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Datta S, Patel M, Sathyaseelan C, Ghosh C, Mudgal A, Patel D, Rathinavelan T, Singh U. G-quadruplex landscape and its regulation revealed by a new antibody capture method. Oncotarget 2024; 15:175-198. [PMID: 38484151 PMCID: PMC10939474 DOI: 10.18632/oncotarget.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Our understanding of DNA G-quadruplexes (G4s) from in vitro studies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s. It remains unknown what fraction of G4s formed in human cells are protein-bound. The G4-chromatin immunoprecipitation (G4-ChIP) method hitherto employed to describe G4 landscapes preferentially reports G4s that get crosslinked to proteins in their proximity. Our current understanding of the G4 landscape is biased against representation of G4s which escape crosslinking as they are not stabilized by protein-binding and presumably transient. We report a protocol that captures G4s from the cells efficiently without any bias as well as eliminates the detection of G4s formed artifactually on crosslinked sheared chromatin post-fixation. We discover that G4s form sparingly at SINEs. An application of this method shows that depletion of a repeat-binding protein CGGBP1 enhances net G4 capture at CGGBP1-dependent CTCF-binding sites and regions of sharp interstrand G/C-skew transitions. Thus, we present an improved method for G4 landscape determination and by applying it we show that sequence property-specific constraints of the nuclear environment mitigate G4 formation.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Chandrama Ghosh
- Azrieli Faculty of Medicine, Bar-Ilan University, Henrietta Szold 8A, Safed 1311502, Israel
| | - Akanksha Mudgal
- Department of Biopharmacy, Medical University of Lublin, Lublin 20059, Poland
| | - Divyesh Patel
- Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | | | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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Datta S, Patel M, Kashyap S, Patel D, Singh U. Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1. Oncotarget 2022; 13:136-155. [PMID: 35070079 PMCID: PMC8765472 DOI: 10.18632/oncotarget.28174] [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: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Sukesh Kashyap
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Current address: Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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Patel M, Patel D, Datta S, Singh U. CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity. BMC Genet 2020; 21:84. [PMID: 32727353 PMCID: PMC7392725 DOI: 10.1186/s12863-020-00894-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
Background The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown. Results By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Conclusion Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
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Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India.
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Patel D, Patel M, Datta S, Singh U. CGGBP1 regulates CTCF occupancy at repeats. Epigenetics Chromatin 2019; 12:57. [PMID: 31547883 PMCID: PMC6757366 DOI: 10.1186/s13072-019-0305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/27/2022] Open
Abstract
Background CGGBP1 is a repeat-binding protein with diverse functions in the regulation of gene expression, cytosine methylation, repeat silencing and genomic integrity. CGGBP1 has also been identified as a cooperator of histone-modifying enzymes and as a component of CTCF-containing complexes that regulate the enhancer–promoter looping. CGGBP1–CTCF cross talk in chromatin regulation has been hitherto unknown. Results Here, we report that the occupancy of CTCF at repeats depends on CGGBP1. Using ChIP-sequencing for CTCF, we describe its occupancy at repetitive DNA. Our results show that endogenous level of CGGBP1 ensures CTCF occupancy preferentially on repeats over canonical CTCF motifs. By combining CTCF ChIP-sequencing results with ChIP sequencing for three different kinds of histone modifications (H3K4me3, H3K9me3 and H3K27me3), we show that the CGGBP1-dependent repeat-rich CTCF-binding sites regulate histone marks in flanking regions. Conclusion CGGBP1 affects the pattern of CTCF occupancy. Our results posit CGGBP1 as a regulator of CTCF and its binding sites in interspersed repeats.
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Affiliation(s)
- Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
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Patel D, Patel M, Westermark B, Singh U. Dynamic bimodal changes in CpG and non-CpG methylation genome-wide upon CGGBP1 loss-of-function. BMC Res Notes 2018; 11:419. [PMID: 29966527 PMCID: PMC6027561 DOI: 10.1186/s13104-018-3516-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Although CpG methylation is well studied, mechanisms of non-CpG methylation in mammals remains elusive. Studying proteins with non-CpG cytosine methylation-sensitive DNA-binding, such as human CGGBP1, can unveil cytosine methylation regulatory mechanisms. Here we have resequenced a published genome-wide bisulfite sequencing library and analyzed it at base level resolution. CpG, CHG and CHH (where H is any nucleotide other than G) methylation states in non-targeting or CGGBP1-targeting shmiR lentivirus-transduced cells have been analyzed to identify how CGGBP1 regulates CpG and non-CpG methylation. RESULTS We report that CGGBP1 acts as a dynamic bimodal balancer of methylation. Both gain and loss of methylation observed upon CGGBP1 depletion were spatially overlapping at annotated functional regions and not identifiable with any sequence motifs but clearly associated with GC-skew. CGGBP1 depletion caused clustered methylation changes in cis, upstream of R-loop forming promoters. This was complemented by clustered occurrences of methylation changes in proximity of transcription start sites of known cytosine methylation regulatory genes, altered expression of which can regulate cytosine methylation in trans. Despite low coverage, our data provide reliable estimates of the spectrum of methylation changes regulated by CGGBP1 in all cytosine contexts genome-wide through a combination of cis and trans-acting mechanisms.
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Affiliation(s)
- Divyesh Patel
- HoMeCell Laboratory, Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gujarat, 382355, India
| | - Manthan Patel
- HoMeCell Laboratory, Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gujarat, 382355, India
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory, Uppsala University, 75185, Uppsala, Sweden
| | - Umashankar Singh
- HoMeCell Laboratory, Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gujarat, 382355, India.
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Patel M, Patel D, Agrawal P, Singh U. Genome-wide CpG and non-CpG methylation regulation by CGGBP1. CANADIAN JOURNAL OF BIOTECHNOLOGY 2017. [DOI: 10.24870/cjb.2017-a97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mauro M, Caradonna F, Klein CB. Dysregulation of DNA methylation induced by past arsenic treatment causes persistent genomic instability in mammalian cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:137-50. [PMID: 26581878 PMCID: PMC5008255 DOI: 10.1002/em.21987] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/29/2015] [Accepted: 10/31/2015] [Indexed: 05/21/2023]
Abstract
The mechanisms by which arsenic-induced genomic instability is initiated and maintained are poorly understood. To investigate potential epigenetic mechanisms, in this study we evaluated global DNA methylation levels in V79 cells and human HaCaT keratinocytes at several time points during expanded growth of cell cultures following removal of arsenite exposures. We have found altered genomic methylation patterns that persisted up to 40 cell generations in HaCaT cells after the treatments were withdrawn. Moreover, mRNA expression levels were evaluated by RT-PCR for DNMT1, DNMT3A, DNMT3B, HMLH1, and HMSH2 genes, demonstrating that the down regulation of DNMT3A and DNMT3B genes, but not DNMT1, occurred in an arsenic dose-dependent manner, and persisted for many cell generations following removal of the arsenite, offering a plausible mechanism of persistently genotoxic arsenic action. Analyses of promoter methylation status of the DNA mismatch repair genes HMLH1 and HMSH2 show that HMSH2, but not HMLH1, was epigenetically regulated by promoter hypermethylation changes following arsenic treatment. The results reported here demonstrate that arsenic exposure promptly induces genome-wide global DNA hypomethylation, and some specific gene promoter methylation changes, that persist for many cell generations following withdrawal of arsenite, supporting the hypothesis that the cells undergo epigenetic reprogramming at both the gene and genome level that is durable over many cell generations in the absence of further arsenic treatment. These DNA methylation changes, in concert with other known epigenome alterations, are likely contributing to long-lasting arsenic-induced genomic instability that manifests in several ways, including aberrant chromosomal effects.
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Affiliation(s)
- Maurizio Mauro
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF, Sezione Di Biologia Cellulare) Universita Di Palermo, Italia
| | - Fabio Caradonna
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF, Sezione Di Biologia Cellulare) Universita Di Palermo, Italia
| | - Catherine B. Klein
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987
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Abstract
The human genome contains multiple stretches of CGG trinucleotide repeats, which act as transcription- and translation-regulatory elements but at the same time form secondary structures that impede replication and give rise to sites of chromosome fragility. Proteins binding to such DNA elements may be involved in divergent cellular processes such as transcription, DNA damage, and epigenetic state of the chromatin. We review here the work done on CGG repeats and associated proteins with special focus on a factor called CGGBP1. CGGBP1 presents with an interesting example of factors that do not have any single dedicated function, but participate indispensably in multiple processes. Both experimental results and data from cancer genome sequencing have revealed that any alteration in CGGBP1 that compromises its function is not tolerated by normal or cancer cells alike. Based upon a large amount of published data, information from databases, and unpublished results, we decipher in this review how CGGBP1 is a classic example of the 'one factor, divergent functions' paradigm of cytoprotection. By taking cues from the studies on CGGBP1, more such factors can be discovered for a better understanding of the evolution of mechanisms of cellular survival.
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Affiliation(s)
- Umashankar Singh
- Biological Sciences and Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, India
- Correspondence: Umashankar Singh, Biological Sciences and Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, India.
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
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