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Sharma M, Larow VM, Dobychina N, Kessler DS, Krasilnikova MM, Yaklichkin S. The evolutionary loss of the Eh1 motif in FoxE1 in the lineage of placental mammals. PLoS One 2023; 18:e0296176. [PMID: 38150428 PMCID: PMC10752562 DOI: 10.1371/journal.pone.0296176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Forkhead box E1 (FoxE1) protein is a transcriptional regulator known to play a major role in the development of the thyroid gland. By performing sequence alignments, we detected a deletion in FoxE1, which occurred in the evolution of mammals, near the point of divergence of placental mammals. This deletion led to the loss of the majority of the Eh1 motif, which was important for interactions with transcriptional corepressors. To investigate a potential mechanism for this deletion, we analyzed replication through the deletion area in mammalian cells with two-dimensional gel electrophoresis, and in vitro, using a primer extension reaction. We demonstrated that the area of the deletion presented an obstacle for replication in both assays. The exact position of polymerization arrest in primer extension indicated that it was most likely caused by a quadruplex DNA structure. The quadruplex structure hypothesis is also consistent with the exact borders of the deletion. The exact roles of these evolutionary changes in FoxE1 family proteins are still to be determined.
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Affiliation(s)
- Mahak Sharma
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Victoria M. Larow
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Nataliia Dobychina
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Daniel S. Kessler
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maria M. Krasilnikova
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Sergey Yaklichkin
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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2
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Huda A, Arakawa H, Mazzucco G, Galli M, Petrocelli V, Casola S, Chen L, Doksani Y. The telomerase reverse transcriptase elongates reversed replication forks at telomeric repeats. SCIENCE ADVANCES 2023; 9:eadf2011. [PMID: 36947627 PMCID: PMC10032592 DOI: 10.1126/sciadv.adf2011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The telomerase reverse transcriptase elongates telomeres to prevent replicative senescence. This process requires exposure of the 3'-end, which is thought to occur when two sister telomeres are generated at replication completion. Using two-dimensional agarose gel electrophoresis (2D-gels) and electron microscopy, we found that telomeric repeats are hotspots for replication fork reversal. Fork reversal generates 3' telomeric ends before replication completion. To verify whether these ends are elongated by telomerase, we probed de novo telomeric synthesis in situ and at replication intermediates by reconstituting mutant telomerase that adds a variant telomere sequence. We found variant telomeric repeats overlapping with telomeric reversed forks in 2D-gels, but not with normal forks, nontelomeric reversed forks, or telomeric reversed forks with a C-rich 3'-end. Our results define reversed telomeric forks as a substrate of telomerase during replication.
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Affiliation(s)
- Armela Huda
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiroshi Arakawa
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giulia Mazzucco
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Martina Galli
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Valentina Petrocelli
- Institute for Tumor Biology and Experimental Therapy, Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefano Casola
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Lu Chen
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Ylli Doksani
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
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3
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Abstract
TelN and tos are a unique DNA linearization unit isolated from bacteriophage N15. While being transferable, the TelN cleaving-rejoining activities remained stable to function on tos in both bacterial and mammalian environments. However, TelN contribution in linear plasmid replication in mammalian cells remains unknown. Herein, we investigated the association of TelN in linear tos-containing DNA (tos-DNA) replication in mammalian cells. Additionally, the mammalian origin of replication (ori) that is well-known to initiate the replication event of plasmid vectors was also studied. In doing so, we identified that both TelN and mammalian initiation sites were essential for the replication of linear tos-DNA, determined by using methylation sensitive DpnI/MboI digestion and polymerase chain reaction (PCR) amplification approaches. Furthermore, we engineered the linear tos-DNA to be able to retain in mammalian cells using S/MAR technology. The resulting S/MAR containing tos-DNA was robust for at least 15 days, with (1) continuous tos-DNA replication, (2) correct splicing of gene transcripts, and (3) stable exogenous gene expression that was statistically comparable to the endogenous gene expression level. Understanding the activities of TelN and tos in mammalian cells can potentially provide insights for adapting this simple DNA linearization unit in developing novel genetic engineering tools, especially to the eukaryotic telomere/telomerase study.
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Affiliation(s)
- Pei Sheng Liew
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Tze Hao Tan
- Faculty of Science, Kyushu University, Ito campus, Fukuoka 819-0395, Japan
| | - Yin Cheng Wong
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Edmund Ui Hang Sim
- Faculty of Resource Sciences and Technology, University Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | - Choon Weng Lee
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
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Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition. Mol Cell 2018; 72:222-238.e11. [PMID: 30293786 DOI: 10.1016/j.molcel.2018.08.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023]
Abstract
DNA polymerase stalling activates the ATR checkpoint kinase, which in turn suppresses fork collapse and breakage. Herein, we describe use of ATR inhibition (ATRi) as a means to identify genomic sites of problematic DNA replication in murine and human cells. Over 500 high-resolution ATR-dependent sites were ascertained using two distinct methods: replication protein A (RPA)-chromatin immunoprecipitation (ChIP) and breaks identified by TdT labeling (BrITL). The genomic feature most strongly associated with ATR dependence was repetitive DNA that exhibited high structure-forming potential. Repeats most reliant on ATR for stability included structure-forming microsatellites, inverted retroelement repeats, and quasi-palindromic AT-rich repeats. Notably, these distinct categories of repeats differed in the structures they formed and their ability to stimulate RPA accumulation and breakage, implying that the causes and character of replication fork collapse under ATR inhibition can vary in a DNA-structure-specific manner. Collectively, these studies identify key sources of endogenous replication stress that rely on ATR for stability.
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5
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Keogh N, Chan KY, Li GM, Lahue RS. MutSβ abundance and Msh3 ATP hydrolysis activity are important drivers of CTG•CAG repeat expansions. Nucleic Acids Res 2017; 45:10068-10078. [PMID: 28973443 PMCID: PMC5622409 DOI: 10.1093/nar/gkx650] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/14/2017] [Indexed: 01/01/2023] Open
Abstract
CTG•CAG repeat expansions cause at least twelve inherited neurological diseases. Expansions require the presence, not the absence, of the mismatch repair protein MutSβ (Msh2-Msh3 heterodimer). To evaluate properties of MutSβ that drive expansions, previous studies have tested under-expression, ATPase function or polymorphic variants of Msh2 and Msh3, but in disparate experimental systems. Additionally, some variants destabilize MutSβ, potentially masking the effects of biochemical alterations of the variations. Here, human Msh3 was mutated to selectively inactivate MutSβ. Msh3-/- cells are severely defective for CTG•CAG repeat expansions but show full activity on contractions. Msh3-/- cells provide a single, isogenic system to add back Msh3 and test key biochemical features of MutSβ on expansions. Msh3 overexpression led to high expansion activity and elevated levels of MutSβ complex, indicating that MutSβ abundance drives expansions. An ATPase-defective Msh3 expressed at normal levels was as defective in expansions as Msh3-/- cells, indicating that Msh3 ATPase function is critical for expansions. Expression of two Msh3 polymorphic variants at normal levels showed no detectable change in expansions, suggesting these polymorphisms primarily affect Msh3 protein stability, not activity. In summary, CTG•CAG expansions are limited by the abundance of MutSβ and rely heavily on Msh3 ATPase function.
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Affiliation(s)
- Norma Keogh
- Centre for Chromosome Biology, National University of Ireland Galway, Newcastle Road, Galway H91T K33, Ireland
| | - Kara Y Chan
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Guo-Min Li
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY 40536, USA.,Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Robert S Lahue
- Centre for Chromosome Biology, National University of Ireland Galway, Newcastle Road, Galway H91T K33, Ireland.,NCBES Galway Neuroscience Centre, National University of Ireland Galway, Newcastle Road, Galway H91T K33, Ireland
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Krasilnikova MM. Complexes between two GAA Repeats within DNA introduced into Cos-1 cells. Mob Genet Elements 2014; 2:267-271. [PMID: 23481169 PMCID: PMC3575420 DOI: 10.4161/mge.23194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have recently shown that GAA repeats severely impede replication elongation during the first replication cycle of transfected DNA wherein the chromatin is still at the formation stage.1 Here we extend this study by showing that two GAA repeats located within the same plasmid in the direct orientation can form complexes upon transient transfection of mammalian Cos-1 cells. However, these complexes do not form in DNA that went through several replication rounds in mammalian cells. We suggest that formation of such complexes in mammalian genomes can contribute to genomic instability.
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Chen X, Liu G, Leffak M. Activation of a human chromosomal replication origin by protein tethering. Nucleic Acids Res 2013; 41:6460-74. [PMID: 23658226 PMCID: PMC3711443 DOI: 10.1093/nar/gkt368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The specification of mammalian chromosomal replication origins is incompletely understood. To analyze the assembly and activation of prereplicative complexes (pre-RCs), we tested the effects of tethered binding of chromatin acetyltransferases and replication proteins on chromosomal c-myc origin deletion mutants containing a GAL4-binding cassette. GAL4DBD (DNA binding domain) fusions with Orc2, Cdt1, E2F1 or HBO1 coordinated the recruitment of the Mcm7 helicase subunit, the DNA unwinding element (DUE)-binding protein DUE-B and the minichromosome maintenance (MCM) helicase activator Cdc45 to the replicator, and restored origin activity. In contrast, replication protein binding and origin activity were not stimulated by fusion protein binding in the absence of flanking c-myc DNA. Substitution of the GAL4-binding site for the c-myc replicator DUE allowed Orc2 and Mcm7 binding, but eliminated origin activity, indicating that the DUE is essential for pre-RC activation. Additionally, tethering of DUE-B was not sufficient to recruit Cdc45 or activate pre-RCs formed in the absence of a DUE. These results show directly in a chromosomal background that chromatin acetylation, Orc2 or Cdt1 suffice to recruit all downstream replication initiation activities to a prospective origin, and that chromosomal origin activity requires singular DNA sequences.
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Affiliation(s)
- Xiaomi Chen
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells. G3-GENES GENOMES GENETICS 2013; 3:451-63. [PMID: 23450065 PMCID: PMC3583453 DOI: 10.1534/g3.112.005173] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 12/30/2012] [Indexed: 12/19/2022]
Abstract
Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSα and MutLα complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletion or expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.
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Gaspar VM, Cruz C, Queiroz JA, Pichon C, Correia IJ, Sousa F. Sensitive Detection of Peptide–Minicircle DNA Interactions by Surface Plasmon Resonance. Anal Chem 2013; 85:2304-11. [DOI: 10.1021/ac303288x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Vítor M. Gaspar
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - João A. Queiroz
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Chantal Pichon
- Centre de Biophysique Moléculaire
CNRS UPR4301, INSERM and University of Orléans, F-45071 Orléans cedex 2, France
| | - Ilídio J. Correia
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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Chandok GS, Patel MP, Mirkin SM, Krasilnikova MM. Effects of Friedreich's ataxia GAA repeats on DNA replication in mammalian cells. Nucleic Acids Res 2012; 40:3964-74. [PMID: 22262734 PMCID: PMC3351192 DOI: 10.1093/nar/gks021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/20/2011] [Accepted: 01/04/2012] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a common hereditary degenerative neuro-muscular disorder caused by expansions of the (GAA)n repeat in the first intron of the frataxin gene. The expanded repeats from parents frequently undergo further significant length changes as they are passed on to progeny. Expanded repeats also show an age-dependent instability in somatic cells, albeit on a smaller scale than during intergenerational transmissions. Here we studied the effects of (GAA)n repeats of varying lengths and orientations on the episomal DNA replication in mammalian cells. We have recently shown that the very first round of the transfected DNA replication occurs in the lack of the mature chromatin, does not depend on the episomal replication origin and initiates at multiple single-stranded regions of plasmid DNA. We now found that expanded GAA repeats severely block this first replication round post plasmid transfection, while the subsequent replication cycles are only mildly affected. The fact that GAA repeats affect various replication modes in a different way might shed light on their differential expansions characteristic for FRDA.
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Affiliation(s)
- Gurangad S. Chandok
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802 and Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Mayank P. Patel
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802 and Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M. Mirkin
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802 and Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Maria M. Krasilnikova
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802 and Department of Biology, Tufts University, Medford, MA 02155, USA
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Abstract
In this issue of Cell Stem Cell, Ku et al. (2010) demonstrate that iPSCS derived from Friedreich's ataxia patients exhibit expansion of the causative (GAA)(n) repeat, consistent with the repeat instability observed during intergenerational transmissions in humans. Furthermore, the epigenetic signature of the disease remains intact in Friedreich's ataxia iPSCs.
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McIver LJ, Fondon JW, Skinner MA, Garner HR. Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments. Genomics 2011; 97:193-9. [PMID: 21223998 DOI: 10.1016/j.ygeno.2011.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/14/2010] [Accepted: 01/03/2011] [Indexed: 12/18/2022]
Abstract
We performed an analysis of global microsatellite variation on the two kindreds sequenced at high depth (~20×-60×) in the 1000 Genomes Project pilot studies because alterations in these highly mutable repetitive sequences have been linked with many phenotypes and disease risks. The standard alignment technique performs poorly in microsatellite regions as a consequence of low effective coverage (~1×-5×) resulting in 79% of the informative loci exhibiting non-Mendelian inheritance patterns. We used a more stringent approach in computing robust allelotypes resulting in 94.4% of the 1095 informative repeats conforming to traditional inheritance. The high-confidence allelotypes were analyzed to obtain an estimate of the minimum polymorphism rate as a function of motif length, motif sequence, and distribution within the genome.
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Affiliation(s)
- L J McIver
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0477, USA
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