1
|
Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. Nat Commun 2024; 15:6636. [PMID: 39107287 PMCID: PMC11303717 DOI: 10.1038/s41467-024-50348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
Collapse
Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
- Department of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA.
| |
Collapse
|
2
|
Yang Y, Wang Y, Yan Z, Li Z, Guo P. Effects of interrupting residues on DNA dumbbell structures formed by CCTG tetranucleotide repeats associated with myotonic dystrophy type 2. FEBS Lett 2024. [PMID: 38922834 DOI: 10.1002/1873-3468.14952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024]
Abstract
Myotonic dystrophy type 2 (DM2) is a neurogenerative disease caused by caprylic/capric triglyceride (CCTG) tetranucleotide repeat expansions in intron 1 of the cellular nucleic acid-binding protein (CNBP) gene. Non-B DNA structures formed by CCTG repeats can promote genetic instability, whereas interrupting motifs of NCTG (N = A/T/G) within CCTG repeats help to maintain genomic stability. However, whether the interrupting motifs can affect DNA structures of CCTG repeats remains unclear. Here, we report that four CCTG repeats with an interrupting 3'-A/T/G residue formed dumbbell structures, whereas a non-interrupting 3'-C residue resulted in a multi-loop structure exhibiting conformational dynamics that may contribute to a higher tendency of escaping from DNA mismatch repair and causing repeat expansions. The results provide new structural insights into the genetic instability of CCTG repeats in DM2.
Collapse
Affiliation(s)
- Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM) Chinese Academy of Sciences, China
| | - Yang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM) Chinese Academy of Sciences, China
- School of Materials Science and Engineering, Tianjin University, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM) Chinese Academy of Sciences, China
| | - Zhigang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM) Chinese Academy of Sciences, China
| |
Collapse
|
3
|
Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.563609. [PMID: 38014227 PMCID: PMC10680705 DOI: 10.1101/2023.11.15.563609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
Collapse
Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | | |
Collapse
|
4
|
Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (BETHESDA, MD.) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
Collapse
Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| |
Collapse
|
5
|
Marzullo M, Coni S, De Simone A, Canettieri G, Ciapponi L. Modeling Myotonic Dystrophy Type 2 Using Drosophila melanogaster. Int J Mol Sci 2023; 24:14182. [PMID: 37762484 PMCID: PMC10532015 DOI: 10.3390/ijms241814182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Myotonic dystrophy 2 (DM2) is a genetic multi-systemic disease primarily affecting skeletal muscle. It is caused by CCTGn expansion in intron 1 of the CNBP gene, which encodes a zinc finger protein. DM2 disease has been successfully modeled in Drosophila melanogaster, allowing the identification and validation of new pathogenic mechanisms and potential therapeutic strategies. Here, we describe the principal tools used in Drosophila to study and dissect molecular pathways related to muscular dystrophies and summarize the main findings in DM2 pathogenesis based on DM2 Drosophila models. We also illustrate how Drosophila may be successfully used to generate a tractable animal model to identify novel genes able to affect and/or modify the pathogenic pathway and to discover new potential drugs.
Collapse
Affiliation(s)
- Marta Marzullo
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Sonia Coni
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Assia De Simone
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
- Istituto Pasteur Italia, Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Laura Ciapponi
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| |
Collapse
|
6
|
Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Kolar K, Mirkin SM, Kim JC. Massive contractions of Myotonic Dystrophy Type 2-associated CCTG tetranucleotide repeats occur via double strand break repair with distinct requirements for helicases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548036. [PMID: 37461657 PMCID: PMC10350092 DOI: 10.1101/2023.07.06.548036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Myotonic Dystrophy Type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75-11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are required for these massive contractions, indicating a mechanism that involves homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a low-repeat control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kara Kolar
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Jane C. Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078
| |
Collapse
|
7
|
Kouzine F, Wojtowicz D, Przytycka TM, Levens D. Detection of Z-DNA Structures in Supercoiled Genome. Methods Mol Biol 2023; 2651:179-193. [PMID: 36892768 PMCID: PMC10512777 DOI: 10.1007/978-1-0716-3084-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Z-DNAs are nucleic acid secondary structures that form within a special pattern of nucleotides and are promoted by DNA supercoiling. Through Z-DNA formation, DNA encodes information by dynamic changes in its secondary structure. A growing body of evidence indicates that Z-DNA formation can play a role in gene regulation; it can affect chromatin architecture and demonstrates its association with genomic instability, genetic diseases, and genome evolution. Many functional roles of Z-DNA are yet to be discovered highlighting the need for techniques to detect genome-wide folding of DNA into this structure. Here, we describe an approach to convert linear genome into supercoiled genome sponsoring Z-DNA formation. Applying permanganate-based methodology and high-throughput sequencing to supercoiled genome allows genome-wide detection of single-stranded DNA. Single-stranded DNA is characteristic of the junctions between the classical B-form of DNA and Z-DNA. Consequently, analysis of single-stranded DNA map provides snapshots of the Z-DNA conformation over the whole genome.
Collapse
Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology, NCI/NIH, Bethesda, MD, USA.
| | | | | | - David Levens
- Laboratory of Pathology, NCI/NIH, Bethesda, MD, USA
| |
Collapse
|
8
|
Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
Collapse
Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
9
|
Vasiliskov VA, Shershov VE, Miftahov RA, Kuznetsova VE, Radko SP, Lisitsa AV, Lapa SA, Surzhikov SA, Timofeev EN, Zasedatelev AS, Chudinov AV. Slippage of the Primer Strand in the Primer Extension Reaction with Modified 2'-Deoxyuridine Triphosphates. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202003022x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Ravichandran S, Subramani VK, Kim KK. Z-DNA in the genome: from structure to disease. Biophys Rev 2019; 11:383-387. [PMID: 31119604 DOI: 10.1007/s12551-019-00534-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 12/17/2022] Open
Abstract
The scope of studies investigating the architecture of genomic DNA has progressed steadily since the elucidation of the structure of B-DNA. In recent years, several non-canonical DNA structures including Z-DNA, G-quadruplexes, H-DNA, cruciform DNA, and i-motifs have been reported to form in genomic DNA and are closely related to the evolution and development of disease. The ability of these structures to form in genomic DNA indicates that they might have important cellular roles and are therefore retained during evolution. Understanding the impact of the formation of these secondary structures on cellular processes can enable identification of new targets for therapeutics. In this review, we report the state of understanding of Z-DNA structure and formation and their implication in disease. Finally, we state our perspective on the potential of Z-DNA as a therapeutic target.
Collapse
Affiliation(s)
- Subramaniyam Ravichandran
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Vinod Kumar Subramani
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea.
| |
Collapse
|
11
|
Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion. Proc Natl Acad Sci U S A 2017; 114:9535-9540. [PMID: 28827328 DOI: 10.1073/pnas.1708691114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.
Collapse
|
12
|
Yenigun VB, Sirito M, Amcheslavky A, Czernuszewicz T, Colonques-Bellmunt J, García-Alcover I, Wojciechowska M, Bolduc C, Chen Z, López Castel A, Krahe R, Bergmann A. (CCUG) n RNA toxicity in a Drosophila model of myotonic dystrophy type 2 (DM2) activates apoptosis. Dis Model Mech 2017. [PMID: 28623239 PMCID: PMC5560059 DOI: 10.1242/dmm.026179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The myotonic dystrophies are prototypic toxic RNA gain-of-function diseases. Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are caused by different unstable, noncoding microsatellite repeat expansions – (CTG)DM1 in DMPK and (CCTG)DM2 in CNBP. Although transcription of mutant repeats into (CUG)DM1 or (CCUG)DM2 appears to be necessary and sufficient to cause disease, their pathomechanisms remain incompletely understood. To study the mechanisms of (CCUG)DM2 toxicity and develop a convenient model for drug screening, we generated a transgenic DM2 model in the fruit fly Drosophila melanogaster with (CCUG)n repeats of variable length (n=16 and 106). Expression of noncoding (CCUG)106, but not (CCUG)16, in muscle and retinal cells led to the formation of ribonuclear foci and mis-splicing of genes implicated in DM pathology. Mis-splicing could be rescued by co-expression of human MBNL1, but not by CUGBP1 (CELF1) complementation. Flies with (CCUG)106 displayed strong disruption of external eye morphology and of the underlying retina. Furthermore, expression of (CCUG)106 in developing retinae caused a strong apoptotic response. Inhibition of apoptosis rescued the retinal disruption in (CCUG)106 flies. Finally, we tested two chemical compounds that have shown therapeutic potential in DM1 models. Whereas treatment of (CCUG)106 flies with pentamidine had no effect, treatment with a PKR inhibitor blocked both the formation of RNA foci and apoptosis in retinae of (CCUG)106 flies. Our data indicate that expression of expanded (CCUG)DM2 repeats is toxic, causing inappropriate cell death in affected fly eyes. Our Drosophila DM2 model might provide a convenient tool for in vivo drug screening. Summary: A Drosophila model of myotonic dystrophy type 2 (DM2) recapitulates several features of the human disease, identifies apoptosis as a contributing factor to DM2, and is likely to provide a convenient tool for drug screening.
Collapse
Affiliation(s)
- Vildan Betul Yenigun
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA
| | - Mario Sirito
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alla Amcheslavky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tomek Czernuszewicz
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Marzena Wojciechowska
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clare Bolduc
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihong Chen
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ralf Krahe
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA.,Graduate Programs in Human & Molecular Genetics, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, Texas, USA
| | - Andreas Bergmann
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA.,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
13
|
Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. Cell Syst 2017; 4:344-356.e7. [PMID: 28237796 DOI: 10.1016/j.cels.2017.01.013] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022]
Abstract
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.
Collapse
|
14
|
Gadgil R, Barthelemy J, Lewis T, Leffak M. Replication stalling and DNA microsatellite instability. Biophys Chem 2016; 225:38-48. [PMID: 27914716 DOI: 10.1016/j.bpc.2016.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023]
Abstract
Microsatellites are short, tandemly repeated DNA motifs of 1-6 nucleotides, also termed simple sequence repeats (SRSs) or short tandem repeats (STRs). Collectively, these repeats comprise approximately 3% of the human genome Subramanian et al. (2003), Lander and Lander (2001) [1,2], and represent a large reservoir of loci highly prone to mutations Sun et al. (2012), Ellegren (2004) [3,4] that contribute to human evolution and disease. Microsatellites are known to stall and reverse replication forks in model systems Pelletier et al. (2003), Samadashwily et al. (1997), Kerrest et al. (2009) [5-7], and are hotspots of chromosomal double strand breaks (DSBs). We briefly review the relationship of these repeated sequences to replication stalling and genome instability, and present recent data on the impact of replication stress on DNA fragility at microsatellites in vivo.
Collapse
Affiliation(s)
- R Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - J Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - T Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - M Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
| |
Collapse
|
15
|
Shin SI, Ham S, Park J, Seo SH, Lim CH, Jeon H, Huh J, Roh TY. Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome. DNA Res 2016; 23:477-486. [PMID: 27374614 PMCID: PMC5066173 DOI: 10.1093/dnares/dsw031] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
Z-DNA, a left-handed double helical DNA is structurally different from the most abundant B-DNA. Z-DNA has been known to play a significant role in transcription and genome stability but the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. To obtain genome-wide map of ZFSs, Zaa with two Z-DNA-binding domains was used for ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examined in vivo. A large portion of ZFSs was enriched in the promoter regions and contain sequences with high potential to form Z-DNA. Genes containing ZFSs were occupied by RNA polymerase II at the promoters and showed high levels of expression. Moreover, ZFSs were significantly related to active histone marks such as H3K4me3 and H3K9ac. The association of Z-DNA with active transcription was confirmed by the reporter assay system. Overall, our results suggest that Z-DNA formation depends on chromatin structure as well as sequence composition, and is associated with active transcription in human cells. The global information about ZFSs positioning will provide a useful resource for further understanding of DNA structure-dependent transcriptional regulation.
Collapse
Affiliation(s)
| | | | - Jihwan Park
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Chae Hyun Lim
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | | | - Tae-Young Roh
- Department of Life Sciences.,Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| |
Collapse
|
16
|
Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. Nucleic Acids Res 2013; 41:5965-77. [PMID: 23620297 PMCID: PMC3695496 DOI: 10.1093/nar/gkt308] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although the right-handed double helical B-form DNA is most common under physiological conditions, DNA is dynamic and can adopt a number of alternative structures, such as the four-stranded G-quadruplex, left-handed Z-DNA, cruciform and others. Active transcription necessitates strand separation and can induce such non-canonical forms at susceptible genomic sequences. Therefore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcription. Such conjecture has been supported in higher eukaryotes by direct studies of several individual genes, as well as a number of large-scale analyses. However, the role of non-B DNA structures in many lower organisms, in particular proteobacteria, remains poorly understood and incompletely documented. In this study, we performed the first comprehensive study of the occurrence of B DNA-non-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure of the Escherichia coli genome. We compared the distributions of non-B DNA motifs in the regulatory regions of operons with those from internal regions. We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this enrichment cannot be simply explained by base composition bias in these regions. We also showed that the distribution of several non-B DNA motifs within intergenic regions separating divergently oriented operons differs from the distribution found between convergent ones. In particular, we found a strong enrichment of cruciforms in the termination region of operons; this enrichment was observed for operons with Rho-dependent, as well as Rho-independent terminators. Finally, a preference for some non-B DNA motifs was observed near transcription factor-binding sites. Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome.
Collapse
Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA
| | | | | | | | | | | |
Collapse
|
17
|
Maruyama A, Mimura J, Harada N, Itoh K. Nrf2 activation is associated with Z-DNA formation in the human HO-1 promoter. Nucleic Acids Res 2013; 41:5223-34. [PMID: 23571756 PMCID: PMC3664823 DOI: 10.1093/nar/gkt243] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Using a luciferase reporter assay, we previously demonstrated that a Z-DNA-forming sequence of alternating thymine-guanine repeats in the human heme oxygenase-1 gene (HO-1) promoter is involved in nuclear factor erythroid-derived 2 (NF-E2)-related factor 2 (Nrf2)-mediated HO-1 promoter activation. However, the actual Z-DNA formation in this native genomic locus has not been experimentally demonstrated. To detect Z-DNA formation in vivo, we generated a construct containing the Z-DNA-binding domain of human adenosine deaminase acting on double-stranded RNA 1 fused with enhanced green fluorescence protein, designated as the Z-probe. A chromatin immunoprecipitation assay using an anti-GFP antibody showed that the Z-probe detects the well-characterized Z-DNA formation in the CSF1 promoter. Using this detection system, we demonstrated that the glutathione-depleting agent, diethyl maleate, induced Nrf2-dependent Z-DNA formation in the HO-1 promoter, but not in the thioredoxin reductase 1 gene promoter. Moreover, a time course analysis revealed that Z-DNA formation precedes HO-1 transcriptional activation. Concurrent with Z-DNA formation, nucleosome occupancy was reduced, and the recruitment of RNA polymerase II was enhanced in the HO-1 promoter region, suggesting that Z-DNA formation enhances HO-1 gene transcription. Furthermore, Nrf2-induced BRG1 recruitment to the HO-1 promoter temporarily occurred simultaneously with Z-DNA formation. Thus, these results implicate Nrf2-dependent Z-DNA formation in HO-1 transcriptional activation and suggest the involvement of BRG1 in Z-DNA formation.
Collapse
Affiliation(s)
- Atsushi Maruyama
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | | | | | | |
Collapse
|
18
|
Sawaya SM, Lennon D, Buschiazzo E, Gemmell N, Minin VN. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model. Genome Biol Evol 2012; 4:636-47. [PMID: 22593552 PMCID: PMC3516246 DOI: 10.1093/gbe/evs050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites.
Collapse
Affiliation(s)
- Sterling M Sawaya
- Centre for Reproduction and Genomics, Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand
| | | | | | | | | |
Collapse
|
19
|
Promoter microsatellites as modulators of human gene expression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 769:41-54. [PMID: 23560304 DOI: 10.1007/978-1-4614-5434-2_4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microsatellites in and around genes have been shown to modulate levels of gene expression in multiple organisms, ranging from bacteria to humans. Here we will discuss promoter microsatellites known to modulate gene expression, with a few key examples related to the human brain. Many of the microsatellites we discuss are highly conserved in mammals, indicating that selection may favor their retention as "tuning knobs" of gene expression. We will also discuss the mechanisms by which microsatellites in promoters can alter gene expression as they expand and contract, with particular attention to secondary structures like Z-DNA and H-DNA. We suggest that promoter microsatellites, especially those that are highly conserved, may be an important source of human phenotypic variation.
Collapse
|
20
|
Abstract
CCTG tetranucleotide repeat expansion is associated with a hereditary neurological disease called myotonic dystrophy type 2 (DM2). The underlying reasons that lead to genetic instability and thus repeat expansion during DNA replication remains elusive. Here, we have shown CCTG repeats have a high propensity to form metastable hairpin and dumbbell structures using high-resolution nuclear magnetic resonance (NMR) spectroscopy. When the repeat length is equal to three, a hairpin with a two-residue CT loop is formed. In addition to the hairpin, a dumbbell structure with two CT-loops is formed when the repeat length is equal to four. Nuclear Overhauser effect (NOE) and chemical shift data reveal both the hairpin and dumbbell structures contain a flexible stem comprising a C-bulge and a T·T mismatch. With the aid of single-site mutation samples, NMR results show these peculiar structures undergo dynamic conformational exchange. In addition to the intrinsic flexibility in the stem region of these structures, the exchange process also serves as an origin of genetic instability that leads to repeat expansion during DNA replication. The structural features provide important drug target information for developing therapeutics to inhibit the expansion process and thus the onset of DM2.
Collapse
Affiliation(s)
- Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | | | | | | |
Collapse
|
21
|
Shimada N, Yamamoto M, Kano A, Maruyama A. Cationic Graft Copolymer as a DNA B-Z Transition Inducer: Effect of Copolymer Structure. Biomacromolecules 2010; 11:3043-8. [DOI: 10.1021/bm100870b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naohiko Shimada
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan, and CREST, Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Miyuki Yamamoto
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan, and CREST, Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Arihiro Kano
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan, and CREST, Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Atsushi Maruyama
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan, and CREST, Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| |
Collapse
|
22
|
López Castel A, Cleary JD, Pearson CE. Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 2010; 11:165-70. [PMID: 20177394 DOI: 10.1038/nrm2854] [Citation(s) in RCA: 325] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Expansions of repetitive DNA sequences cause numerous human neurological and neuromuscular diseases. Ongoing repeat expansions in patients can exacerbate disease progression and severity. As pathogenesis is connected to repeat length, a potential therapeutic avenue is to modulate disease by manipulating repeat expansion size--targeting DNA, the root-cause of symptoms. How repeat instability is mediated by DNA replication, repair, recombination, transcription and epigenetics may explain its contribution to pathogenesis and give insights into therapeutic strategies to block expansions or induce contractions.
Collapse
Affiliation(s)
- Arturo López Castel
- Program of Genetics & Genome Biology, The Hospital for Sick Children, 101 College Avenue, East Tower 15-312, TMDT Toronto, Ontario, Canada, M5G 1L7
| | | | | |
Collapse
|
23
|
Edwards SF, Hashem VI, Klysik EA, Sinden RR. Genetic instabilities of (CCTG)·(CAGG) and (ATTCT)·(AGAAT) disease-associated repeats reveal multiple pathways for repeat deletion. Mol Carcinog 2009; 48:336-49. [DOI: 10.1002/mc.20534] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|