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Yang N, Srivastav SP, Rahman R, Ma Q, Dayama G, Li S, Chinen M, Lei EP, Rosbash M, Lau NC. Transposable element landscapes in aging Drosophila. PLoS Genet 2022; 18:e1010024. [PMID: 35239675 PMCID: PMC8893327 DOI: 10.1371/journal.pgen.1010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic mechanisms that repress transposable elements (TEs) in young animals decline during aging, as reflected by increased TE expression in aged animals. Does increased TE expression during aging lead to more genomic TE copies in older animals? To address this question, we quantified TE Landscapes (TLs) via whole genome sequencing of young and aged Drosophila strains of wild-type and mutant backgrounds. We quantified TLs in whole flies and dissected brains and validated the feasibility of our approach in detecting new TE insertions in aging Drosophila genomes when small RNA and RNA interference (RNAi) pathways are compromised. We also describe improved sequencing methods to quantify extra-chromosomal DNA circles (eccDNAs) in Drosophila as an additional source of TE copies that accumulate during aging. Lastly, to combat the natural progression of aging-associated TE expression, we show that knocking down PAF1, a conserved transcription elongation factor that antagonizes RNAi pathways, may bolster suppression of TEs during aging and extend lifespan. Our study suggests that in addition to a possible influence by different genetic backgrounds, small RNA and RNAi mechanisms may mitigate genomic TL expansion despite the increase in TE transcripts during aging. Transposable elements, also called transposons, are genetic parasites found in all animal genomes. Normally, transposons are compacted away in silent chromatin in young animals. But, as animals age and transposon-silencing defense mechanisms break down, transposon RNAs accumulate to significant levels in old animals like fruit flies. An open question is whether the increased levels of transposon RNAs in older animals also correspond to increased genomic copies of transposons. This study approached this question by sequencing the whole genomes of young and old wild-type and mutant flies lacking a functional RNA interference (RNAi) pathway, which naturally silences transposon RNAs. Although the wild-type flies with intact RNAi activity had little new accumulation of transposon copies, the sequencing approach was able to detect several transposon accumulation occurrences in some RNAi mutants. In addition, we found that some fly transposon families can also accumulate as extra-chromosomal circular DNA copies. Lastly, we showed that genetically augmenting the expression of RNAi factors can counteract the rising transposon RNA levels in aging and promote longevity. This study improves our understanding of the animal host genome relationship with transposons during natural aging processes.
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Affiliation(s)
- Nachen Yang
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Satyam P. Srivastav
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Reazur Rahman
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Gargi Dayama
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Sizheng Li
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Madoka Chinen
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Michael Rosbash
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Nelson C. Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
- Boston University Genome Science Institute, Boston, Massachusetts, United States of America
- * E-mail:
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2
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O'Brochta DA, Stosic CD, Pilitt K, Subramanian RA, Hice RH, Atkinson PW. Transpositionally active episomal hAT elements. BMC Mol Biol 2009; 10:108. [PMID: 20003420 PMCID: PMC2803484 DOI: 10.1186/1471-2199-10-108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 12/14/2009] [Indexed: 01/31/2023] Open
Abstract
Background hAT elements and V(D)J recombination may have evolved from a common ancestral transposable element system. Extrachromosomal, circular forms of transposable elements (referred to here as episomal forms) have been reported yet their biological significance remains unknown. V(D)J signal joints, which resemble episomal transposable elements, have been considered non-recombinogenic products of V(D)J recombination and a safe way to dispose of excised chromosomal sequences. V(D)J signal joints can, however, participate in recombination reactions and the purpose of this study was to determine if hobo and Hermes episomal elements are also recombinogenic. Results Up to 50% of hobo/Hermes episomes contained two intact, inverted-terminal repeats and 86% of these contained from 1-1000 bp of intercalary DNA. Episomal hobo/Hermes elements were recovered from Musca domestica (a natural host of Hermes), Drosophila melanogaster (a natural host of hobo) and transgenic Drosophila melanogaster and Aedes aegypti (with autonomous Hermes elements). Episomal Hermes elements were recovered from unfertilized eggs of M. domestica and D. melanogaster demonstrating their potential for extrachromosomal, maternal transmission. Reintegration of episomal Hermes elements was observed in vitro and in vivo and the presence of Hermes episomes resulted in lower rates of canonical Hermes transposition in vivo. Conclusion Episomal hobo/Hermes elements are common products of element excision and can be maternally transmitted. Episomal forms of Hermes are capable of integration and also of influencing the transposition of canonical elements suggesting biological roles for these extrachromosomal elements in element transmission and regulation.
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Affiliation(s)
- David A O'Brochta
- Center for Biosystems Research, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.
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3
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Musatov SA, Dudus L, Parrish CM, Scully TA, Fisher KJ. Spontaneous mobilization of integrated recombinant adenoassociated virus in a cell culture model of virus latency. Virology 2002; 294:151-69. [PMID: 11886274 DOI: 10.1006/viro.2001.1267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A cell line containing integrated recombinant adenoassociated virus (AAV) was investigated for spontaneous mobilization of vector sequence. Detection of these rare events was facilitated by using a vector design that allowed the circular rescue product (cAAV) to be individually scored by bacterial transformation. Restriction and sequence analysis of captured clones revealed five highly ordered classes of cAAV, each of which contained a defined segment of the integrated vector locus. A common feature of all cAAV classes was the presence of a modified inverted terminal repeat that joined the ends of the liberated sequence. Assembly of extrachromosomal vector genomes was accompanied by deletions in the integration locus that could be mapped to one of the five cAAV classes, suggesting an excision-type mechanism. We propose that the spontaneous deletion and mobilization of vector sequence from the recombinant adenoassociated virus (rAAV) integration locus is mediated by a recombination event between the inverted terminal repeats that define the boundaries of the individual genome subunits.
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Affiliation(s)
- Sergei A Musatov
- Department of Pathology and Laboratory Medicine, Tulane University Medical Center, New Orleans, Louisiana, USA
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4
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Boldog F, Gemmill RM, West J, Robinson M, Robinson L, Li E, Roche J, Todd S, Waggoner B, Lundstrom R, Jacobson J, Mullokandov MR, Klinger H, Drabkin HA. Chromosome 3p14 homozygous deletions and sequence analysis of FRA3B. Hum Mol Genet 1997; 6:193-203. [PMID: 9063739 DOI: 10.1093/hmg/6.2.193] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Loss of heterozygosity (LOH) involving 3p occurs in many carcinomas but is complicated by the identification of four distinct homozygous deletion regions. One putative target, 3p14.2, contains the common fragile site, FRA3B, a hereditary renal carcinoma-associated 3;8 translocation and the candidate tumor suppressor gene, FHIT. Using a approximately 300 kb comsid/lambda contig, we identified homozygous deletions in cervix, breast, lung and colorectal carcinoma cell lines. The smallest deletion (CC19) was shown not to involve FHIT coding exons and no DNA sequence alterations were present in the transcript. We also detected discontinuous deletions as well as deletions in non-tumor DNAs, suggesting that FHIT is not a selective target. Further, we demonstrate that some reported FHIT aberrations represent normal splicing variation. DNA sequence analysis of 110 kb demonstrated that the region is high in A-T content, LINEs and MER repeats, whereas Alu elements are reduced. We note an intriguing similarity in repeat sequence composition between FRA3B and a 152 kb segment from the Fragile-X region. We also identified similarity between a FRA3B segment and a small polydispersed circular DNA. In contrast to the selective loss of a tumor suppressor gene, we propose an alternative hypothesis, that some putative targets including FRA3B may undergo loss as a consequence of genomic instability. This instability is not due to DNA mismatch repair deficiency, but may correlate in part with p53 inactivation.
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Affiliation(s)
- F Boldog
- Division of Medical Oncology, University of Colorado Health Sciences Center, Denver 80262, USA
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5
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Cohen S, Lavi S. Induction of circles of heterogeneous sizes in carcinogen-treated cells: two-dimensional gel analysis of circular DNA molecules. Mol Cell Biol 1996; 16:2002-14. [PMID: 8628266 PMCID: PMC231187 DOI: 10.1128/mcb.16.5.2002] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Extrachromosomal circular DNA molecules are associated with genomic instability, and circles containing inverted repeats were suggested to be the early amplification products. Here we present for the first time the use of neutral-neutral two-dimensional (2D) gel electrophoresis as a technique for the identification, isolation, and characterization of heterogeneous populations of circular molecules. Using this technique, we demonstrated that in N-methyl-N'-nitro-N-nitrosoguanidine-treated simian virus 40-transformed Chinese hamster cells (CO60 cells), the viral sequences are amplified as circular molecules of various sizes. The supercoiled circular fraction was isolated and was shown to contain molecules with inverted repeats. 2D gel analysis of extrachromosomal DNA from CHO cells revealed circular molecules containing highly repetitive DNA which are similar in size to the simian virus 40-amplified molecules. Moreover, enhancement of the amount of circular DNA was observed upon N-methyl-N'-nitro-N-nitrosoguanidine treatment of CHO cells. The implications of these findings regarding the processes of gene amplification and genomic instability and the possible use of the 2D gel technique to study these phenomena are discussed.
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MESH Headings
- Animals
- CHO Cells
- Carcinogens/toxicity
- Cell Line
- Cell Line, Transformed
- Cell Transformation, Viral
- Cricetinae
- DNA Replication/drug effects
- DNA, Circular/biosynthesis
- DNA, Circular/chemistry
- DNA, Circular/ultrastructure
- DNA, Viral/biosynthesis
- DNA, Viral/chemistry
- DNA, Viral/ultrastructure
- Methylnitronitrosoguanidine/toxicity
- Microscopy, Electron
- Models, Structural
- Nucleic Acid Conformation
- Repetitive Sequences, Nucleic Acid
- Simian virus 40/genetics
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Affiliation(s)
- S Cohen
- Department of Cell Research and Immunology, Tel Aviv University, Israel
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6
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Abstract
Retroelements comprise a substantial portion of the human genome. Their large number and ubiquitous distribution has led scientists to speculate about their evolutionary origin and their biological functions. Human endogenous retroviruses and their retrotransposon relatives represent a reservoir of possibly pathogenic retroviral genes that may be activated spontaneously or by environmental conditions. They can act as insertion mutagens and activate or inactivate cellular genes, or may be involved in chromosome aberrations by recombination of related elements on different chromosomal locations. Retroviral gene products themselves may also be pathogenic and, for example, could be implicated in the development of tumors and autoimmune diseases. On the other hand, endogenous retroviral elements and nonviral retroposons are thought to have played an important role in shaping the genomes of vertebrates by intracellular transposition events and by generating hot spots of recombination. In the course of time, some of these elements have acquired cellular functions, such as, for instance, in the regulation of gene expression. Therefore, the role of human endogenous retroviruses and retroposons in biological processes is currently a subject of great interest.
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Affiliation(s)
- C Leib-Mösch
- III. Medizinische Klinik, Klinikum Mannheim, Universität Heidelberg, Mannheim, Federal Republic of Germany
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7
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McNaughton JC, Marshall CJ, Broom JE, Hughes G, Jones WA, Stockwell PA, Petersen GB. Phylogenetic relationships among transposon-like elements in human and primate DNA. J Mol Evol 1995; 40:127-35. [PMID: 7699719 DOI: 10.1007/bf00167108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A THE-1 sequence in intron 7 of the human dystrophin gene has been found to represent a new subfamily of THE-1 elements. The sequence is closely related to the MstII family of repetitive sequences and is more like single-copy sequences found in the galago genome than any other THE-1 sequence previously reported. This new THE-1 sequence has been compared with two other complete THE-1 sequences and three related long-terminal repeat elements that we have previously found in intron 7 of the dystrophin gene, and with members of the same family from elsewhere in the primate genome. Parsimony and deletion analysis show that the cluster of THE-1 sequences in intron 7 of the dystrophin gene has arisen from at least three individual insertion events, rather than from the insertion and duplication of a single progenitor sequence.
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Affiliation(s)
- J C McNaughton
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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8
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Monckton DG, Neumann R, Guram T, Fretwell N, Tamaki K, MacLeod A, Jeffreys AJ. Minisatellite mutation rate variation associated with a flanking DNA sequence polymorphism. Nat Genet 1994; 8:162-70. [PMID: 7842015 DOI: 10.1038/ng1094-162] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Human minisatellite mutation in the male germline frequently involves complex interallelic gene conversion events restricted to one end of the tandem repeat array. Some alleles at minisatellite MS32 show reduced variability in human populations and are associated with a G to C transversion upstream of the array. Analysis of single sperm demonstrated a frequently profound reduction in mutation rate at alleles carrying the C variant. This mutation suppression acts in cis, but does not affect the ability of an allele to act as sequence donor during gene conversion. This mutation rate polymorphism provides strong evidence for elements near the minisatellite that regulate tandem repeat instability.
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Affiliation(s)
- D G Monckton
- Department of Genetics, University of Leicester, UK
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9
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Hakim I, Amariglio N, Grossman Z, Simoni-Brok F, Ohno S, Rechavi G. The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence. Proc Natl Acad Sci U S A 1994; 91:7967-9. [PMID: 8058743 PMCID: PMC44525 DOI: 10.1073/pnas.91.17.7967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Amplification of rearranged human immunoglobulin heavy-chain genes using the polymerase chain reaction resulted unexpectedly in the amplification of human transposable repetitive element genomes. These were identified as members of the THE I (transposon-like human element I) transposable element family. Analysis of the THE I sequences revealed the presence of several copies of the ancestral building block described > 10 years ago by Ohno and coworkers as the primordial immunoglobulin sequence. The frequency and degree of homology of the repeats of the basic unit were similar for the two genes, as well as for two murine intracisternal A particles. These findings suggest that both the transposable genetic elements and the immunoglobulin genes originated from a common ancestral building block.
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Affiliation(s)
- I Hakim
- Institute of Hematology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
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10
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van Loon N, Miller D, Murnane JP. Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination. Nucleic Acids Res 1994; 22:2447-52. [PMID: 8041604 PMCID: PMC308194 DOI: 10.1093/nar/22.13.2447] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) generated from chromosomal DNA is found in all mammalian cells and increases with cell stress or aging. Studies of eccDNA structure and mode of formation provide insight into mechanisms of instability of the mammalian genome. Previous studies have suggested that eccDNA is generated through a process involving recombination between repetitive sequences. However, we observed that approximately one half of the small eccDNA fragments cloned from HeLa S3 cells were composed entirely of nonrepetitive or low-copy DNA sequences. We analyzed four of these fragments by polymerase chain reaction and nucleotide sequencing and found that they were complete eccDNAs. We then screened a human genomic library with the eccDNAs to isolate the complementary chromosomal sequences. Comparing the recombination junctions within the eccDNAs with the chromosomal sequences from which they were derived revealed that nonhomologous recombination was involved in their formation. One of the eccDNAs was composed of two separate sequences from different parts of the genome. These results suggest that rejoining of ends of fragmented DNA is responsible for the generation of a substantial portion of the eccDNAs found in HeLa S3 cells.
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Affiliation(s)
- N van Loon
- Laboratory of Radiobiology and Environmental Health, University of California, San Francisco 94143-0750
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11
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Plattner R, Heerema NA, Yurov YB, Palmer CG. Efficient identification of marker chromosomes in 27 patients by stepwise hybridization with alpha-satellite DNA probes. Hum Genet 1993; 91:131-40. [PMID: 8462972 DOI: 10.1007/bf00222713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Using a procedure involving stepwise hybridization of alpha-satellite DNA probes at various conditions of stringency, 33 marker chromosomes from 27 patients were identified. The markers were ascertained prenatally in fetal amniotic fluid and chorionic villi samples or postnatally in blood from liveborn children. The marker chromosomes first were characterized by cytogenetic techniques and later identified by fluorescence in situ hybridization. There were 14 bisatellited markers, 3 metacentric nonsatellited marker chromosomes, 2 nonsupernumerary sex-chromosomal rings, and 9 patients carrying markers that appeared to be small rings. Multiple stringency conditions were used for the identification of 14 supernumerary ringlike chromosomes detected in 8 patients. Ring-like markers were initially screened at low stringency and grouped into alpha-satellite families. Subsequent higher stringency hybridization led to marker identification. Ringlike chromosomes originated from chromosomes 1, 2, 8, 12, 13 or 21, 14 or 22, 15, 18, and X. Multiple ringlike markers ascertained in a single patient were determined to originate from different chromosomes.
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Affiliation(s)
- R Plattner
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis 46202
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12
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Abstract
We report a collection of 53 prototypic sequences representing known families of repetitive elements from the human genome. The prototypic sequences are either consensus sequences or selected examples of repetitive sequences. The collection includes: prototypes for high and medium reiteration frequency interspersed repeats, long terminal repeats of endogenous retroviruses, alphoid repeats, telomere-associated repeats, and some miscellaneous repeats. The collection is annotated and available electronically.
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Affiliation(s)
- J Jurka
- Linus Pauling Institute of Science and Medicine, Palo Alto, CA 94306
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13
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Pizzuti A, Pieretti M, Fenwick RG, Gibbs RA, Caskey CT. A transposon-like element in the deletion-prone region of the dystrophin gene. Genomics 1992; 13:594-600. [PMID: 1322353 DOI: 10.1016/0888-7543(92)90129-g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The central portion of the dystrophin gene locus is a preferential site for deletions causing progressive muscular dystrophy of the Duchenne type (DMD). The nucleotide sequence of a deletion junction fragment from a DMD patient was determined, revealing that the proximal breakpoint of the deletion in intron 43 fell within the sequence of a transposon-like element. This segment, belonging to the THE-1 family of human transposable elements, is normally present in a complete form in intron 43 of the dystrophin gene. The deletion mutation was maternally transmitted and eliminated two-thirds of the THE-1 element. Analysis of DNA from additional DMD patients revealed a second deletion with the proximal breakpoint mapping within the same THE-1 element.
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Affiliation(s)
- A Pizzuti
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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14
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Fields CA, Grady DL, Moyzis RK. The human THE-LTR(O) and MstII interspersed repeats are subfamilies of a single widely distributed highly variable repeat family. Genomics 1992; 13:431-6. [PMID: 1319393 DOI: 10.1016/0888-7543(92)90264-s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fifteen examples of the transposon-like human element (THE) LTR and thirteen examples of the MstII interspersed repeat are aligned to generate new consensus sequences for these human repetitive elements. The consensus sequences of these elements are very similar, indicating that they compose subfamilies of a single human interspersed repetitive sequence family. Members of this highly polymorphic repeat family have been mapped to at least 11 chromosomes. Seven examples of the THE internal sequence are also aligned to generate a new consensus sequence for this element. Estimates of the abundance of this repetitive sequence family, derived from both hybridization analysis and frequency of occurrence in GenBank, indicate that THE-LTR/MstII sequences are present every 100-3000 kb in human DNA. The widespread occurrence of members of this family makes them useful landmarks, like Alu, L1, and (GT)n repeats, for physical and genetic mapping of human DNA.
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Affiliation(s)
- C A Fields
- Computing Research Laboratory, New Mexico State University, Las Cruces 88003-0001
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15
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Motejlek K, Assum G, Krone W, Kleinschmidt AK. The size of small polydisperse circular DNA (spcDNA) in angiofibroma-derived cell cultures from patients with tuberous sclerosis (TSC) differs from that in fibroblasts. Hum Genet 1991; 87:6-10. [PMID: 1645325 DOI: 10.1007/bf01213083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cell cultures were derived from angiofibromas of three patients with tuberous sclerosis (TSC), from the unaffected skin of these patients, and from the skin of five healthy donors. The length distributions of the small polydisperse circular DNA (spcDNA) fraction of these cell cultures were then analyzed. Nearly half the spcDNA molecules from the angiofibroma cultures were longer than 0.4 micron, whereas only about 7% exceeded this threshold in the spcDNA preparations from the skin fibroblast cultures. The percentage of the larger size class of spcDNA showed an increase at higher numbers of in vitro passages in all three types of cultures, but this effect was much more conspicuous in the angiofibroma-derived cultures than in those from the skin fibroblasts. An age-dependent increase in the overall amount of spcDNA was only seen in the angiofibroma-derived cultures. Our earlier finding of elevated amounts of spcDNA in angiofibroma cultures was confirmed in cultures from an additional TSC patient.
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Affiliation(s)
- K Motejlek
- Abteilung Humangenetik der Universität, Ulm, Federal Republic of Germany
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16
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Manoharan TH, Somasundaram T, Chinnadurai G. Localization of a transcription start point within the human Hinf element. Gene X 1989; 83:173-9. [PMID: 2591745 DOI: 10.1016/0378-1119(89)90416-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Hinf family is a repetitive nucleotide sequence of the human genome. Certain structural features of Hinf DNA resemble the eukaryotic RNA polymerase II promoters. Therefore, we studied the ability of the Hinf element to function as a transcriptional promoter in mammalian cells. We placed the Hinf element upstream from the thymidine kinase-encoding (tk) sequence in a plasmid construct, pAC401 and introduced it into Ltk- mouse cells. The Hinf-tk plasmid was able to transform Ltk- cells to Tk+ phenotype. In another plasmid construct, pAC Hinf-neo, the Hinf element was inserted upstream from the sequence encoding neomycin (Nm) resistance (neo), and this plasmid was able to confer Nm resistance to HeLa cells. The nature of transcription initiation of the tk gene in four of the Tk+ clones transformed by pAC401 was examined by S1 nuclease analysis, and the transcription start point (tsp) for the tk gene in these clones was mapped within the Hinf element. The same tsp in the Hinf element was found in HeLa cells. Our studies show that the Hinf element functions as a weak promoter.
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Affiliation(s)
- T H Manoharan
- St. Louis University School of Medicine, Institute for Molecular Virology, MO 63110
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17
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Misra R, Matera AG, Schmid CW, Rush MG. Recombination mediates production of an extrachromosomal circular DNA containing a transposon-like human element, THE-1. Nucleic Acids Res 1989; 17:8327-41. [PMID: 2478961 PMCID: PMC334967 DOI: 10.1093/nar/17.20.8327] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An abundant class of HeLa extrachromosomal circular DNA containing the transposon-like element, THE-1, is shown to arise via site specific recombination. The chromosomal locus from which these circles are derived, however, is single-copy. Northern blot analysis detects homology to two polyadenylated RNAs in HeLa cells. The possible presence of an origin of replication and its role in generating these small polydisperse circles is discussed.
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Affiliation(s)
- R Misra
- Department of Biochemistry, New York University School of Medicine, NY 10016
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18
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Degroote F, Pont G, Micard D, Picard G. Extrachromosomal circular DNAs in Drosophila melanogaster: comparison between embryos and Kc0% cells. Chromosoma 1989; 98:201-6. [PMID: 2510979 DOI: 10.1007/bf00329684] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We established the size distribution of extrachromosomal covalently closed circular DNA molecules from embryos of various Drosophila melanogaster strains and from Kc0% tissue culture cells. In embryos, more than 80% of the circular DNA molecules are smaller than 2.5 kb and all the distributions show a peak of molecules of between 200 and 400 bp. The Kc0% cell distribution differs mainly from that of embryos in that 48% of the molecules have a size between 4 and 8 kb. Correlating with this, circular molecules homologous to copia, 412 and 297 were detected only in Kc0% cells. The three tandemly repeated families containing the 5S genes, the histone genes and the 240 bp repeat of the ribosomal DNA intergenic spacer, which had previously been identified in circular DNAs from embryos, were also found in cultured cells. A fourth tandemly repeated family corresponding to the 1.688 g/cm3 satellite DNA was detected, both in embryos and Kc0% cells. It consists of circular multimeric molecules containing multiple copies of the 359 bp repeated unit. No circular DNA molecules homologous to the actin genes, the type I ribosomal DNA insertion, or the F and I transposable elements were found in embryos or Kc0% cells. Thus it appears that the extrachromosomal circular DNA molecules from embryos and from tissue culture cells differ mainly in the presence of circular copies of the copia-like transposable elements.
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Affiliation(s)
- F Degroote
- Laboratoire de Génétique, UA 360 CNRS, Université Blaise-Pascal Clermont-Ferrand II, Aubière, France
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Shih A, Misra R, Rush MG. Detection of multiple, novel reverse transcriptase coding sequences in human nucleic acids: relation to primate retroviruses. J Virol 1989; 63:64-75. [PMID: 2462064 PMCID: PMC247658 DOI: 10.1128/jvi.63.1.64-75.1989] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A variety of chemically synthesized oligonucleotides designed on the basis of amino acid and/or nucleotide sequence data were used to detect a large number of novel reverse transcriptase coding sequences in human and mouse DNAs. Procedures involving Southern blotting, library screening, and the polymerase chain reaction were all used to detect such sequences; the polymerase chain reaction was the most rapid and productive approach. In the polymerase chain reaction, oligonucleotide mixtures based on consensus sequence homologies to reverse transcriptase coding sequences and unique oligonucleotides containing perfect homology to the coding sequences of human T-cell leukemia virus types I and II were both effective in amplifying reverse transcriptase-related DNA. It is shown that human DNA contains a wide spectrum of retrovirus-related reverse transcriptase coding sequences, including some that are clearly related to human T-cell leukemia virus types I and II, some that are related to the L-1 family of long interspersed nucleotide sequences, and others that are related to previously described human endogenous proviral DNAs. In addition, human T-cell leukemia virus type I-related sequences appear to be transcribed in both normal human T cells and in a cell line derived from a human teratocarcinoma.
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Affiliation(s)
- A Shih
- Department of Biochemistry, New York University School of Medicine, New York 10016
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Sunnerhagen P, Sjöberg RM, Bjursell G. Increase of extrachromosomal circular DNA in mouse 3T6 cells on perturbation of DNA synthesis: implications for gene amplification. SOMATIC CELL AND MOLECULAR GENETICS 1989; 15:61-70. [PMID: 2492679 DOI: 10.1007/bf01534670] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have analyzed the amount of extrachromosomal double-stranded covalently closed circular nonmitochondrial DNA in mouse 3T6 cells by Southern blotting and electron microscopy. Treatment with 7,1-dimethylbenz[a]anthracene, known to promote amplification of integrated SV40 genomes, elevated the amount of circular DNA. Inhibition of DNA synthesis with hydroxyurea, earlier shown to enhance amplification of the cellular dihydrofolate reductase gene, resulted in yet higher levels. Thus, elevation of the frequency of gene amplification and generation of extrachromosomal circular DNA seem to accompany each other in the situations studied in this paper. Two other DNA synthesis inhibitors, aphidicolin and thymidine, had markedly lesser effects on circular DNA. The significance of these findings for the mechanism of gene amplification is discussed.
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Affiliation(s)
- P Sunnerhagen
- Department of Medical Biochemistry, University of Göteborg, Sweden
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Affiliation(s)
- G Echalier
- URA 7 CNRS, Laboratoire de Zoologie, Université Pierre et Marie Curie, Paris, France
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Pont G, Degroote F, Picard G. Illegitimate recombination in the histone multigenic family generates circular DNAs in Drosophila embryos. Nucleic Acids Res 1988; 16:8817-33. [PMID: 3140219 PMCID: PMC338637 DOI: 10.1093/nar/16.18.8817] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
From extrachromosomal covalently closed circular DNA molecules purified from Drosophila melanogaster embryos, we have isolated 24 clones homologous to the histone tandemly repeated gene family. Some of the clones harbor one of the two main types of genomic repeated units of 4.8 and 5.0 kb. and probably result from homologous recombination. The remaining clones have a size ranging from 0.2 to 2.5 kb. and most of them carry a single fragment of the repeated unit. Nucleotide sequences of the junction region of six of these clones indicate they are generated by illegitimate recombination between short (8-15 bp.) imperfect direct repeats. The data suggest that most of the histone homologous circular DNA molecules are deleted histone units.
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Affiliation(s)
- G Pont
- Laboratoire de Génétique, UA 360 CNRS, Université Blaise Pascal-Clermont-Fd. II, Aubière, France
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Deka N, Willard CR, Wong E, Schmid CW. Human transposon-like elements insert at a preferred target site: evidence for a retrovirally mediated process. Nucleic Acids Res 1988; 16:1143-51. [PMID: 2830591 PMCID: PMC334743 DOI: 10.1093/nar/16.3.1143] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Members of the human transposon-like family of repetitive sequences (called THE 1 repeats) like many other repetitive DNA sequences are flanked by short direct repeats. Comparison of the base sequences of twelve examples of these flanking direct repeats indicates that THE 1 repeats insert into a preferred genomic target site. In one case, we have identified the sequence of an empty site into which a THE 1 element inserted. The sequence of this empty site and sequences of truncated THE 1 LTRs are consistent with a retroviral mechanism for the insertion of THE 1 elements. Truncated transposon structures illustrate for the first time that intermediate structures of retrotransposition may also be integrated into the genome.
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Affiliation(s)
- N Deka
- Department of Chemistry, University of California, Davis 95616
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