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Ward JR, Khan A, Torres S, Crawford B, Nock S, Frisbie T, Moran J, Longworth M. Condensin I and condensin II proteins form a LINE-1 dependent super condensin complex and cooperate to repress LINE-1. Nucleic Acids Res 2022; 50:10680-10694. [PMID: 36169232 PMCID: PMC9561375 DOI: 10.1093/nar/gkac802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Condensin I and condensin II are multi-subunit complexes that are known for their individual roles in genome organization and preventing genomic instability. However, interactions between condensin I and condensin II subunits and cooperative roles for condensin I and condensin II, outside of their genome organizing functions, have not been reported. We previously discovered that condensin II cooperates with Gamma Interferon Activated Inhibitor of Translation (GAIT) proteins to associate with Long INterspersed Element-1 (LINE-1 or L1) RNA and repress L1 protein expression and the retrotransposition of engineered L1 retrotransposition in cultured human cells. Here, we report that the L1 3'UTR is required for condensin II and GAIT association with L1 RNA, and deletion of the L1 RNA 3'UTR results in increased L1 protein expression and retrotransposition. Interestingly, like condensin II, we report that condensin I also binds GAIT proteins, associates with the L1 RNA 3'UTR, and represses L1 retrotransposition. We provide evidence that the condensin I protein, NCAPD2, is required for condensin II and GAIT protein association with L1 RNA. Furthermore, condensin I and condensin II subunits interact to form a L1-dependent super condensin complex (SCC) which is located primarily within the cytoplasm of both transformed and primary epithelial cells. These data suggest that increases in L1 expression in epithelial cells promote cytoplasmic condensin protein associations that facilitate a feedback loop in which condensins may cooperate to mediate L1 repression.
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Affiliation(s)
- Jacqueline R Ward
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Afshin Khan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bert Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sarah Nock
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Trenton Frisbie
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, USA
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2
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Komissarov AS, Galkina SA, Koshel EI, Kulak MM, Dyomin AG, O'Brien SJ, Gaginskaya ER, Saifitdinova AF. New high copy tandem repeat in the content of the chicken W chromosome. Chromosoma 2017; 127:73-83. [PMID: 28951974 DOI: 10.1007/s00412-017-0646-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.
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Affiliation(s)
- Aleksey S Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy av. 41, 199034, Saint Petersburg, Russia
| | - Svetlana A Galkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
- Saint Petersburg Association of Scientists and Scholars, Universitetskaya emb. 5, Saint Petersburg, 199034, Russia
| | - Elena I Koshel
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Maria M Kulak
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Aleksander G Dyomin
- Saint Petersburg Association of Scientists and Scholars, Universitetskaya emb. 5, Saint Petersburg, 199034, Russia
- Chromas Research Resource Center, Saint Petersburg State University, Oranienbaumskoye sh. 2, 198504, Saint Petersburg, Russia
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy av. 41, 199034, Saint Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, 33004, USA
| | - Elena R Gaginskaya
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Alsu F Saifitdinova
- Chromas Research Resource Center, Saint Petersburg State University, Oranienbaumskoye sh. 2, 198504, Saint Petersburg, Russia.
- International Centre of Reproductive Medicine, Komendantskiy av. 53-1, Saint Petersburg, 197350, Russia.
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3
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Hayward BE, Zavanelli M, Furano AV. Recombination creates novel L1 (LINE-1) elements in Rattus norvegicus. Genetics 1997; 146:641-54. [PMID: 9178013 PMCID: PMC1208004 DOI: 10.1093/genetics/146.2.641] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian L1 (long interspersed repeated DNA. LINE-1) retrotransposons consist of a 5' untranslated region (UTR) with regulatory properties, two protein encoding regions (ORF I, ORF II, which encodes a reverse transcriptase) and a 3' UTR. L1 elements have been evolving in mammals for > 100 million years and this process continues to generate novel L1 subfamilies in modern species. Here we characterized the youngest known subfamily in Rattus norvegicus, L1mlvi2, and unexpectedly found that this element has a dual ancestry. While its 3' UTR shares the same lineage as its nearest chronologically antecedent subfamilies, L13 and L14, its ORF I sequence does not. The L1mlvi2 ORF I was derived from an ancestral ORF I sequence that was the evolutionary precursor of the L13 and L14 ORF I. We suggest that an ancestral ORF I sequence was recruited into the modern L1mlvi2 subfamily by recombination that possibly could have resulted from template strand switching by the reverse transcriptase during L1 replication. This mechanism could also account for some of the structural features of rodent L1 5' UTR and ORF I sequences including one of the more dramatic features of L1 evolution in mammals, namely the repeated acquisition of novel 5' UTRs.
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Affiliation(s)
- B E Hayward
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Maryland 20892-0830, USA
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Nishikawa N, Kanda N, Oishi M, Kiyama R. Enrichment of oligo(dG).oligo(dC)-containing fragments from human genomic DNA by Mg 2+-dependent triplex affinity capture. Nucleic Acids Res 1997; 25:1701-8. [PMID: 9108150 PMCID: PMC146659 DOI: 10.1093/nar/25.9.1701] [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: 02/04/2023] Open
Abstract
Oligo(dG).oligo(dC)- or short poly(dG).poly(dC)-containing fragments were enriched and cloned by means of Mg2+-dependent triplex affinity capture and subsequent cloning procedures. A library constructed after three cycles of enrichment showed that approximately 80% of the clones in the supercoiled form formed a complex with labeled oligonucleotide (dG)34. However, while the rest of the clones retained the ability to form a complex (type I clones), 90.9% failed to form a complex when they were linearized. This group of DNA was abundant in the genomic DNA, although it showed only approximately 3-fold enrichment by one cycle of affinity capture. This group was further classified into two species (types II and III) based on complex formation ability after phenol extraction. Type II clones retained the complex formation ability after treatment, while the human telomere [(TTAGGG)n] and telomere-like [(TGGAA)n] or [(TGGAG)n] sequences belonging to type III clones did not. Serial deletion experiments and the binding assays using oligonucleotides confirmed that the repetitive units containing T(G)nT ( n = 3-5) tracts or (G)n-motifs (n >/= 3) were the sites of complex formation for type II and III clones. On the other hand, type I clones contained poly(dG).poly(dC) tracts at least 10 nt long, and DNase I-footprinting analysis indicated that these tracts were the sites of complex formation.
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Affiliation(s)
- N Nishikawa
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113, Japan
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Daniels GA, Lieber MR. RNA:DNA complex formation upon transcription of immunoglobulin switch regions: implications for the mechanism and regulation of class switch recombination. Nucleic Acids Res 1995; 23:5006-11. [PMID: 8559658 PMCID: PMC307506 DOI: 10.1093/nar/23.24.5006] [Citation(s) in RCA: 170] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Central the regulation and mechanism of class switch recombination is the understanding of the relationship between transcription and DNA recombination. We demonstrated previously, using mini-chromosome substrates, that physiologically oriented transcription is required for recombination to occur between switch regions. In this report, we demonstrate the formation of an RNA:DNA complex under in vitro transcription conditions for these same and other switch DNA fragments. We find that cell-free transcription of repetitive murine switch regions (Smu, S gamma 2b and S gamma 3) leads to altered DNA mobility on agarose gels. These altered mobilities are resistant to RNase A but sensitive to RNase H. Transcription in the presence of labeled ribonucleotides demonstrates the stable physical association of the RNA with the DNA. Importantly, complex formation only occurs upon transcription in the physiologic orientation. Reaban and Griffin [1990 Nature, 348, 342-344] found an RNA:DNA hybrid structure that was limited to an atypical 143 nucleotide purine region within a 2.3 kb S alpha segment. Here we demonstrate RNA:DNA hybrid formation in more typical switch sequences (lacking the atypical 143 nucleotide purine tract) from a variety of switch regions that are only 60-70% purine on the non-template strand. These results suggest a general model involving an RNA:DNA complex as an intermediate during class switch recombination.
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Affiliation(s)
- G A Daniels
- Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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6
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Furano AV, Usdin K. DNA "fossils" and phylogenetic analysis. Using L1 (LINE-1, long interspersed repeated) DNA to determine the evolutionary history of mammals. J Biol Chem 1995; 270:25301-4. [PMID: 7592685 DOI: 10.1074/jbc.270.43.25301] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- A V Furano
- Section on Genomic Structure and Function, NIDDK, National Institutes of Health, Bethesda, Maryland 20893-0830, USA
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8
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Gualberto A, Patrick RM, Walsh K. Nucleic acid specificity of a vertebrate telomere-binding protein: evidence for G-G base pair recognition at the core-binding site. Genes Dev 1992; 6:815-24. [PMID: 1577275 DOI: 10.1101/gad.6.5.815] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A factor from avian cells formed complexes with telomeric sequences and other single-stranded probes that contained tracts of guanine residues. Nucleoprotein complexes with telomere probes required two or more of the telomeric repeats that were incapable of Watson-Crick base-pairing. Methylation interference and protection experiments identified guanine N7 residues that were critical for the formation of the nucleoprotein complex and for the formation of a higher-order structure that occurred in the absence of the protein. Substitutions of deoxyinosine (dI) for deoxyguanosine (dG) demonstrated that the exocyclic N2 amino groups in the internal telomeric repeat, but not the terminal repeat, were required for the formation of the chemically protected structure and for protein binding. On the basis of these data we propose that the factor specifically recognizes a hairpin DNA structure that is stabilized by intramolecular G-G base-pairing between the telomere repeats. The positions of the critical guanine N2 and N7 groups indicate a G-G base-pairing configuration, where guanines function as hydrogen bond donors at the internal telomeric repeat and hydrogen bond acceptors at the terminal telomeric repeat.
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Affiliation(s)
- A Gualberto
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
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9
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Satyanarayana K, Strominger JL. DNA sequences near a meiotic recombinational breakpoint within the human HLA-DQ region. Immunogenetics 1992; 35:235-40. [PMID: 1541483 DOI: 10.1007/bf00166828] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular organization of HLA-DQ regions derived from DR7, DQw2, and DR4, DQw3 parental haplotypes and DR7, DQw3, a presumed recombinant haplotype, have been studied to define the sequences between DQA1 and DQB1 which may have been involved in this recombinational event. The breakpoint was localized in the intergenic region near the 3' end of the DQB1 gene by restriction mapping. DNA sequences in the immediate vicinity of the breakpoint in DR7, DQw2 (parental), and DR7, DQw3 (recombinant) haplotypes revealed the presence of (CA)22 repeats, minisatellite-related sequences and GC-rich sequences. The intergenic regions varied considerably depending on the haplotype and contained several additional types of repetitive sequences including Alu and LINE repeats. Some of these sequences are related to sequences previously suggested to be involved in meiotic or somatic recombination. In particular, (CA)n repeats, which can adopt the Z-DNA conformation, have previously been shown to promote recombination in several systems.
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Affiliation(s)
- K Satyanarayana
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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10
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Abstract
The DNA of telomeres--the terminal DNA-protein complexes of chromosomes--differs notably from other DNA sequences in both structure and function. Recent work has highlighted its remarkable mode of synthesis by the ribonucleoprotein reverse transcriptase, telomerase, as well as its ability to form unusual structures in vitro. Moreover, telomere synthesis by telomerase has been shown to be essential for telomere maintenance and long-term viability.
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11
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Abstract
A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.
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MESH Headings
- Animals
- Base Sequence
- Chromosomes/ultrastructure
- DNA/drug effects
- DNA/metabolism
- DNA/ultrastructure
- DNA Helicases/metabolism
- DNA Replication
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/metabolism
- DNA, Single-Stranded/ultrastructure
- DNA, Superhelical/drug effects
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/metabolism
- Endonucleases/metabolism
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation/drug effects
- Nucleic Acid Denaturation
- Plasmids
- Transcription, Genetic
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Affiliation(s)
- G Yagil
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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12
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Pascale E, Valle E, Furano AV. Amplification of an ancestral mammalian L1 family of long interspersed repeated DNA occurred just before the murine radiation. Proc Natl Acad Sci U S A 1990; 87:9481-5. [PMID: 2251288 PMCID: PMC55190 DOI: 10.1073/pnas.87.23.9481] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Each mammalian genus examined so far contains 50,000-100,000 members of an L1 (LINE 1) family of long interspersed repeated DNA elements. Current knowledge on the evolution of L1 families presents a paradox because, although L1 families have been in mammalian genomes since before the mammalian radiation approximately 80 million years ago, most members of the L1 families are only a few million years old. Accordingly it has been suggested either that the extensive amplification that characterizes present-day L1 families did not occur in the past or that old members were removed as new ones were generated. However, we show here that an ancestral rodent L1 family was extensively amplified approximately 10 million years ago and that the relics (approximately 60,000 copies) of this amplification have persisted in modern murine genomes (Old World rats and mice). This amplification occurred just before the divergence of modern murine genera from their common ancestor and identifies the murine node in the lineage of modern muroid rodents. Our results suggest that repeated amplification of L1 elements is a feature of the evolution of mammalian genomes and that ancestral amplification events could provide a useful tool for determining mammalian lineages.
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Affiliation(s)
- E Pascale
- Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892
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13
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Weinreb A, Collier DA, Birshtein BK, Wells RD. Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40021-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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The Structure of the Guanine-rich Polypurine: Polypyrimidine Sequence at the Right End of the Rat L1 (LINE) Element. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84886-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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