1
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Xu H, Ye J, Zhang KX, Hu Q, Cui T, Tong C, Wang M, Geng H, Shui KM, Sun Y, Wang J, Hou X, Zhang K, Xie R, Yin Y, Chen N, Chen JY. Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA. Nat Chem 2024:10.1038/s41557-024-01609-7. [PMID: 39223307 DOI: 10.1038/s41557-024-01609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Triplex DNA structures, formed when a third DNA strand wraps around the major groove of DNA, are key molecular regulators and genomic threats. However, the regulatory network governing triplex DNA dynamics remains poorly understood. Here we reveal the binding and functional repertoire of proteins that interact with triplex DNA through chemoproteomic profiling in living cells. We develop a chemical probe that exhibits exceptional specificity towards triplex DNA. By employing a co-binding-mediated proximity capture strategy, we enrich triplex DNA interactome for quantitative proteomics analysis. This enables the identification of a comprehensive list of proteins that interact with triplex DNA, characterized by diverse binding properties and regulatory mechanisms in their native chromatin context. As a demonstration, we validate DDX3X as an ATP-independent triplex DNA helicase to unwind substrates with a 5' overhang to prevent DNA damage. Overall, our study provides a valuable resource for exploring the biology and translational potential of triplex DNA.
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Affiliation(s)
- Hongzhan Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jing Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Kui-Xing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Chong Tong
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Huichao Geng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Kun-Ming Shui
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Yan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jian Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Xiaomeng Hou
- ChomiX Biotech (Nanjing) Co. Ltd., Nanjing, China
| | - Kai Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nan Chen
- ChomiX Biotech (Nanjing) Co. Ltd., Nanjing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China.
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, China.
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2
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Bai G, Endres T, Kühbacher U, Mengoli V, Greer BH, Peacock EM, Newton MD, Stanage T, Dello Stritto MR, Lungu R, Crossley MP, Sathirachinda A, Cortez D, Boulton SJ, Cejka P, Eichman BF, Cimprich KA. HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability. Mol Cell 2024; 84:3044-3060.e11. [PMID: 39142279 PMCID: PMC11366124 DOI: 10.1016/j.molcel.2024.07.018] [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: 11/29/2023] [Revised: 05/29/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes. Their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected role for the double-stranded DNA (dsDNA) translocase helicase-like transcription factor (HLTF) in responding to G4s. We show that HLTF, which is enriched at G4s in the human genome, can directly unfold G4s in vitro and uses this ATP-dependent translocase function to suppress G4 accumulation throughout the cell cycle. Additionally, MSH2 (a component of MutS heterodimers that bind G4s) and HLTF act synergistically to suppress G4 accumulation, restrict alternative lengthening of telomeres, and promote resistance to G4-stabilizing drugs. In a discrete but complementary role, HLTF restrains DNA synthesis when G4s are stabilized by suppressing primase-polymerase (PrimPol)-dependent repriming. Together, the distinct roles of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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Affiliation(s)
- Gongshi Bai
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Theresa Endres
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ulrike Kühbacher
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Valentina Mengoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Briana H Greer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Emma M Peacock
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Matthew D Newton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Roxana Lungu
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Magdalena P Crossley
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ataya Sathirachinda
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Karlene A Cimprich
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA.
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3
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Todkari IA, Chaudhary P, Kulkarni MJ, Ganesh KN. Supramolecular polyplexes from Janus peptide nucleic acids (bm-PNA-G5): self-assembled bm-PNA G-quadruplex and its tetraduplex with DNA. Org Biomol Chem 2024; 22:6810-6821. [PMID: 39113548 DOI: 10.1039/d4ob00968a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Nucleic acids (DNA and RNA) can form diverse secondary structures ranging from hairpins to duplex, triplex, G4-tetraplex and C4-i-motifs. Many of the DNA analogues designed as antisense oligonucleotides (ASO) are also adept at embracing such folded structures, although to different extents with altered stabilities. One such analogue, peptide nucleic acid (PNA), which is uncharged and achiral, forms hybrids with complementary DNA/RNA with greater stability and specificity than DNA:DNA/RNA hybrids. Like DNAs, these single-stranded PNAs can form PNA:DNA/RNA duplexes, PNA:DNA:PNA triplexes, PNA-G4 tetraplexes and PNA-C4-i-motifs. We have recently designed Janus-like bimodal PNAs endowed with two different nucleobase sequences on either side of a single aminoethylglycyl (aeg) PNA backbone and shown that these can simultaneously bind to two complementary DNA sequences from both faces of PNA. This leads to the formation of supramolecular polyplexes such as double duplexes, triple duplexes and triplexes of double duplexes with appropriate complementary DNA/RNA. Herein, we demonstrate that Janus/bimodal PNA with a poly G-sequence on the triazole side of the PNA backbone and mixed bases on the t-amide side, templates the initial formation of a (PNA-G5)4 tetraplex (triazole side), followed by the formation of a PNA:DNA duplex (t-amide side). Such a polyplex shows synergistic overall stabilisation compared to the isolated duplexes/quadruplex. The assembly of polyplexes with a shared backbone for duplexes and tetraplexes is programmable and may have potential applications in the self-assembly of nucleic acid nano- and origami structures. It is also shown that Janus PNAs enter the cells better than the standard aeg-PNA oligomers, and hence have implications for in vivo applications as well.
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Affiliation(s)
- Iranna Annappa Todkari
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Preeti Chaudhary
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
| | - Mahesh J Kulkarni
- Division of Biochemistry, CSIR-National Chemical Laboratory, Pashan Road, Pune 411008, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, India
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4
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Hisey JA, Radchenko EA, Mandel NH, McGinty R, Matos-Rodrigues G, Rastokina A, Masnovo C, Ceschi S, Hernandez A, Nussenzweig A, Mirkin S. Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures. Nucleic Acids Res 2024; 52:4361-4374. [PMID: 38381906 PMCID: PMC11077069 DOI: 10.1093/nar/gkae124] [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: 07/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
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 pathogenic (A2G3)n and 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 vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the 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
| | | | | | - Ryan J McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115, USA
| | | | | | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD20892, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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5
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Krasilnikova MM, Humphries CL, Shinsky EM. Friedreich's ataxia: new insights. Emerg Top Life Sci 2023; 7:313-323. [PMID: 37698160 DOI: 10.1042/etls20230017] [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: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Friedreich ataxia (FRDA) is an inherited disease that is typically caused by GAA repeat expansion within the first intron of the FXN gene coding for frataxin. This results in the frataxin deficiency that affects mostly muscle, nervous, and cardiovascular systems with progressive worsening of the symptoms over the years. This review summarizes recent progress that was achieved in understanding of molecular mechanism of the disease over the last few years and latest treatment strategies focused on overcoming the frataxin deficiency.
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Affiliation(s)
- Maria M Krasilnikova
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
| | - Casey L Humphries
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
| | - Emily M Shinsky
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
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6
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Bai G, Endres T, Kühbacher U, Greer BH, Peacock EM, Crossley MP, Sathirachinda A, Cortez D, Eichman BF, Cimprich KA. HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.563641. [PMID: 37961428 PMCID: PMC10634870 DOI: 10.1101/2023.10.27.563641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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7
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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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8
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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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