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Schwaiger M, Mohn F, Bühler M, Kaaij LJT. guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel. BMC Genomics 2024; 25:732. [PMID: 39075377 DOI: 10.1186/s12864-024-10625-3] [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: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024] Open
Abstract
Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) liberation. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of any type of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we present a cost-effective, scalable, and customizable target enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.
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Affiliation(s)
- Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
- Swiss Institute of Bioinformatics, Basel, 4056, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, 4056, Switzerland
- University of Basel, Basel, 4003, Switzerland
| | - Lucas J T Kaaij
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands.
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Sorwar E, Oliveira JIN, Malar C M, Krüger M, Corradi N. Assembly and comparative analyses of the Geosiphon pyriformis metagenome. Environ Microbiol 2024; 26:e16681. [PMID: 39054868 DOI: 10.1111/1462-2920.16681] [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: 04/09/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.
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Affiliation(s)
- Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Institute of Experimental Botany, The Czech Academy of Science, Prague, Czech Republic
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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Flores-Fernández CN, Lin D, Robins K, O'Callaghan CA. DNA methylases for site-selective inhibition of type IIS restriction enzyme activity. Appl Microbiol Biotechnol 2024; 108:174. [PMID: 38270650 PMCID: PMC10810934 DOI: 10.1007/s00253-024-13015-7] [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: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. KEY POINTS: • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly.
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Affiliation(s)
- Carol N Flores-Fernández
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Triple Helix Biotechnology Ltd, Moneta Building (B280), Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK
| | - Katherine Robins
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Complete Regulatory, 19-20 King Edward Street, Macclesfield, SK10 1AQ, UK
| | - Chris A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Miura F, Miura M, Shibata Y, Furuta Y, Miyamura K, Ino Y, Bayoumi AMA, Oba U, Ito T. Correction: Identifcation, expression, and purifcation of DNA cytosine 5-methyltransferases with short recognition sequences. BMC Biotechnol 2022; 22:37. [PMID: 36457075 PMCID: PMC9716734 DOI: 10.1186/s12896-022-00770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Fumihito Miura
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Miki Miura
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Yukiko Shibata
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Yoshikazu Furuta
- grid.39158.360000 0001 2173 7691Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020 Japan
| | - Keisuke Miyamura
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Yuki Ino
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Asmaa M. A. Bayoumi
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Pharmacy, Minia University, El-Minia, 61511 Egypt
| | - Utako Oba
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan ,grid.177174.30000 0001 2242 4849Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
| | - Takashi Ito
- grid.177174.30000 0001 2242 4849Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582 Japan
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