201
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McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH. Mosaic copy number variation in human neurons. Science 2013; 342:632-7. [PMID: 24179226 DOI: 10.1126/science.1243472] [Citation(s) in RCA: 406] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We used single-cell genomic approaches to map DNA copy number variation (CNV) in neurons obtained from human induced pluripotent stem cell (hiPSC) lines and postmortem human brains. We identified aneuploid neurons, as well as numerous subchromosomal CNVs in euploid neurons. Neurotypic hiPSC-derived neurons had larger CNVs than fibroblasts, and several large deletions were found in hiPSC-derived neurons but not in matched neural progenitor cells. Single-cell sequencing of endogenous human frontal cortex neurons revealed that 13 to 41% of neurons have at least one megabase-scale de novo CNV, that deletions are twice as common as duplications, and that a subset of neurons have highly aberrant genomes marked by multiple alterations. Our results show that mosaic CNV is abundant in human neurons.
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Affiliation(s)
- Michael J McConnell
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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202
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Bohr J, Olsen KW. Total positive curvature of circular DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052714. [PMID: 24329303 DOI: 10.1103/physreve.88.052714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 08/15/2013] [Indexed: 06/03/2023]
Abstract
The properties of double-stranded DNA and other chiral molecules depend on the local geometry, i.e., on curvature and torsion, yet the paths of closed chain molecules are globally restricted by topology. When both of these characteristics are to be incorporated in the description of circular chain molecules, e.g., plasmids, it is shown to have implications for the total positive curvature integral. For small circular micro-DNAs it follows as a consequence of Fenchel's inequality that there must exist a minimum length for the circular plasmids to be double stranded. It also follows that all circular micro-DNAs longer than the minimum length must be concave, a result that is consistent with typical atomic force microscopy images of plasmids. Predictions for the total positive curvature of circular micro-DNAs are given as a function of length, and comparisons with circular DNAs from the literature are presented.
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Affiliation(s)
- Jakob Bohr
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kasper W Olsen
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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203
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Biological Water Dynamics and Entropy: A Biophysical Origin of Cancer and Other Diseases. ENTROPY 2013. [DOI: 10.3390/e15093822] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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204
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Abstract
Genome instability has long been implicated as the main causal factor in aging. Somatic cells are continuously exposed to various sources of DNA damage, from reactive oxygen species to UV radiation to environmental mutagens. To cope with the tens of thousands of chemical lesions introduced into the genome of a typical cell each day, a complex network of genome maintenance systems acts to remove damage and restore the correct base pair sequence. Occasionally, however, repair is erroneous, and such errors, as well as the occasional failure to correctly replicate the genome during cell division, are the basis for mutations and epimutations. There is now ample evidence that mutations accumulate in various organs and tissues of higher animals, including humans, mice, and flies. What is not known, however, is whether the frequency of these random changes is sufficient to cause the phenotypic effects generally associated with aging. The exception is cancer, an age-related disease caused by the accumulation of mutations and epimutations. Here, we first review current concepts regarding the relationship between DNA damage, repair, and mutation, as well as the data regarding genome alterations as a function of age. We then describe a model for how randomly induced DNA sequence and epigenomic variants in the somatic genomes of animals can result in functional decline and disease in old age. Finally, we discuss the genetics of genome instability in relation to longevity to address the importance of alterations in the somatic genome as a causal factor in aging and to underscore the opportunities provided by genetic approaches to develop interventions that attenuate genome instability, reduce disease risk, and increase life span.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA.
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205
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206
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Bhattacharya D, Pelletreau KN, Price DC, Sarver KE, Rumpho ME. Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc. Mol Biol Evol 2013; 30:1843-52. [PMID: 23645554 PMCID: PMC3708498 DOI: 10.1093/molbev/mst084] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea. The “stolen” plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University
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207
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Kwon SM, Kim DS, Won NH, Park SJ, Chwae YJ, Kang HC, Lee SH, Baik EJ, Thorgeirsson SS, Woo HG. Genomic copy number alterations with transcriptional deregulation at 6p identify an aggressive HCC phenotype. Carcinogenesis 2013; 34:1543-50. [PMID: 23508637 DOI: 10.1093/carcin/bgt095] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic analyses have revealed the enormous heterogeneity in essentially all cancer types. However, the identification of precise subtypes, which are biologically informative and clinically useful, remains a challenge. The application of integrative analysis of multilayered genomic profiles to define the chromosomal regions of genomic copy number alterations with concomitant transcriptional deregulation is posited to provide a promising strategy to identify driver targets. In this study, we performed an integrative analysis of the DNA copy numbers and gene expression profiles of hepatocellular carcinoma (HCC). By comparing DNA copy numbers between HCC subtypes based on gene expression pattern, we revealed the DNA copy number alteration with concordant gene expression changes at 6p21-p24 particularly in the HCC subtype of aggressive phenotype without expressing stemness genes. Among the genes at 6p21-p24, we identified IER3 as a potential driver. The clinical utility of IER3 copy numbers was demonstrated by validating its clinical correlation with independent cohorts. In addition, short hairpin RNA-mediated knock-down experiment revealed the functional relevance of IER3 in liver cancer progression. In conclusion, our results suggest that genomic copy number alterations with transcriptional deregulation at 6p21-p24 identify an aggressive HCC phenotype and a novel functional biomarker.
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Affiliation(s)
- So Mee Kwon
- Department of Physiology, Ajou University School of Medicine, Suwon 443-721, Korea
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208
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Affiliation(s)
- Wenwen Fang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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209
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Mukherjee K, Storici F. A mechanism of gene amplification driven by small DNA fragments. PLoS Genet 2012; 8:e1003119. [PMID: 23271978 PMCID: PMC3521702 DOI: 10.1371/journal.pgen.1003119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s). Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA) occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB) external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation in nature.
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Affiliation(s)
- Kuntal Mukherjee
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Francesca Storici
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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210
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Lanza AM, Cheng JK, Alper HS. Emerging synthetic biology tools for engineering mammalian cell systems and expediting cell line development. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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211
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Gong Z, Wu Y, Koblížková A, Torres GA, Wang K, Iovene M, Neumann P, Zhang W, Novák P, Buell CR, Macas J, Jiang J. Repeatless and repeat-based centromeres in potato: implications for centromere evolution. THE PLANT CELL 2012; 24:3559-74. [PMID: 22968715 PMCID: PMC3480287 DOI: 10.1105/tpc.112.100511] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/18/2012] [Accepted: 08/30/2012] [Indexed: 05/18/2023]
Abstract
Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats. By contrast, most newly formed centromeres (neocentromeres) do not contain satellite repeats and instead include DNA sequences representative of the genome. An unknown question in centromere evolution is how satellite repeat-based centromeres evolve from neocentromeres. We conducted a genome-wide characterization of sequences associated with CENH3 nucleosomes in potato (Solanum tuberosum). Five potato centromeres (Cen4, Cen6, Cen10, Cen11, and Cen12) consisted primarily of single- or low-copy DNA sequences. No satellite repeats were identified in these five centromeres. At least one transcribed gene was associated with CENH3 nucleosomes. Thus, these five centromeres structurally resemble neocentromeres. By contrast, six potato centromeres (Cen1, Cen2, Cen3, Cen5, Cen7, and Cen8) contained megabase-sized satellite repeat arrays that are unique to individual centromeres. The satellite repeat arrays likely span the entire functional cores of these six centromeres. At least four of the centromeric repeats were amplified from retrotransposon-related sequences and were not detected in Solanum species closely related to potato. The presence of two distinct types of centromeres, coupled with the boom-and-bust cycles of centromeric satellite repeats in Solanum species, suggests that repeat-based centromeres can rapidly evolve from neocentromeres by de novo amplification and insertion of satellite repeats in the CENH3 domains.
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Affiliation(s)
- Zhiyun Gong
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yufeng Wu
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre, Academy of Sciences of the Czech Republic, CZ-37005 Ceske Budejovice, Czech Republic
| | - Giovana A. Torres
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, Minas Gerais 37200, Brazil
| | - Kai Wang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Marina Iovene
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre, Academy of Sciences of the Czech Republic, CZ-37005 Ceske Budejovice, Czech Republic
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre, Academy of Sciences of the Czech Republic, CZ-37005 Ceske Budejovice, Czech Republic
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre, Academy of Sciences of the Czech Republic, CZ-37005 Ceske Budejovice, Czech Republic
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
- Address correspondence to
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212
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Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep 2012; 2:69-75. [PMID: 22840398 DOI: 10.1016/j.celrep.2012.06.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/27/2012] [Accepted: 06/12/2012] [Indexed: 12/15/2022] Open
Abstract
Genomic imprinting occurs when expression of an allele differs based on the sex of the parent that transmitted the allele. In D. melanogaster, imprinting can occur, but its impact on allelic expression genome-wide is unclear. Here, we search for imprinted genes in D. melanogaster using RNA-seq to compare allele-specific expression between pools of 7- to 10-day-old adult female progeny from reciprocal crosses. We identified 119 genes with allelic expression consistent with imprinting, and these genes showed significant clustering within the genome. Surprisingly, additional analysis of several of these genes showed that either genomic heterogeneity or high levels of intrinsic noise caused imprinting-like allelic expression. Consequently, our data provide no convincing evidence of imprinting for D. melanogaster genes in their native genomic context. Elucidating sources of false-positive signals for imprinting in allele-specific RNA-seq data, as done here, is critical given the growing popularity of this method for identifying imprinted genes.
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213
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Kwon SM, Cho H, Choi JH, Jee BA, Jo Y, Woo HG. Perspectives of integrative cancer genomics in next generation sequencing era. Genomics Inform 2012; 10:69-73. [PMID: 23105932 PMCID: PMC3480879 DOI: 10.5808/gi.2012.10.2.69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 05/15/2012] [Accepted: 05/23/2012] [Indexed: 12/18/2022] Open
Abstract
The explosive development of genomics technologies including microarrays and next generation sequencing (NGS) has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.
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Affiliation(s)
- So Mee Kwon
- Department of Physiology, Ajou University School of Medicine, Suwon 443-721, Korea
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214
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New family of DNA molecule found in mammals. Nat Rev Genet 2012. [DOI: 10.1038/nrg3232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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