1
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Fang Y, Bansal K, Mostafavi S, Benoist C, Mathis D. AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization. Nature 2024; 628:400-407. [PMID: 38480882 PMCID: PMC11091860 DOI: 10.1038/s41586-024-07169-7] [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: 02/14/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells1-4. The biological logic of AIRE's target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE's cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice5. Both approaches nominated Z-DNA and NFE2-MAF as putative positive influences on AIRE's target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene's promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.
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Affiliation(s)
- Yuan Fang
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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2
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Liang HT, Yan JY, Yao HJ, Zhang XN, Xing ZM, Liu L, Chen YQ, Li GR, Huang J, He YD, Zheng KW. G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity. Nucleic Acids Res 2024; 52:2142-2156. [PMID: 38340342 PMCID: PMC10954455 DOI: 10.1093/nar/gkae073] [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: 10/21/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.
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Affiliation(s)
- Hui-ting Liang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jiang-yu Yan
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Hao-jun Yao
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Xue-nan Zhang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Zhi-ming Xing
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yao-qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Guo-rui Li
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Yi-de He
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Ke-wei Zheng
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
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3
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Esain-Garcia I, Kirchner A, Melidis L, Tavares RDCA, Dhir S, Simeone A, Yu Z, Madden SK, Hermann R, Tannahill D, Balasubramanian S. G-quadruplex DNA structure is a positive regulator of MYC transcription. Proc Natl Acad Sci U S A 2024; 121:e2320240121. [PMID: 38315865 PMCID: PMC10873556 DOI: 10.1073/pnas.2320240121] [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: 11/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. G4 loss leads to suppression of MYC transcription from the P1 promoter that is mediated by the deposition of a de novo nucleosome alongside alterations in RNA polymerase recruitment. We also show that replacement of the endogenous MYC G4 with a different G4 structure from the KRAS oncogene restores G4 folding and MYC transcription. Moreover, we demonstrate that the MYC G4 structure itself, rather than its sequence, recruits transcription factors and histone modifiers. Overall, our work establishes that G4 structures are important features of transcriptional regulation that coordinate recruitment of key chromatin proteins and the transcriptional machinery through interactions with DNA secondary structure, rather than primary sequence.
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Affiliation(s)
- Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Angie Kirchner
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Somdutta Dhir
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Angela Simeone
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Zutao Yu
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sarah K. Madden
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Regina Hermann
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - David Tannahill
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- School of Clinical Medicine, University of Cambridge, CambridgeCB2 0SP, United Kingdom
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4
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Lahnsteiner A, Craig SJC, Kamali K, Weissensteiner B, McGrath B, Risch A, Makova KD. In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq). Methods Enzymol 2024; 695:159-191. [PMID: 38521584 DOI: 10.1016/bs.mie.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively called 'non-B DNA'), which DNA molecules can adopt beyond the B conformation. DNA secondary structures have significant biological roles, and their landscape is dynamic and can rearrange due to various factors, including changes in cellular conditions, temperature, and DNA-binding proteins. Understanding this dynamic nature is crucial for unraveling their functions in cellular processes. Detecting DNA secondary structures remains a challenge. Conventional methods, such as gel electrophoresis and chemical probing, have limitations in terms of sensitivity and specificity. Emerging techniques, including next-generation sequencing and single-molecule approaches, offer promise but face challenges since these techniques are mostly limited to only one type of secondary structure. Here we describe an updated version of a technique permanganate/S1 nuclease footprinting, which uses potassium permanganate to trap single-stranded DNA regions as found in many non-B structures, in combination with S1 nuclease digest and adapter ligation to detect genome-wide non-B formation. To overcome technical hurdles, we combined this method with direct adapter ligation and sequencing (PDAL-Seq). Furthermore, we established a user-friendly pipeline available on Galaxy to standardize PDAL-Seq data analysis. This optimized method allows the analysis of many types of DNA secondary structures that form in a living cell and will advance our knowledge of their roles in health and disease.
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Affiliation(s)
- Angelika Lahnsteiner
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), University of Salzburg, Salzburg, Austria; Cancer Cluster Salzburg, Salzburg, Austria.
| | - Sarah J C Craig
- Department of Biology, Penn State University, Wartik Laboratory, University Park, PA, United States
| | - Kaivan Kamali
- Department of Biology, Penn State University, Wartik Laboratory, University Park, PA, United States
| | | | - Barbara McGrath
- Department of Biology, Penn State University, Wartik Laboratory, University Park, PA, United States
| | - Angela Risch
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), University of Salzburg, Salzburg, Austria; Cancer Cluster Salzburg, Salzburg, Austria
| | - Kateryna D Makova
- Department of Biology, Penn State University, Wartik Laboratory, University Park, PA, United States.
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5
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Benham CJ. DNA superhelicity. Nucleic Acids Res 2024; 52:22-48. [PMID: 37994702 PMCID: PMC10783518 DOI: 10.1093/nar/gkad1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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6
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Shang G, Yang M, Li M, Ma L, Liu Y, Ma J, Chen Y, Wang X, Fan S, Xie M, Wu W, Dai S, Chen Z. Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A. Int J Mol Sci 2024; 25:686. [PMID: 38255759 PMCID: PMC10815869 DOI: 10.3390/ijms25020686] [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: 12/08/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
N6-methyladenine (6mA) of DNA is an emerging epigenetic mark in the genomes of Chlamydomonas, Caenorhabditis elegans, and mammals recently. Levels of 6mA undergo drastic fluctuation and thus affect fertility during meiosis and early embryogenesis. Here, we showed three complex structures of 6mA demethylase C. elegans NMAD-1A, a canonical isoform of NMAD-1 (F09F7.7). Biochemical results revealed that NMAD-1A prefers 6mA Bubble or Bulge DNAs. Structural studies of NMAD-1A revealed an unexpected "stretch-out" conformation of its Flip2 region, a conserved element that is usually bent over the catalytic center to facilitate substrate base flipping in other DNA demethylases. Moreover, the wide channel between the Flip1 and Flip2 of the NMAD-1A explained the observed preference of NMAD-1A for unpairing substrates, of which the flipped 6mA was primed for catalysis. Structural analysis and mutagenesis studies confirmed that key elements such as carboxy-terminal domain (CTD) and hypothetical zinc finger domain (ZFD) critically contributed to structural integrity, catalytic activity, and nucleosome binding. Collectively, our biochemical and structural studies suggest that NMAD-1A prefers to regulate 6mA in the unpairing regions and is thus possibly associated with dynamic chromosome regulation and meiosis regulation.
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Affiliation(s)
- Guohui Shang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiting Yang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Lulu Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunlong Liu
- School of Life Sciences, Tiangong University, Tianjin 300387, China
| | - Jun Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiyun Chen
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Xue Wang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shilong Fan
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Mengjia Xie
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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7
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Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571946. [PMID: 38168392 PMCID: PMC10760177 DOI: 10.1101/2023.12.15.571946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CDCA7 , encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.
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8
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Maria G, Andrey P, Artem S, Nikita T, Andrey K, Evgeny K, Oxana R, Maxim F, Veniamin F. Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease. Epigenetics Chromatin 2023; 16:48. [PMID: 38072950 PMCID: PMC10712037 DOI: 10.1186/s13072-023-00524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
This study presents a novel approach for mapping global chromatin interactions using S1 nuclease, a sequence-agnostic enzyme. We develop and outline a protocol that leverages S1 nuclease's ability to effectively introduce breaks into both open and closed chromatin regions, allowing for comprehensive profiling of chromatin properties. Our S1 Hi-C method enables the preparation of high-quality Hi-C libraries, marking a significant advancement over previously established DNase I Hi-C protocols. Moreover, S1 nuclease's capability to fragment chromatin to mono-nucleosomes suggests the potential for mapping the three-dimensional organization of the genome at high resolution. This methodology holds promise for an improved understanding of chromatin state-dependent activities and may facilitate the development of new genomic methods.
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Affiliation(s)
- Gridina Maria
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Popov Andrey
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Shadskiy Artem
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Torgunakov Nikita
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Kechin Andrey
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Khrapov Evgeny
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - Filipenko Maxim
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Fishman Veniamin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
- Artificial Intelligence Research Institute, AIRI, Moscow, Russia.
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9
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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10
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Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J. CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. Nat Commun 2023; 14:7346. [PMID: 37963886 PMCID: PMC10645931 DOI: 10.1038/s41467-023-43158-6] [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: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe "CHEX-seq" which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3'-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.
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Affiliation(s)
- Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jaehee Lee
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jifen Li
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Srinivasa Rao Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jinhui Wang
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin L Bullaughey
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean G Rosario
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, Children's Hospital of Philadelphia, ARC 517, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Alexandra V Ulyanova
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - H Isaac Chen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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11
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Yella VR, Vanaja A. Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes. Biochimie 2023; 214:101-111. [PMID: 37311475 DOI: 10.1016/j.biochi.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
The promoter regions of gene regulation are under evolutionary constraints and earlier studies uncovered that they are characterized by enrichment of functional non-B DNA structural signatures like curved DNA, cruciform DNA, G-quadruplex, triple-helical DNA, slipped DNA structures, and Z-DNA. However, these studies are restricted to a few model organisms, single non-B DNA motif types, or whole genomic sequences, and their comparative accumulation in promoter regions of different domains of life has not been reported comprehensively. In this study, for the first time, we investigated the preponderance of non-B DNA-prone motifs in promoter regions in 1180 genomes belonging to 28 taxonomic groups using the non-B DNA Motif Search Tool (nBMST). The trends suggest that they are predominant in promoters compared to the upstream and downstream regions of all three domains of life and variably linked to taxonomic groups. Cruciform DNA motif is the most abundant form of non-B DNA, spanning from archaea to lower eukaryotes. Curved DNA motifs are prominent in host-associated bacteria, and suppressed in mammals. Triplex-DNA and slipped DNA structure repeats are discretely dispersed in all lineages. G-quadruplex motifs are significantly enriched in mammals. We also observed that the unique enrichment of non-B DNA in promoters is strongly linked to genome GC, size, evolutionary time divergence, and ecological adaptations. Overall, our work systematically reports the unique non-B DNA structural landscape of cellular organisms from the perspective of the cis-regulatory code of genomes.
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Affiliation(s)
- Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India.
| | - Akkinepally Vanaja
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India; KL College of Pharmacy, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India
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12
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Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
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Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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13
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Maldonado R, Längst G. The chromatin - triple helix connection. Biol Chem 2023; 404:1037-1049. [PMID: 37506218 DOI: 10.1515/hsz-2023-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.
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Affiliation(s)
- Rodrigo Maldonado
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile
| | - Gernot Längst
- Regensburg Center for Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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14
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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15
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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16
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Herbert A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem 2023; 299:105140. [PMID: 37544644 PMCID: PMC10474125 DOI: 10.1016/j.jbc.2023.105140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
The role of alternate DNA conformations such as Z-DNA in the regulation of transcription is currently underappreciated. These structures are encoded by sequences called flipons, many of which are enriched in promoter and enhancer regions. Through a change in their conformation, flipons provide a tunable mechanism to mechanically reset promoters for the next round of transcription. They act as actuators that capture and release energy to ensure that the turnover of the proteins at promoters is optimized to cell state. Likewise, the single-stranded DNA formed as flipons cycle facilitates the docking of RNAs that are able to microcode promoter conformations and canalize the pervasive transcription commonly observed in metazoan genomes. The strand-specific nature of the interaction between RNA and DNA likely accounts for the known asymmetry of epigenetic marks present on the histone tetramers that pair to form nucleosomes. The role of these supercoil-dependent processes in promoter choice and transcriptional interference is reviewed. The evolutionary implications are examined: the resilience and canalization of flipon-dependent gene regulation is contrasted with the rapid adaptation enabled by the spread of flipon repeats throughout the genome. Overall, the current findings underscore the important role of flipons in modulating the readout of genetic information and how little we know about their biology.
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Affiliation(s)
- Alan Herbert
- Discovery Division, InsideOutBio, Charlestown, Massachusetts, USA.
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17
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Xu D, Huang Y, Luo L, Tang L, Lu M, Cao H, Wang F, Diao Y, Lyubchenko L, Kapranov P. Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method. Int J Mol Sci 2023; 24:12062. [PMID: 37569439 PMCID: PMC10418711 DOI: 10.3390/ijms241512062] [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: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity, much of which remains to be fully understood. Here, we established the SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions. We applied this method to profile essDNA in both human mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNA regions were found to be enriched in certain types of functional genomic elements, particularly, the origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, interestingly, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus could represent yet unknown functional elements.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lingcong Luo
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Meng Lu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Liudmila Lyubchenko
- National Medical Research Center for Radiology, Ministry of Health of Russia, 125284 Moscow, Russia
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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18
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Hisey JA, Radchenko EA, Ceschi S, Rastokina A, Mandel NH, McGinty RJ, Matos-Rodrigues G, Hernandez A, Nussenzweig A, Mirkin SM. Pathogenic CANVAS (AAGGG) n repeats stall DNA replication due to the formation of alternative DNA structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550509. [PMID: 37546920 PMCID: PMC10402041 DOI: 10.1101/2023.07.25.550509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the main pathogenic (A2G3)n and the main nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in supercoiled DNA reveals triplex H-DNA formation by the pathogenic repeat. Consistently, bioinformatic analysis of the S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs in vivo. Finally, the pathogenic, but not the non-pathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A. Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | | | - Ryan J. McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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19
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Umerenkov D, Herbert A, Konovalov D, Danilova A, Beknazarov N, Kokh V, Fedorov A, Poptsova M. Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease. Life Sci Alliance 2023; 6:e202301962. [PMID: 37164635 PMCID: PMC10172764 DOI: 10.26508/lsa.202301962] [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: 01/31/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
Identifying roles for Z-DNA remains challenging given their dynamic nature. Here, we perform genome-wide interrogation with the DNABERT transformer algorithm trained on experimentally identified Z-DNA forming sequences (Z-flipons). The algorithm yields large performance enhancements (F1 = 0.83) over existing approaches and implements computational mutagenesis to assess the effects of base substitution on Z-DNA formation. We show Z-flipons are enriched in promoters and telomeres, overlapping quantitative trait loci for RNA expression, RNA editing, splicing, and disease-associated variants. We cross-validate across a number of orthogonal databases and define BZ junction motifs. Surprisingly, many effects we delineate are likely mediated through Z-RNA formation. A shared Z-RNA motif is identified in SCARF2, SMAD1, and CACNA1 transcripts, whereas other motifs are present in noncoding RNAs. We provide evidence for a Z-RNA fold that promotes adaptive immunity through alternative splicing of KRAB domain zinc finger proteins. An analysis of OMIM and presumptive gnomAD loss-of-function datasets reveals an overlap of Z-flipons with disease-causing variants in 8.6% and 2.9% of Mendelian disease genes, respectively, greatly extending the range of phenotypes mapped to Z-flipons.
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Affiliation(s)
| | - Alan Herbert
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
- InsideOutBio, Charlestown, MA, USA
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Anna Danilova
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | | | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
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20
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Hosseini M, Palmer A, Manka W, Grady PGS, Patchigolla V, Bi J, O'Neill RJ, Chi Z, Aguiar D. Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures. Bioinformatics 2023; 39:i242-i251. [PMID: 37387144 DOI: 10.1093/bioinformatics/btad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated with genomic instability, gene regulation, and oncogenesis. Experimental methods are low-throughput and can detect only a limited set of non-B DNA structures, while computational methods rely on non-B DNA base motifs, which are necessary but not sufficient indicators of non-B structures. Oxford Nanopore sequencing is an efficient and low-cost platform, but it is currently unknown whether nanopore reads can be used for identifying non-B structures. RESULTS We build the first computational pipeline to predict non-B DNA structures from nanopore sequencing. We formalize non-B detection as a novelty detection problem and develop the GoFAE-DND, an autoencoder that uses goodness-of-fit (GoF) tests as a regularizer. A discriminative loss encourages non-B DNA to be poorly reconstructed and optimizing Gaussian GoF tests allows for the computation of P-values that indicate non-B structures. Based on whole genome nanopore sequencing of NA12878, we show that there exist significant differences between the timing of DNA translocation for non-B DNA bases compared with B-DNA. We demonstrate the efficacy of our approach through comparisons with novelty detection methods using experimental data and data synthesized from a new translocation time simulator. Experimental validations suggest that reliable detection of non-B DNA from nanopore sequencing is achievable. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/bayesomicslab/ONT-nonb-GoFAE-DND.
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Affiliation(s)
- Marjan Hosseini
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
| | - Aaron Palmer
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
| | - William Manka
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
| | - Patrick G S Grady
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3003, United States
| | - Venkata Patchigolla
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
| | - Jinbo Bi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3003, United States
| | - Zhiyi Chi
- Department of Statistics, University of Connecticut, Storrs, CT 06269-4120, United States
| | - Derek Aguiar
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-4155, United States
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21
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Zhang ZH, Qian SH, Wei D, Chen ZX. In vivo dynamics and regulation of DNA G-quadruplex structures in mammals. Cell Biosci 2023; 13:117. [PMID: 37381029 DOI: 10.1186/s13578-023-01074-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
G-quadruplex (G4) is a four-stranded helical DNA secondary structure formed by guanine-rich sequence folding, and G4 has been computationally predicted to exist in a wide range of species. Substantial evidence has supported the formation of endogenous G4 (eG4) in living cells and revealed its regulatory dynamics and critical roles in several important biological processes, making eG4 a regulator of gene expression perturbation and a promising therapeutic target in disease biology. Here, we reviewed the methods for prediction of potential G4 sequences (PQS) and detection of eG4s. We also highlighted the factors affecting the dynamics of eG4s and the effects of eG4 dynamics. Finally, we discussed the future applications of eG4 dynamics in disease therapy.
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Affiliation(s)
- Ze-Hao Zhang
- Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Hu Qian
- Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengguo Wei
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
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22
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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23
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Amgalan B, Wojtowicz D, Kim YA, Przytycka TM. Influence network model uncovers relations between biological processes and mutational signatures. Genome Med 2023; 15:15. [PMID: 36879282 PMCID: PMC9987115 DOI: 10.1186/s13073-023-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND There has been a growing appreciation recently that mutagenic processes can be studied through the lenses of mutational signatures, which represent characteristic mutation patterns attributed to individual mutagens. However, the causal links between mutagens and observed mutation patterns as well as other types of interactions between mutagenic processes and molecular pathways are not fully understood, limiting the utility of mutational signatures. METHODS To gain insights into these relationships, we developed a network-based method, named GENESIGNET that constructs an influence network among genes and mutational signatures. The approach leverages sparse partial correlation among other statistical techniques to uncover dominant influence relations between the activities of network nodes. RESULTS Applying GENESIGNET to cancer data sets, we uncovered important relations between mutational signatures and several cellular processes that can shed light on cancer-related processes. Our results are consistent with previous findings, such as the impact of homologous recombination deficiency on clustered APOBEC mutations in breast cancer. The network identified by GENESIGNET also suggest an interaction between APOBEC hypermutation and activation of regulatory T Cells (Tregs), as well as a relation between APOBEC mutations and changes in DNA conformation. GENESIGNET also exposed a possible link between the SBS8 signature of unknown etiology and the Nucleotide Excision Repair (NER) pathway. CONCLUSIONS GENESIGNET provides a new and powerful method to reveal the relation between mutational signatures and gene expression. The GENESIGNET method was implemented in python, and installable package, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/GeneSigNet.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA
| | - Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA.,Current address: Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, ul. Banacha 2, 02-097, Warszawa, Poland
| | - Yoo-Ah Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA.
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24
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Herbert A, Pavlov F, Konovalov D, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations. Int J Mol Sci 2023; 24:ijms24054884. [PMID: 36902315 PMCID: PMC10003719 DOI: 10.3390/ijms24054884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10-116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Correspondence:
| | - Fedor Pavlov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
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25
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Makova KD, Weissensteiner MH. Noncanonical DNA structures are drivers of genome evolution. Trends Genet 2023; 39:109-124. [PMID: 36604282 PMCID: PMC9877202 DOI: 10.1016/j.tig.2022.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023]
Abstract
In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
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Affiliation(s)
- Kateryna D Makova
- Department of Biology, Penn State University, 310 Wartik Laboratory, University Park, PA 16802, USA.
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26
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Non-B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes. Proc Natl Acad Sci U S A 2023; 120:e2211683120. [PMID: 36574697 PMCID: PMC9910436 DOI: 10.1073/pnas.2211683120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Centromeres are the specialized regions of the chromosomes that direct faithful chromosome segregation during cell division. Despite their functional conservation, centromeres display features of rapidly evolving DNA and wide evolutionary diversity in size and organization. Previous work found that the noncanonical B-form DNA structures are abundant in the centromeres of several eukaryotic species with a possible implication for centromere specification. Thus far, systematic studies into the organization and function of non-B-form DNA in plants remain scarce. Here, we applied the oat system to investigate the role of non-B-form DNA in centromeres. We conducted chromatin immunoprecipitation sequencing using an antibody to the centromere-specific histone H3 variant (CENH3); this accurately positioned oat centromeres with different ploidy levels and identified a series of centromere-specific sequences including minisatellites and retrotransposons. To define genetic characteristics of oat centromeres, we surveyed the repeat sequences and found that dyad symmetries were abundant in oat centromeres and were predicted to form non-B-DNA structures in vivo. These structures including bent DNA, slipped DNA, Z-DNA, G-quadruplexes, and R-loops were prone to form within CENH3-binding regions. Dynamic conformational changes of predicted non-B-DNA occurred during the evolution from diploid to tetraploid to hexaploid oat. Furthermore, we applied the single-molecule technique of AFM and DNA:RNA immunoprecipitation with deep sequencing to validate R-loop enrichment in oat centromeres. Centromeric retrotransposons exhibited strong associations with R-loop formation. Taken together, our study elucidates the fundamental character of non-B-form DNA in the oat genome and reveals its potential role in centromeres.
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27
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Beknazarov N, Poptsova M. DeepZ: A Deep Learning Approach for Z-DNA Prediction. Methods Mol Biol 2023; 2651:217-226. [PMID: 36892770 DOI: 10.1007/978-1-0716-3084-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Here we describe an approach that uses deep learning neural networks such as CNN and RNN to aggregate information from DNA sequence; physical, chemical, and structural properties of nucleotides; and omics data on histone modifications, methylation, chromatin accessibility, and transcription factor binding sites and data from other available NGS experiments. We explain how with the trained model one can perform whole-genome annotation of Z-DNA regions and feature importance analysis in order to define key determinants for functional Z-DNA regions.
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Affiliation(s)
- Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia.
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28
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Lee SK, Kim YG. Construction of a Z-DNA-Specific Recombinant Nuclease Zαα-FOK for Conformation Studies. Methods Mol Biol 2023; 2651:143-155. [PMID: 36892765 DOI: 10.1007/978-1-0716-3084-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Development of FokI-based engineered nucleases has been a platform technology that enables creation of novel sequence-specific nucleases as well as structure-specific nucleases. Z-DNA-specific nucleases have been constructed by fusing a Z-DNA-binding domain to the nuclease domain of FokI (FN). In particular, Zαα, an engineered Z-DNA-binding domain with a high affinity, is an ideal fusion partner to generate a highly efficient Z-DNA-specific cutter. Here, we describe construction, expression, and purification of Zαα-FOK (Zαα-FN) nuclease in detail. In addition, Z-DNA-specific cleavage is demonstrated by the use of Zαα-FOK.
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Affiliation(s)
- Seul Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea.
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29
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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.
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Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology, NCI/NIH, Bethesda, MD, USA.
| | | | | | - David Levens
- Laboratory of Pathology, NCI/NIH, Bethesda, MD, USA
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30
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Herbert A. Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate. Bioessays 2022; 44:e2200166. [DOI: 10.1002/bies.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
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31
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Correspondence may also be addressed to Christine J. Cardin. Tel: +44 118 378 8215;
| | - David Monchaud
- To whom correspondence should be addressed. Tel: +33 380 399 043;
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32
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Ajoge HO, Kohio HP, Paparisto E, Coleman MD, Wong K, Tom SK, Bain KL, Berry CC, Arts EJ, Barr SD. G-Quadruplex DNA and Other Non-Canonical B-Form DNA Motifs Influence Productive and Latent HIV-1 Integration and Reactivation Potential. Viruses 2022; 14:v14112494. [PMID: 36423103 PMCID: PMC9692945 DOI: 10.3390/v14112494] [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: 09/12/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The integration of the HIV-1 genome into the host genome is an essential step in the life cycle of the virus and it plays a critical role in the expression, long-term persistence, and reactivation of HIV expression. To better understand the local genomic environment surrounding HIV-1 proviruses, we assessed the influence of non-canonical B-form DNA (non-B DNA) on the HIV-1 integration site selection. We showed that productively and latently infected cells exhibit different integration site biases towards non-B DNA motifs. We identified a correlation between the integration sites of the latent proviruses and non-B DNA features known to potently influence gene expression (e.g., cruciform, guanine-quadruplex (G4), triplex, and Z-DNA). The reactivation potential of latent proviruses with latency reversal agents also correlated with their proximity to specific non-B DNA motifs. The perturbation of G4 structures in vitro using G4 structure-destabilizing or -stabilizing ligands resulted in a significant reduction in integration within 100 base pairs of G4 motifs. The stabilization of G4 structures increased the integration within 300-500 base pairs from G4 motifs, increased integration near transcription start sites, and increased the proportion of latently infected cells. Moreover, we showed that host lens epithelium-derived growth factor (LEDGF)/p75 and cleavage and polyadenylation specificity factor 6 (CPSF6) influenced the distribution of integration sites near several non-B DNA motifs, especially G4 DNA. Our findings identify non-B DNA motifs as important factors that influence productive and latent HIV-1 integration and the reactivation potential of latent proviruses.
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Affiliation(s)
- Hannah O. Ajoge
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Hinissan P. Kohio
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Ermela Paparisto
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Macon D. Coleman
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Kemen Wong
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Sean K. Tom
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Katie L. Bain
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Charles C. Berry
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA
| | - Eric J. Arts
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Stephen D. Barr
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
- Correspondence:
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33
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Shi X, Teng H, Sun Z. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops. Brief Bioinform 2022; 23:6751149. [PMID: 36208174 PMCID: PMC9677470 DOI: 10.1093/bib/bbac441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple types of non-canonical nucleic acid structures play essential roles in DNA recombination and replication, transcription, and genomic instability and have been associated with several human diseases. Thus, an increasing number of experimental and bioinformatics methods have been developed to identify these structures. To date, most reviews have focused on the features of non-canonical DNA/RNA structure formation, experimental approaches to mapping these structures, and the association of these structures with diseases. In addition, two reviews of computational algorithms for the prediction of non-canonical nucleic acid structures have been published. One of these reviews focused only on computational approaches for G4 detection until 2020. The other mainly summarized the computational tools for predicting cruciform, H-DNA and Z-DNA, in which the algorithms discussed were published before 2012. Since then, several experimental and computational methods have been developed. However, a systematic review including the conformation, sequencing mapping methods and computational prediction strategies for these structures has not yet been published. The purpose of this review is to provide an updated overview of conformation, current sequencing technologies and computational identification methods for non-canonical nucleic acid structures, as well as their strengths and weaknesses. We expect that this review will aid in understanding how these structures are characterised and how they contribute to related biological processes and diseases.
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Affiliation(s)
- Xiaohui Shi
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Ouhai District, Wenzhou 325000, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Ouhai District, Wenzhou 325000, China
| | - Zhongsheng Sun
- Corresponding author: Zhongsheng Sun, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The 1st Affiliated Hospital of WMU, Nanbaixiang Wenyi Yiyuan Xinyuan District, Ouhai District, Wenzhou 325000, China. E-mail:
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34
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Matos-Rodrigues G, van Wietmarschen N, Wu W, Tripathi V, Koussa NC, Pavani R, Nathan WJ, Callen E, Belinky F, Mohammed A, Napierala M, Usdin K, Ansari AZ, Mirkin SM, Nussenzweig A. S1-END-seq reveals DNA secondary structures in human cells. Mol Cell 2022; 82:3538-3552.e5. [PMID: 36075220 PMCID: PMC9547894 DOI: 10.1016/j.molcel.2022.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/25/2022] [Accepted: 08/04/2022] [Indexed: 11/15/2022]
Abstract
DNA becomes single stranded (ssDNA) during replication, transcription, and repair. Transiently formed ssDNA segments can adopt alternative conformations, including cruciforms, triplexes, and quadruplexes. To determine whether there are stable regions of ssDNA in the human genome, we utilized S1-END-seq to convert ssDNA regions to DNA double-strand breaks, which were then processed for high-throughput sequencing. This approach revealed two predominant non-B DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulate in microsatellite unstable human cancer cell lines and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine mirror repeats common across a variety of cell lines. We show that H-DNA is enriched during replication, that its genomic location is highly conserved, and that H-DNA formed by (GAA)n repeats can be disrupted by treatment with a (GAA)n-binding polyamide. Finally, we show that triplex-forming repeats are hotspots for mutagenesis. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability.
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Affiliation(s)
| | | | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Veenu Tripathi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Natasha C Koussa
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Frida Belinky
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ashraf Mohammed
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marek Napierala
- Department of Neurology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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35
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Miglietta G, Marinello J, Russo M, Capranico G. Ligands stimulating antitumour immunity as the next G-quadruplex challenge. Mol Cancer 2022; 21:180. [PMID: 36114513 PMCID: PMC9482198 DOI: 10.1186/s12943-022-01649-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractG-quadruplex (G4) binders have been investigated to discover new anticancer drugs worldwide in past decades. As these ligands are generally not highly cytotoxic, the discovery rational was mainly based on increasing the cell-killing potency. Nevertheless, no G4 binder has been shown yet to be effective in cancer patients. Here, G4 binder activity at low dosages will be discussed as a critical feature to discover ligands with therapeutic effects in cancer patients. Specific effects of G4 binders al low doses have been reported to occur in cancer and normal cells. Among them, genome instability and the stimulation of cytoplasmic processes related to autophagy and innate immune response open to the use of G4 binders as immune-stimulating agents. Thus, we propose a new rational of drug discovery, which is not based on cytotoxic potency but rather on immune gene activation at non-cytotoxic dosage.
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36
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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.
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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
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37
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High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol 2022; 23:159. [PMID: 35851062 PMCID: PMC9290270 DOI: 10.1186/s13059-022-02727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary structures. The roles of DNA and RNA secondary structures in transcriptional regulation remain incompletely understood. However, advances in high-throughput assays have enabled genome wide characterization of some secondary structures. Here, we describe their regulatory functions in promoters and 3’UTRs, providing insights into key mechanisms through which they regulate gene expression. We discuss their implication in human disease, and how advances in molecular technologies and emerging high-throughput experimental methods could provide additional insights.
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38
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Meng Y, Wang G, He H, Lau KH, Hurt A, Bixler BJ, Parham A, Jin SG, Xu X, Vasquez KM, Pfeifer GP, Szabó PE. Z-DNA is remodelled by ZBTB43 in prospermatogonia to safeguard the germline genome and epigenome. Nat Cell Biol 2022; 24:1141-1153. [PMID: 35787683 PMCID: PMC9276527 DOI: 10.1038/s41556-022-00941-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/17/2022] [Indexed: 12/12/2022]
Abstract
Mutagenic purine–pyrimidine repeats can adopt the left-handed Z-DNA conformation. DNA breaks at potential Z-DNA sites can lead to somatic mutations in cancer or to germline mutations that are transmitted to the next generation. It is not known whether any mechanism exists in the germ line to control Z-DNA structure and DNA breaks at purine–pyrimidine repeats. Here we provide genetic, epigenomic and biochemical evidence for the existence of a biological process that erases Z-DNA specifically in germ cells of the mouse male foetus. We show that a previously uncharacterized zinc finger protein, ZBTB43, binds to and removes Z-DNA, preventing the formation of DNA double-strand breaks. By removing Z-DNA, ZBTB43 also promotes de novo DNA methylation at CG-containing purine–pyrimidine repeats in prospermatogonia. Therefore, the genomic and epigenomic integrity of the species is safeguarded by remodelling DNA structure in the mammalian germ line during a critical window of germline epigenome reprogramming. Meng et al. show that ZBTB43 alters Z-DNA structures to prevent deleterious double-strand breaks and promote DNA methylation at purine–pyrimidine repeats in the mouse germ line.
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Affiliation(s)
- Yingying Meng
- Capital Normal University College of Life Science, Beijing, China.,Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Hongjuan He
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.,School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Hurt
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Brianna J Bixler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Andrea Parham
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.,Van Andel Institute Graduate School, Grand Rapids, MI, USA
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Xingzhi Xu
- Capital Normal University College of Life Science, Beijing, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Piroska E Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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39
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APOBEC mutagenesis is low in most types of non-B DNA structures. iScience 2022; 25:104535. [PMID: 35754742 PMCID: PMC9213766 DOI: 10.1016/j.isci.2022.104535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022] Open
Abstract
While somatic mutations are known to be enriched in genome regions with non-canonical DNA secondary structure, the impact of particular mutagens still needs to be elucidated. Here, we demonstrate that in human cancers, the APOBEC mutagenesis is not enriched in direct repeats, mirror repeats, short tandem repeats, and G-quadruplexes, and even decreased below its level in B-DNA for cancer samples with very high APOBEC activity. In contrast, we observe that the APOBEC-induced mutational density is positively associated with APOBEC activity in inverted repeats (cruciform structures), where the impact of cytosine at the 3’-end of the hairpin loop is substantial. Surprisingly, the APOBEC-signature mutation density per TC motif in the single-stranded DNA of a G-quadruplex (G4) is lower than in the four-stranded part of G4 and in B-DNA. The APOBEC mutagenesis, as well as the UV-mutagenesis in melanoma samples, are absent in Z-DNA regions, owing to the depletion of their mutational signature motifs. APOBEC mutagenesis is not enriched in most non-canonical DNA structures Inverted repeats (cruciform structures) show increased APOBEC mutagenesis G-quadruplex’s unstructured strand has low APOBEC-induced mutation density Decrease of APOBEC mutagenesis in non-B DNA possibly associated with PrimPol
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40
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Yu D, Zhou J, Chen Q, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry 2022; 61:1005-1013. [PMID: 35605980 PMCID: PMC9178792 DOI: 10.1021/acs.biochem.2c00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/04/2022] [Indexed: 11/30/2022]
Abstract
PCIF1 and FTO are a pair of human mRNA cap-specific modification enzymes that have opposing activities. PCIF1 adds a methyl group to the N6-position of 2'O-methyladenosine (Am), generating N6, 2'O-dimethyladenosine (m6Am), when Am is the cap-proximal nucleotide. FTO removes the N6-methyl group from m6Am. In addition, FTO has a demethylase activity on a broad spectrum of various RNA substrates, as well as on DNA N6-methyldeoxyadenosine (m6dA). While the existence of m6dA in mammalian DNA remains controversial, we show here that PCIF1 has significant methylation activity on single stranded DNA deoxyadenosine, double stranded RNA/DNA hybrids, and double stranded DNA, though with lower catalytic efficiency than that on its preferred RNA substrate. PCIF1 has activities in the order ssRNA > RNA/DNA hybrid > ssDNA > dsDNA. We discuss the implications of PCIF1 generation, and FTO removal, of DNA adenine methylation.
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Affiliation(s)
- Dan Yu
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jujun Zhou
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Qin Chen
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Tao Wu
- Department
of Molecular & Human Genetics, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Robert M. Blumenthal
- Department
of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life
Sciences, Toledo, Ohio 43614, United States
| | - Xing Zhang
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Xiaodong Cheng
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
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41
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Maekawa K, Yamada S, Sharma R, Chaudhuri J, Keeney S. Triple-helix potential of the mouse genome. Proc Natl Acad Sci U S A 2022; 119:e2203967119. [PMID: 35503911 PMCID: PMC9171763 DOI: 10.1073/pnas.2203967119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023] Open
Abstract
Certain DNA sequences, including mirror-symmetric polypyrimidine•polypurine runs, are capable of folding into a triple-helix–containing non–B-form DNA structure called H-DNA. Such H-DNA–forming sequences occur frequently in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)–specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides an approach for studying DNA secondary structure genome-wide at high spatial resolution.
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Affiliation(s)
- Kaku Maekawa
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Rahul Sharma
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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42
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Koculi E, Cho SS. RNA Post-Transcriptional Modifications in Two Large Subunit Intermediates Populated in E. coli Cells Expressing Helicase Inactive R331A DbpA. Biochemistry 2022; 61:833-842. [PMID: 35481783 DOI: 10.1021/acs.biochem.2c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
23S ribosomal RNA (rRNA) of Escherichia coli 50S large ribosome subunit contains 26 post-transcriptionally modified nucleosides. Here, we determine the extent of modifications in the 35S and 45S large subunit intermediates, accumulating in cells expressing the helicase inactive DbpA protein, R331A, and the native 50S large subunit. The modifications we characterized are 3-methylpseudouridine, 2-methyladenine, 5-hydroxycytidine, and nine pseudouridines. These modifications were detected using 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) treatment followed by alkaline treatment. In addition, KMnO4 treatment of 23S rRNA was employed to detect 5-hydroxycytidine modification. CMCT and KMnO4 treatments produce chemical changes in modified nucleotides that cause reverse transcriptase misincorporations and deletions, which were detected employing next-generation sequencing. Our results show that the 2-methyladenine modification and seven uridines to pseudouridine isomerizations are present in both the 35S and 45S to similar extents as in the 50S. Hence, the enzymes that perform these modifications, namely, RluA, RluB, RluC, RluE, RluF, and RlmN, have already acted in the intermediates. Two uridines to pseudouridine isomerizations, the 3-methylpseudouridine and 5-hydroxycytidine modifications, are significantly less present in the 35S and 45S, as compared to the 50S. Therefore, the enzymes that incorporate these modifications, RluD, RlmH, and RlhA, are in the process of modifying the 35S and 45S or will incorporate these modifications during the later stages of ribosome assembly. Our study employs a novel high throughput and single nucleotide resolution technique for the detection of 2-methyladenine and two novel high throughput and single nucleotide resolution techniques for the detection of 5-hydroxycytidine.
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Affiliation(s)
- Eda Koculi
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Samuel S Cho
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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43
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Abstract
Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long-read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, and new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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44
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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45
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Herbert A, Fedorov A, Poptsova M. Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus. Int J Mol Sci 2022; 23:ijms23063079. [PMID: 35328502 PMCID: PMC8955656 DOI: 10.3390/ijms23063079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022] Open
Abstract
Z-DNA binding protein (ZBP1) very much represents the nuclear option. By initiating inflammatory cell death (ICD), ZBP1 activates host defenses to destroy infectious threats. ZBP1 is also able to induce noninflammatory regulated cell death via apoptosis (RCD). ZBP1 senses the presence of left-handed Z-DNA and Z-RNA (ZNA), including that formed by expression of endogenous retroelements. Viruses such as the Epstein–Barr “kissing virus” inhibit ICD, RCD and other cell death signaling pathways to produce persistent infection. EBV undergoes lytic replication in plasma cells, which maintain detectable levels of basal ZBP1 expression, leading us to suggest a new role for ZBP1 in maintaining EBV latency, one of benefit for both host and virus. We provide an overview of the pathways that are involved in establishing latent infection, including those regulated by MYC and NF-κB. We describe and provide a synthesis of the evidence supporting a role for ZNA in these pathways, highlighting the positive and negative selection of ZNA forming sequences in the EBV genome that underscores the coadaptation of host and virus. Instead of a fight to the death, a state of détente now exists where persistent infection by the virus is tolerated by the host, while disease outcomes such as death, autoimmunity and cancer are minimized. Based on these new insights, we propose actionable therapeutic approaches to unhost EBV.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
- Correspondence:
| | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
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46
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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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47
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Kim S, Hwang S. G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency. Genes (Basel) 2022; 13:genes13030391. [PMID: 35327946 PMCID: PMC8948836 DOI: 10.3390/genes13030391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
How and why distinct genetic alterations, such as BRCA1 mutation, promote tumorigenesis in certain tissues, but not others, remain an important issue in cancer research. The underlying mechanisms may reveal tissue-specific therapeutic vulnerabilities. Although the roles of BRCA1, such as DNA damage repair and stalled fork stabilization, obviously contribute to tumor suppression, these ubiquitously important functions cannot explain tissue-specific tumorigenesis by BRCA1 mutations. Recent advances in our understanding of the cancer genome and fundamental cellular processes on DNA, such as transcription and DNA replication, have provided new insights regarding BRCA1-associated tumorigenesis, suggesting that G-quadruplex (G4) plays a critical role. In this review, we summarize the importance of G4 structures in mutagenesis of the cancer genome and cell type-specific gene regulation, and discuss a recently revealed molecular mechanism of G4/base excision repair (BER)-mediated transcriptional activation. The latter adequately explains the correlation between the accumulation of unresolved transcriptional regulatory G4s and multi-level genomic alterations observed in BRCA1-associated tumors. In summary, tissue-specific tumorigenesis by BRCA1 deficiency can be explained by cell type-specific levels of transcriptional regulatory G4s and the role of BRCA1 in resolving it. This mechanism would provide an integrated understanding of the initiation and development of BRCA1-associated tumors.
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Affiliation(s)
- Sanghyun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
| | - Sohyun Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Sungnam 13496, Korea
- Correspondence:
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48
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Shaheen C, Hastie C, Metera K, Scott S, Zhang Z, Chen S, Gu G, Weber L, Munsky B, Kouzine F, Levens D, Benham C, Leslie S. Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation. Nucleic Acids Res 2022; 50:2754-2764. [PMID: 35188541 PMCID: PMC8934633 DOI: 10.1093/nar/gkac101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
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Affiliation(s)
- Cynthia Shaheen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Cameron Hastie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Shane Scott
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Institute of Materials Science, Kiel University, 24142 Kiel, Germany
| | - Zhi Zhang
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Sitong Chen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Gracia Gu
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Lisa Weber
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Craig Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
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49
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KAS-seq: genome-wide sequencing of single-stranded DNA by N 3-kethoxal-assisted labeling. Nat Protoc 2022; 17:402-420. [PMID: 35013616 PMCID: PMC8923001 DOI: 10.1038/s41596-021-00647-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/22/2021] [Indexed: 02/03/2023]
Abstract
Transcription and its dynamics are crucial for gene expression regulation. However, very few methods can directly read out transcriptional activity with low-input material and high temporal resolution. This protocol describes KAS-seq, a robust and sensitive approach for capturing genome-wide single-stranded DNA (ssDNA) profiles using N3-kethoxal-assisted labeling. We developed N3-kethoxal, an azido derivative of kethoxal that reacts with deoxyguanosine bases of ssDNA in live cells within 5-10 min at 37 °C, allowing the capture of dynamic changes. Downstream biotinylation of labeled DNA occurs via copper-free click chemistry. Altogether, the KAS-seq procedure involves N3-kethoxal labeling, DNA isolation, biotinylation, fragmentation, affinity pull-down, library preparation, sequencing and bioinformatics analysis. The pre-library construction labeling and enrichment can be completed in as little as 3-4 h and is applicable to both animal tissue and as few as 1,000 cultured cells. Our recent study shows that ssDNA signals measured by KAS-seq simultaneously reveal the dynamics of transcriptionally engaged RNA polymerase (Pol) II, transcribing enhancers, RNA Pol I and Pol III activities and potentially non-canonical DNA structures with high analytical sensitivity. In addition to the experimental protocol, we also introduce here KAS-pipe, a user-friendly integrative data analysis pipeline for KAS-seq.
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50
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Liu M, Cui Y, Zhang Y, An R, Li L, Park S, Sugiyama H, Liang X. Single base-modification reports and locates Z-DNA conformation on a Z-B-chimera formed by topological constraint. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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