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Raiber EA, Portella G, Martínez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Liu Z, Dawson MA, Reik W, Balasubramanian S. 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells. Nat Chem 2018; 10:1258-1266. [PMID: 30349137 DOI: 10.1038/s41557-018-0149-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/29/2018] [Indexed: 12/27/2022]
Abstract
Nucleosomes are the basic unit of chromatin that help the packaging of genetic material while controlling access to the genetic information. The underlying DNA sequence, together with transcription-associated proteins and chromatin remodelling complexes, are important factors that influence the organization of nucleosomes. Here, we show that the naturally occurring DNA modification, 5-formylcytosine (5fC) is linked to tissue-specific nucleosome organization. Our study reveals that 5fC is associated with increased nucleosome occupancy in vitro and in vivo. We demonstrate that 5fC-associated nucleosomes at enhancers in the mammalian hindbrain and heart are linked to elevated gene expression. Our study also reveals the formation of a reversible-covalent Schiff base linkage between lysines of histone proteins and 5fC within nucleosomes in a cellular environment. We define their specific genomic loci in mouse embryonic stem cells and look into the biological consequences of these DNA-histone Schiff base sites. Collectively, our findings show that 5fC is a determinant of nucleosome organization and plays a role in establishing distinct regulatory regions that control transcription.
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Affiliation(s)
- Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Sergio Martínez Cuesta
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Robyn Hardisty
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Zhe Li
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Mario Iurlaro
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Julia Spindel
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Dario Beraldi
- Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Zheng Liu
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK. .,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK. .,School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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Raiber EA, Beraldi D, Cuesta SM, McInroy G, Kingsbury Z, Becq J, James T, Lopes M, Allinson K, Field S, Humphray S, Santarius T, Watts C, Bentley D, Balasubramanian S. GENE-46. COMPARISON OF MATCHED GLIOBLASTOMA TUMOR AND MARGIN SAMPLES USING SINGLE BASE RESOLUTION MAPS REVEALS ACQUIRED, EARLY EPIGENETIC CHANGES THAT PREDISPOSE TO MUTATIONS DURING TUMOURIGENESIS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Raiber EA, Beraldi D, Martínez Cuesta S, McInroy GR, Kingsbury Z, Becq J, James T, Lopes M, Allinson K, Field S, Humphray S, Santarius T, Watts C, Bentley D, Balasubramanian S. Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma. NPJ Genom Med 2017; 2:6. [PMID: 29263824 PMCID: PMC5677956 DOI: 10.1038/s41525-017-0007-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/24/2023] Open
Abstract
Aberrant genetic and epigenetic variations drive malignant transformation and are hallmarks of cancer. Using PCR-free sample preparation we achieved the first in-depth whole genome (hydroxyl)-methylcytosine, single-base-resolution maps from a glioblastoma tumour/margin sample of a patient. Our data provide new insights into how genetic and epigenetic variations are interrelated. In the tumour, global hypermethylation with a depletion of 5-hydroxymethylcytosine was observed. The majority of single nucleotide variations were identified as cytosine-to-thymine deamination products within CpG context, where cytosine was preferentially methylated in the margin. Notably, we observe that cells neighbouring tumour cells display epigenetic alterations characteristic of the tumour itself although genetically they appear "normal". This shows the potential transfer of epigenetic information between cells that contributes to the intratumour heterogeneity of glioblastoma. Together, our reference (epi)-genome provides a human model system for future studies that aim to explore the link between genetic and epigenetic variations in cancer progression.
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Affiliation(s)
- Eun-Ang Raiber
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Dario Beraldi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Zoya Kingsbury
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Jennifer Becq
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Terena James
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Margarida Lopes
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Kieren Allinson
- Department of Pathology, Addenbrooke’s Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Sarah Field
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sean Humphray
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Thomas Santarius
- Department of Clinical Neurosciences, Division of Neurosurgery, University of Cambridge, Cambridge, UK
| | - Colin Watts
- Department of Clinical Neurosciences, Division of Neurosurgery, University of Cambridge, Cambridge, UK
| | - David Bentley
- Illumina Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
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Iurlaro M, McInroy GR, Burgess HE, Dean W, Raiber EA, Bachman M, Beraldi D, Balasubramanian S, Reik W. In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine. Genome Biol 2016; 17:141. [PMID: 27356509 PMCID: PMC4928330 DOI: 10.1186/s13059-016-1001-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/06/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown. RESULTS Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development. CONCLUSIONS The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.
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Affiliation(s)
- Mario Iurlaro
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Gordon R McInroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Heather E Burgess
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Wendy Dean
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Eun-Ang Raiber
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
- Present Address: Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Dario Beraldi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
| | - Wolf Reik
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
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McInroy GR, Beraldi D, Raiber EA, Modrzynska K, van Delft P, Billker O, Balasubramanian S. Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments. PLoS One 2016; 11:e0152322. [PMID: 27031619 PMCID: PMC4816320 DOI: 10.1371/journal.pone.0152322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/11/2016] [Indexed: 12/04/2022] Open
Abstract
Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemical treatment causes strand scission, which depletes the number of sequenceable DNA fragments in a library and thus necessitates PCR amplification. The AT-rich nature of the library generated from bisulfite treatment adversely affects this amplification, resulting in the introduction of major biases that can confound methylation analysis. Here, we report a method that enables more accurate methylation analysis, by rebuilding bisulfite-damaged components of a DNA library. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We apply the ReBuilT method for the first whole methylome analysis of the highly AT-rich genome of Plasmodium berghei. Side-by-side comparison to a commercial protocol involving amplification demonstrates a substantial improvement in uniformity of coverage and reduction of sequence context bias. Our method will be widely applicable for quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.
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Affiliation(s)
- Gordon R. McInroy
- Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Dario Beraldi
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, Cambridgeshire, United Kingdom
| | - Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | | | - Pieter van Delft
- Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, Cambridgeshire, United Kingdom
- School of Clinical Medicine, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
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Abstract
The exquisite selectivity of chemical reactions enables the study of rare DNA bases. However, chemical modification of the genome can affect downstream analysis. We report a PCR bias caused by such modification, and exemplify a solution with the synthesis and characterization of a cleavable aldehyde-reactive biotinylation probe.
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Affiliation(s)
- Gordon R McInroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S. 5-Formylcytosine alters the structure of the DNA double helix. Nat Struct Mol Biol 2014; 22:44-49. [PMID: 25504322 PMCID: PMC4287393 DOI: 10.1038/nsmb.2936] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/21/2014] [Indexed: 12/15/2022]
Abstract
The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-Å-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.
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Affiliation(s)
- Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Dario Beraldi
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK.,School of Clinical Medicine, University of Cambridge, Cambridge, UK
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Affiliation(s)
- Michael J Booth
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Eun-Ang Raiber
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Shankar Balasubramanian
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom.,‡Cambridge Institute, Li Ka Shing Centre, Cancer Research U.K., Robinson Way, Cambridge, CB2 0RE United Kingdom.,§School of Clinical Medicine, The University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0SP United Kingdom
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Iurlaro M, Ficz G, Oxley D, Raiber EA, Bachman M, Booth MJ, Andrews S, Balasubramanian S, Reik W. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol 2013; 14:R119. [PMID: 24156278 PMCID: PMC4014808 DOI: 10.1186/gb-2013-14-10-r119] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/24/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins which showed preferential binding to 5-methylcytosine (5mC) and its oxidised forms, where readers for 5mC and 5hmC showed little overlap, and proteins bound to further oxidation forms were enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine using DNA from mouse embryonic stem cell extracts. RESULTS We compared protein enrichments from two DNA probes with different CpG composition and show that, whereas some of the enriched proteins show specificity to cytosine modifications, others are selective for both modification and target sequences. Only a few proteins were identified with a preference for 5hmC (such as RPL26, PRP8 and the DNA mismatch repair protein MHS6), but proteins with a strong preference for 5fC were more numerous, including transcriptional regulators (FOXK1, FOXK2, FOXP1, FOXP4 and FOXI3), DNA repair factors (TDG and MPG) and chromatin regulators (EHMT1, L3MBTL2 and all components of the NuRD complex). CONCLUSIONS Our screen has identified novel proteins that bind to 5fC in genomic sequences with different CpG composition and suggests they regulate transcription and chromatin, hence opening up functional investigations of 5fC readers.
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Affiliation(s)
- Mario Iurlaro
- Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Charterhouse Square, London EC1M 6BQ, UK
| | - David Oxley
- Proteomics Research Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson way, Cambridge CB2 0RE, UK
| | - Michael J Booth
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson way, Cambridge CB2 0RE, UK
- School of Clinical Medicine, The University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0SP, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- 1Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Inside Cover: Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry (Angew. Chem. Int. Ed. 44/2012). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/anie.201207794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Innentitelbild: Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry (Angew. Chem. 44/2012). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA versus DNA G-quadruplex targeting by in situ click chemistry. Angew Chem Int Ed Engl 2012; 51:11073-8. [PMID: 23038154 PMCID: PMC3652031 DOI: 10.1002/anie.201206281] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Indexed: 12/22/2022]
Abstract
It all clicks into place: A potent telomere-targeting small molecule has been identified by using the copper-free 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks catalyzed by a non-Watson-Crick DNA secondary structure (see picture). This method rapidly identifies, otherwise unanticipated, potent small-molecule probes to selectively target a given RNA or DNA.
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Affiliation(s)
- Marco Di Antonio
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206281] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Raiber EA, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ, Reik W, Balasubramanian S. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol 2012; 13:R69. [PMID: 22902005 PMCID: PMC3491369 DOI: 10.1186/gb-2012-13-8-r69] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/17/2012] [Indexed: 11/10/2022] Open
Abstract
Background Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified key players involved in active demethylation pathways, including oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) by the TET enzymes, and excision of 5fC by the base excision repair enzyme thymine DNA glycosylase (TDG). Here, we provide the first genome-wide map of 5fC in mouse embryonic stem (ES) cells and evaluate potential roles for 5fC in differentiation. Results Our method exploits the unique reactivity of 5fC for pulldown and high-throughput sequencing. Genome-wide mapping revealed 5fC enrichment in CpG islands (CGIs) of promoters and exons. CGI promoters in which 5fC was relatively more enriched than 5mC or 5hmC corresponded to transcriptionally active genes. Accordingly, 5fC-rich promoters had elevated H3K4me3 levels, associated with active transcription, and were frequently bound by RNA polymerase II. TDG down-regulation led to 5fC accumulation in CGIs in ES cells, which correlates with increased methylation in these genomic regions during differentiation of ES cells in wild-type and TDG knockout contexts. Conclusions Collectively, our data suggest that 5fC plays a role in epigenetic reprogramming within specific genomic regions, which is controlled in part by TDG-mediated excision. Notably, 5fC excision in ES cells is necessary for the correct establishment of CGI methylation patterns during differentiation and hence for appropriate patterns of gene expression during development.
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Tulone C, Sponaas AM, Raiber EA, Tabor AB, Langhorne J, Chain BM. Differential requirement for cathepsin D for processing of the full length and C-terminal fragment of the malaria antigen MSP1. PLoS One 2011; 6:e24886. [PMID: 22053177 PMCID: PMC3203867 DOI: 10.1371/journal.pone.0024886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 08/23/2011] [Indexed: 11/19/2022] Open
Abstract
Merozoite Surface Protein 1 is expressed on the surface of malaria merozoites and is important for invasion of the malaria parasite into erythrocytes. MSP1-specific CD4 T cell responses and antibody can confer protective immunity in experimental models of malaria. In this study we explore the contributions of cathepsins D and E, two aspartic proteinases previously implicated in antigen processing, to generating MSP1 CD4 T-cell epitopes for presentation. The absence of cathepsin D, a late endosome/lysosomal enzyme, is associated with a reduced presentation of MSP1 both following in vitro processing of the epitope MSP1 from infected erythrocytes by bone marrow-derived dendritic cells, and following in vivo processing by splenic CD11c+ dendritic cells. By contrast, processing and presentation of the soluble recombinant protein fragment of MSP1 is unaffected by the absence of cathepsin D, but is inhibited when both cathepsin D and E are absent. The role of different proteinases in generating the CD4 T cell repertoire, therefore, depends on the context in which an antigen is introduced to the immune system.
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Affiliation(s)
- Calogero Tulone
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Anne-Marit Sponaas
- Division of Parasitology MRC National Institute of Medical Research, London, United Kingdom
| | - Eun-Ang Raiber
- Department of Chemistry, University College London, London, United Kingdom
| | - Alethea B. Tabor
- Department of Chemistry, University College London, London, United Kingdom
| | - Jean Langhorne
- Division of Parasitology MRC National Institute of Medical Research, London, United Kingdom
| | - Benny M. Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail:
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Raiber EA, Kranaster R, Lam E, Nikan M, Balasubramanian S. A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. Nucleic Acids Res 2011; 40:1499-508. [PMID: 22021377 PMCID: PMC3287196 DOI: 10.1093/nar/gkr882] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
SP1 is a ubiquitous transcription factor that is involved in the regulation of various house-keeping genes. It is known that it acts by binding to a double-stranded consensus motif. Here, we have discovered that SP1 binds also to a non-canonical DNA structure, a G-quadruplex, with high affinity. In particular, we have studied the SP1 binding site within the promoter region of the c-KIT oncogene and found that this site can fold into an anti-parallel two-tetrad G-quadruplex. SP1 pull-down experiments from cellular extracts, together with biophysical binding assays revealed that SP1 has a comparable binding affinity for this G-quadruplex structure and the canonical SP1 duplex sequence. Using SP1 ChIP-on-chip data sets, we have also found that 87% of SP1 binding sites overlap with G-quadruplex forming sequences. Furthermore, while many of these immuoprecipitated sequences (36%) even lack the minimal SP1 consensus motif, 5′-GGGCGG-3′, we have shown that 77% of them are putative G-quadruplexes. Collectively, these data suggest that SP1 is able to bind both, canonical SP1 duplex DNA as well as G-quadruplex structures in vitro and we hypothesize that both types of interactions may occur in cells.
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Affiliation(s)
- Eun-Ang Raiber
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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Wang Y, Jimenez M, Hansen AS, Raiber EA, Schreiber SL, Young DW. Control of olefin geometry in macrocyclic ring-closing metathesis using a removable silyl group. J Am Chem Soc 2011; 133:9196-9. [PMID: 21557625 DOI: 10.1021/ja202012s] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Introducing a silyl group at one of the internal olefin positions in diolefinic substrates results in E-selective olefin formation in macrocyclic ring-forming metathesis. The application of this method to a range of macrocyclic (E)-alkenylsiloxanes is described. Protodesilylation of alkenylsiloxane products yields novel Z-configured macrocycles.
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Affiliation(s)
- Yikai Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Körner C, Raiber EA, Keegan SE, Nicolau DC, Sheppard TD, Tabor AB. An expedient synthesis of orthogonally protected lysinoalanine from Aloc-protected Garner’s aldehyde. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.09.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Raiber EA, Tulone C, Zhang Y, Martinez-Pomares L, Steed E, Sponaas AM, Langhorne J, Noursadeghi M, Chain BM, Tabor AB. Targeted delivery of antigen processing inhibitors to antigen presenting cells via mannose receptors. ACS Chem Biol 2010; 5:461-476. [PMID: 20349916 DOI: 10.1021/cb100008p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Improved chemical inhibitors are required to dissect the role of specific antigen processing enzymes and to complement genetic models. In this study we explore the in vitro and in vivo properties of a novel class of targeted inhibitor of aspartic proteinases, in which pepstatin is coupled to mannosylated albumin (MPC6), creating an inhibitor with improved solubility and the potential for selective cell tropism. Using these compounds, we have demonstrated that MPC6 is taken up via mannose receptor facilitated endocytosis, leading to a slow but continuous accumulation of inhibitor within large endocytic vesicles within dendritic cells and a parallel inhibition of intracellular aspartic proteinase activity. Inhibition of intracellular proteinase activity is associated with reduction in antigen processing activity, but this is epitope-specific, preferentially inhibiting processing of T cell epitopes buried within compact proteinase-resistant protein domains. Unexpectedly, we have also demonstrated, using quenched fluorescent substrates, that little or no cleavage of the disulfide linker takes place within dendritic cells. This does not appear to affect the activity of MPC6 as an inhibitor of cathepsins D and E in vitro and in vivo. Finally, we have shown that MPC6 selectively targets dendritic cells and macrophages in spleen in vivo. Preliminary results suggest that access to nonlymphoid tissues is very limited in the steady state but is strongly enhanced at local sites of inflammation. The strategy adopted for MPC6 synthesis may therefore represent a more general way to deliver chemical inhibitors to cells of the innate immune system, especially at sites of inflammation.
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Affiliation(s)
| | | | - Yanjing Zhang
- Division of Infection and Immunity, UCL, London, U.K
| | | | - Emily Steed
- Division of Infection and Immunity, UCL, London, U.K
| | - Anna M. Sponaas
- Division of Parasitology, National Institute for Medical Research, London, U.K
| | - Jean Langhorne
- Division of Parasitology, National Institute for Medical Research, London, U.K
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Mustapa MFM, Grosse SM, Kudsiova L, Elbs M, Raiber EA, Wong JB, Brain APR, Armer HEJ, Warley A, Keppler M, Ng T, Lawrence MJ, Hart SL, Hailes HC, Tabor AB. Stabilized Integrin-Targeting Ternary LPD (Lipopolyplex) Vectors for Gene Delivery Designed To Disassemble Within the Target Cell. Bioconjug Chem 2009; 20:518-32. [DOI: 10.1021/bc800450r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- M. Firouz Mohd Mustapa
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Stephanie M. Grosse
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Laila Kudsiova
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Martin Elbs
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Eun-Ang Raiber
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - John B. Wong
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Anthony P. R. Brain
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Hannah E. J. Armer
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Alice Warley
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Melanie Keppler
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Tony Ng
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - M. Jayne Lawrence
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Stephen L. Hart
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Helen C. Hailes
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
| | - Alethea B. Tabor
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, Wolfson Centre for Gene Therapy of Childhood Disease, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, School of Biomedical and Health Sciences, Pharmaceutical Science Research Division, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, Centre for Ultrastructure Imaging, King’s College London, New Hunt’s House,
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Raiber EA, Wilkinson JA, Manetti F, Botta M, Deakin J, Gallagher J, Lyon M, Ducki SW. Novel heparin/heparan sulfate mimics as inhibitors of HGF/SF-induced MET activation. Bioorg Med Chem Lett 2007; 17:6321-5. [PMID: 17870532 DOI: 10.1016/j.bmcl.2007.08.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 08/30/2007] [Accepted: 08/31/2007] [Indexed: 11/22/2022]
Abstract
The synthesis of simple, non-sugar glycosaminoglycan (GAG) mimics has been achieved and the analogues evaluated for their ability to inhibit the activation of the MET receptor by hepatocyte growth factor/scatter factor (HGF/SF).
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Affiliation(s)
- Eun-Ang Raiber
- Centre for Molecular Drug Design, Cockcroft Building, University of Salford, Salford, UK
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Vu NQ, Dujardin G, Collet SC, Raiber EA, Guingant AY, Evain M. Synthesis of 5-aza-analogues of angucyclines: manipulation of the 2-deoxy-C-glycoside subunit. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.09.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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