequence of relaxed selection. By investigating the correlation of breakpoints with DNA methylation, Hi-C interactions, and histone marks and the substitution patterns of nucleotides near them, we find that breakpoints with the signature of non-allelic homologous recombination (NAHR) are associated with open chromatin. We hypothesize that some NAHR deletions occur without DNA replication and cell division, in embryonic and germline cells. In contrast, breakpoints associated with non-homologous (NH) mechanisms often have sequence micro-insertions, templated from later replicating genomic sites, spaced at two characteristic distances from the breakpoint. These micro-insertions are consistent with template-switching events and suggest a particular spatiotemporal configuration for DNA during the events.
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Affiliation(s)
- Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota 55905, USA
| | - Shantao Li
- 1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Rhee Kim
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | | | - Adrian M Stütz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | | | - Xinmeng Jasmine Mu
- 1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut 06520, USA
| | - Wyatt Clark
- 1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut 06520, USA
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Matthew Hurles
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jan O Korbel
- 1] European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Hugo Y K Lam
- Bina Technologies, Roche Sequencing, Redwood City, California 94065, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030, USA
| | - Mark B Gerstein
- 1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
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193
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Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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194
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Komosa M, Root H, Meyn MS. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH. Nucleic Acids Res 2015; 43:2152-63. [PMID: 25662602 PMCID: PMC4344523 DOI: 10.1093/nar/gkv091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells.
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Affiliation(s)
- Martin Komosa
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Heather Root
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - M Stephen Meyn
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada Department of Paediatrics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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195
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Denoth-Lippuner A, Krzyzanowski MK, Stober C, Barral Y. Role of SAGA in the asymmetric segregation of DNA circles during yeast ageing. eLife 2014; 3. [PMID: 25402830 PMCID: PMC4232608 DOI: 10.7554/elife.03790] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/14/2014] [Indexed: 12/18/2022] Open
Abstract
In eukaryotes, intra-chromosomal recombination generates DNA circles, but little is known about how cells react to them. In yeast, partitioning of such circles to the mother cell at mitosis ensures their loss from the population but promotes replicative ageing. Nevertheless, the mechanisms of partitioning are debated. In this study, we show that the SAGA complex mediates the interaction of non-chromosomal DNA circles with nuclear pore complexes (NPCs) and thereby promotes their confinement in the mother cell. Reciprocally, this causes retention and accumulation of NPCs, which affects the organization of ageing nuclei. Thus, SAGA prevents the spreading of DNA circles by linking them to NPCs, but unavoidably causes accumulation of circles and NPCs in the mother cell, and thereby promotes ageing. Together, our data provide a unifying model for the asymmetric segregation of DNA circles and how age affects nuclear organization. DOI:http://dx.doi.org/10.7554/eLife.03790.001 Budding yeast is a microorganism that has been widely studied to understand how it and many other organisms, including animals, age over time. This yeast is so named because it proliferates by ‘budding’ daughter cells out of the surface of a mother cell. For each daughter cell that buds, the mother cell loses some fitness and eventually dies after a certain number of budding events. This process is called ‘replicative ageing’, and it also resembles the way that stem cells age. In contrast, the newly formed daughters essentially have their age ‘reset to zero’ and grow until they turn into mother cells themselves. Several molecules or factors have been linked to replicative ageing. These are retained in the mother cell during budding, rather than being passed on to the daughters. Non-chromosomal DNA circles, for example, are rings of DNA that detach from chromosomes during DNA repair and that accumulate inside the ageing mother cell over time. How the mother cells retain these circles of DNA is an on-going topic of debate. Similar to plants and animals, chromosomes in yeast cells are confined in a membrane-bound structure known as the cell nucleus. The nuclear membrane is perforated by channels called nuclear pore complexes that ensure the transport of molecules into, and out of, the nucleus. Now, Denoth-Lippuner et al. establish that for the non-chromosomal DNA circles to be efficiently confined in the mother cell, the DNA circles must be anchored to the nuclear pore complexes. Denoth-Lippuner et al. next asked how the DNA circles were anchored to these complexes; and found that another complex of proteins known as SAGA is involved. When components of the SAGA complex were deleted in budding yeast cells, non-chromosomal DNA circles spread into the daughters as well. On the other hand, artificially anchoring these DNA circles to the nuclear pore complex alleviated the need for the SAGA complex, in order to retain these molecules in the mother cell. Denoth-Lippuner et al. also show that SAGA-dependent attachment of the DNA circles to the nuclear pore complexes causes these complexes to remain in the mother cell. As a consequence, these nuclear pore complexes accumulate in the mother cells as they age. The number of nuclear pore complexes in the daughter cells, however, remained fairly constant. Together these data raise the question of whether the effects of DNA circles on the number and activity of the nuclear pores might account for their contribution to ageing, perhaps by affecting the workings of the nucleus. DOI:http://dx.doi.org/10.7554/eLife.03790.002
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Affiliation(s)
| | | | - Catherine Stober
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
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196
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197
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Zoli M. Twist versus nonlinear stacking in short DNA molecules. J Theor Biol 2014; 354:95-104. [DOI: 10.1016/j.jtbi.2014.03.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/02/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
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198
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How a replication origin and matrix attachment region accelerate gene amplification under replication stress in mammalian cells. PLoS One 2014; 9:e103439. [PMID: 25061979 PMCID: PMC4111587 DOI: 10.1371/journal.pone.0103439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
The gene amplification plays a critical role in the malignant transformation of mammalian cells. The most widespread method for amplifying a target gene in cell culture is the use of methotrexate (Mtx) treatment to amplify dihydrofolate reductase (Dhfr). Whereas, we found that a plasmid bearing both a mammalian origin of replication (initiation region; IR) and a matrix attachment region (MAR) was spontaneously amplified in mammalian cells. In this study, we attempted to uncover the underlying mechanism by which the IR/MAR sequence might accelerate Mtx induced Dhfr amplification. The plasmid containing the IR/MAR was extrachromosomally amplified, and then integrated at multiple chromosomal locations within individual cells, increasing the likelihood that the plasmid might be inserted into a chromosomal environment that permits high expression and further amplification. Efficient amplification of this plasmid alleviated the genotoxicity of Mtx. Clone-based cytogenetic and sequence analysis revealed that the plasmid was amplified in a chromosomal context by breakage-fusion-bridge cycles operating either at the plasmid repeat or at the flanking fragile site activated by Mtx. This mechanism explains how a circular molecule bearing IR/MAR sequences of chromosomal origin might be amplified under replication stress, and also provides insight into gene amplification in human cancer.
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199
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Abstract
MYC dysregulation initiates a dynamic process of genomic instability that is linked to tumor initiation. Early studies using MYC-carrying retroviruses showed that these viruses were potent transforming agents. Cell culture models followed that addressed the role of MYC in transformation. With the advent of MYC transgenic mice, it became obvious that MYC deregulation alone was sufficient to initiate B-cell neoplasia in mice. More than 70% of all tumors have some form of c-MYC gene dysregulation, which affects gene regulation, microRNA expression profiles, large genomic amplifications, and the overall organization of the nucleus. These changes set the stage for the dynamic genomic rearrangements that are associated with cellular transformation.
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Affiliation(s)
- Alexandra Kuzyk
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
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200
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Abstract
Recent studies indicate that long interspersed nuclear element-1 (L1) are mobilized in the genome of human neural progenitor cells and enhanced in Rett syndrome and ataxia telangiectasia. However, whether aberrant L1 retrotransposition occurs in mental disorders is unknown. Here, we report high L1 copy number in schizophrenia. Increased L1 was demonstrated in neurons from prefrontal cortex of patients and in induced pluripotent stem (iPS) cell-derived neurons containing 22q11 deletions. Whole-genome sequencing revealed brain-specific L1 insertion in patients localized preferentially to synapse- and schizophrenia-related genes. To study the mechanism of L1 transposition, we examined perinatal environmental risk factors for schizophrenia in animal models and observed an increased L1 copy number after immune activation by poly-I:C or epidermal growth factor. These findings suggest that hyperactive retrotransposition of L1 in neurons triggered by environmental and/or genetic risk factors may contribute to the susceptibility and pathophysiology of schizophrenia.
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