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Abstract
Maintenance of genome stability requires control over the expression of transposable elements (TEs), whose activity can have substantial deleterious effects on the host. Chemical modification of DNA is a commonly used strategy to achieve this, and it has long been argued that the emergence of 5-methylcytosine (5mC) in many species was driven by the requirement to silence TEs. Potential roles in TE regulation have also been suggested for other DNA modifications, such as N6-methyladenine and oxidation derivatives of 5mC, although the underlying mechanistic relationships are poorly understood. Here, we discuss current evidence implicating DNA modifications and DNA-modifying enzymes in TE regulation across different species.
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Affiliation(s)
- Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Jennifer M Frost
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK.
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52
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O'Brown ZK, Boulias K, Wang J, Wang SY, O'Brown NM, Hao Z, Shibuya H, Fady PE, Shi Y, He C, Megason SG, Liu T, Greer EL. Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 2019; 20:445. [PMID: 31159718 PMCID: PMC6547475 DOI: 10.1186/s12864-019-5754-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/30/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relatively abundant in bacteria, occurring in about a percent of all bases of most bacteria. Until recently, 5mC and its oxidized derivatives were thought to be the only directed DNA methylation events in metazoa. New and more sensitive detection techniques (ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-ms/ms) and single molecule real-time sequencing (SMRTseq)) have suggested that 6mA and 4mC modifications could be present in a variety of metazoa. RESULTS Here, we find that both of these techniques are prone to inaccuracies, which overestimate DNA methylation concentrations in metazoan genomic DNA. Artifacts can arise from methylated bacterial DNA contamination of enzyme preparations used to digest DNA and contaminating bacterial DNA in eukaryotic DNA preparations. Moreover, DNA sonication introduces a novel modified base from 5mC that has a retention time near 4mC that can be confused with 4mC. Our analyses also suggest that SMRTseq systematically overestimates 4mC in prokaryotic and eukaryotic DNA and 6mA in DNA samples in which it is rare. Using UHPLC-ms/ms designed to minimize and subtract artifacts, we find low to undetectable levels of 4mC and 6mA in genomes of representative worms, insects, amphibians, birds, rodents and primates under normal growth conditions. We also find that mammalian cells incorporate exogenous methylated nucleosides into their genome, suggesting that a portion of 6mA modifications could derive from incorporation of nucleosides from bacteria in food or microbiota. However, gDNA samples from gnotobiotic mouse tissues found rare (0.9-3.7 ppm) 6mA modifications above background. CONCLUSIONS Altogether these data demonstrate that 6mA and 4mC are rarer in metazoa than previously reported, and highlight the importance of careful sample preparation and measurement, and need for more accurate sequencing techniques.
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Affiliation(s)
- Zach K O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Konstantinos Boulias
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Wang
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Natasha M O'Brown
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ziyang Hao
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Hiroki Shibuya
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Present address: Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Paul-Enguerrand Fady
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chuan He
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tao Liu
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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53
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DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning. Bioinformatics 2019; 35:4586-4595. [DOI: 10.1093/bioinformatics/btz276] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/06/2019] [Accepted: 04/11/2019] [Indexed: 01/19/2023] Open
Abstract
Abstract
Motivation
The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are required to improve the accuracy and robustness of DNA methylation state prediction using Nanopore reads.
Results
In this study, we develop DeepSignal, a deep learning method to detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads of Homo sapiens (H. sapiens), Escherichia coli (E. coli) and pUC19 shows that DeepSignal can achieve higher performance at both read level and genome level on detecting 6 mA and 5mC methylation states comparing to previous hidden Markov model (HMM) based methods. DeepSignal achieves similar performance cross different DNA methylation bases, different DNA methylation motifs and both singleton and mixed DNA CpG. Moreover, DeepSignal requires much lower coverage than those required by HMM and statistics based methods. DeepSignal can achieve 90% above accuracy for detecting 5mC and 6 mA using only 2× coverage of reads. Furthermore, for DNA CpG methylation state prediction, DeepSignal achieves 90% correlation with bisulfite sequencing using just 20× coverage of reads, which is much better than HMM based methods. Especially, DeepSignal can predict methylation states of 5% more DNA CpGs that previously cannot be predicted by bisulfite sequencing. DeepSignal can be a robust and accurate method for detecting methylation states of DNA bases.
Availability and implementation
DeepSignal is publicly available at https://github.com/bioinfomaticsCSU/deepsignal.
Supplementary information
Supplementary data are available at bioinformatics online.
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54
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Kweon SM, Chen Y, Moon E, Kvederaviciutė K, Klimasauskas S, Feldman DE. An Adversarial DNA N 6-Methyladenine-Sensor Network Preserves Polycomb Silencing. Mol Cell 2019; 74:1138-1147.e6. [PMID: 30982744 PMCID: PMC6591016 DOI: 10.1016/j.molcel.2019.03.018] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/12/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
Adenine N6 methylation in DNA (6mA) is widespread among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplored. Here we show that 6mA deposition and removal are catalyzed by the Mettl4 methyltransferase and Alkbh4 dioxygenase, respectively, and that 6mA accumulation in genic elements corresponds with transcriptional silencing. Inactivation of murine Mettl4 depletes 6mA and causes sublethality and craniofacial dysmorphism in incross progeny. We identify distinct 6mA sensor domains of prokaryotic origin within the MPND deubiquitinase and ASXL1, a component of the Polycomb repressive deubiquitinase (PR-DUB) complex, both of which act to remove monoubiquitin from histone H2A (H2A-K119Ub), a repressive mark. Deposition of 6mA by Mettl4 triggers the proteolytic destruction of both sensor proteins, preserving genome-wide H2A-K119Ub levels. Expression of the bacterial 6mA methyltransferase Dam, in contrast, fails to destroy either sensor. These findings uncover a native, adversarial 6mA network architecture that preserves Polycomb silencing. 6mA deposition and erasure by mammalian Mettl4 and Alkbh4, respectively Mettl4-deficient mice display craniofacial dysmorphism 6mA triggers proteolysis of its cognate sensor proteins ASXL1 and MPND Adversarial 6mA network architecture preserves Polycomb silencing
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Affiliation(s)
- Soo-Mi Kweon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Eugene Moon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Kotryna Kvederaviciutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Douglas E Feldman
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA.
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55
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Pacini CE, Bradshaw CR, Garrett NJ, Koziol MJ. Characteristics and homogeneity of N6-methylation in human genomes. Sci Rep 2019; 9:5185. [PMID: 30914725 PMCID: PMC6435722 DOI: 10.1038/s41598-019-41601-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022] Open
Abstract
A novel DNA modification, N-6 methylated deoxyadenosine (m6dA), has recently been discovered in eukaryotic genomes. Despite its low abundance in eukaryotes, m6dA is implicated in human diseases such as cancer. It is therefore important to precisely identify and characterize m6dA in the human genome. Here, we identify m6dA sites at nucleotide level, in different human cells, genome wide. We compare m6dA features between distinct human cells and identify m6dA characteristics in human genomes. Our data demonstrates for the first time that despite low m6dA abundance, the m6dA mark does often occur consistently at the same genomic location within a given human cell type, demonstrating m6dA homogeneity. We further show, for the first time, higher levels of m6dA homogeneity within one chromosome. Most m6dA are found on a single chromosome from a diploid sample, suggesting inheritance. Our transcriptome analysis not only indicates that human genes with m6dA are associated with higher RNA transcript levels but identifies allele-specific gene transcripts showing haplotype-specific m6dA methylation, which are implicated in different biological functions. Our analyses demonstrate the precision and consistency by which the m6dA mark occurs within the human genome, suggesting that m6dA marks are precisely inherited in humans.
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Affiliation(s)
- Clare E Pacini
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Charles R Bradshaw
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nigel J Garrett
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK.
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK.
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56
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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57
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Ye G, Zhang H, Chen B, Nie S, Liu H, Gao W, Wang H, Gao Y, Gu L. De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:779-794. [PMID: 30427081 DOI: 10.1111/tpj.14159] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 05/18/2023]
Abstract
Casuarina equisetifolia (C. equisetifolia), a conifer-like angiosperm with resistance to typhoon and stress tolerance, is mainly cultivated in the coastal areas of Australasia. C. equisetifolia, making it a valuable model to study secondary growth associated genes and stress-tolerance traits. However, the genome sequence is unavailable and therefore wood-associated growth rate and stress resistance at the molecular level is largely unexplored. We therefore constructed a high-quality draft genome sequence of C. equisetifolia by a combination of Illumina second-generation sequencing reads and Pacific Biosciences single-molecule real-time (SMRT) long reads to advance the investigation of this species. Here, we report the genome assembly, which contains approximately 300 megabases (Mb) and scaffold size of N50 is 1.06 Mb. Additionally, gene annotation, assisted by a combination of prediction and RNA-seq data, generated 29 827 annotated protein-coding genes and 1983 non-coding genes, respectively. Furthermore, we found that the total number of repetitive sequences account for one-third of the genome assembly. Here we also construct the genome-wide map of DNA modification, such as two novel forms N6 -adenine (6mA) and N4-methylcytosine (4mC) at the level of single-nucleotide resolution using single-molecule real-time (SMRT) sequencing. Interestingly, we found that 17% of 6mA modification genes and 15% of 4mC modification genes also included alternative splicing events. Finally, we investigated cellulose, hemicellulose, and lignin-related genes, which were associated with secondary growth and contained different DNA modifications. The high-quality genome sequence and annotation of C. equisetifolia in this study provide a valuable resource to strengthen our understanding of the diverse traits of trees.
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Affiliation(s)
- Gongfu Ye
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
- Fujian Casuarina Engineering Technology Research Center, Fuzhou, Fujian, 350012, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bihua Chen
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Sen Nie
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Hai Liu
- Fujian Forestry Investigations and Planning Institute, Fuzhou, Fujian, 350003, China
| | - Wei Gao
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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58
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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59
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Koh C, Goh YT, Toh J, Neo SP, Ng S, Gunaratne J, Gao YG, Quake SR, Burkholder W, Goh W. Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome. Nucleic Acids Res 2018; 46:11659-11670. [PMID: 30412255 PMCID: PMC6294517 DOI: 10.1093/nar/gky1104] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 01/08/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single-stranded DNA-binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homologue 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.
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Affiliation(s)
- Casslynn W Q Koh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yeek Teck Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Joel D W Toh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Suat Peng Neo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Sarah B Ng
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Stephen R Quake
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - William F Burkholder
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Wee Siong S Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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60
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Zhang Q, Liang Z, Cui X, Ji C, Li Y, Zhang P, Liu J, Riaz A, Yao P, Liu M, Wang Y, Lu T, Yu H, Yang D, Zheng H, Gu X. N 6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses. MOLECULAR PLANT 2018; 11:1492-1508. [PMID: 30448535 DOI: 10.1016/j.molp.2018.11.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/03/2018] [Accepted: 11/11/2018] [Indexed: 05/23/2023]
Abstract
N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.
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Affiliation(s)
- Qian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhe Liang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Xuean Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Yun Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingrong Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pu Yao
- Biomarker Technologies, Beijing 101300, China
| | - Min Liu
- Biomarker Technologies, Beijing 101300, China
| | - Yunpeng Wang
- Institute of Clinical Medicine, University of Oslo, Oslo 0450, Norway
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Donglei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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61
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Xie Q, Wu TP, Gimple RC, Li Z, Prager BC, Wu Q, Yu Y, Wang P, Wang Y, Gorkin DU, Zhang C, Dowiak AV, Lin K, Zeng C, Sui Y, Kim LJY, Miller TE, Jiang L, Lee-Poturalski C, Huang Z, Fang X, Zhai K, Mack SC, Sander M, Bao S, Kerstetter-Fogle AE, Sloan AE, Xiao AZ, Rich JN. N 6-methyladenine DNA Modification in Glioblastoma. Cell 2018; 175:1228-1243.e20. [PMID: 30392959 PMCID: PMC6433469 DOI: 10.1016/j.cell.2018.10.006] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023]
Abstract
Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. Although the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obscure. Here, we report the identification of novel N6-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic mark in human disease, specifically the highly malignant brain cancer glioblastoma. Glioblastoma markedly upregulated N6-mA levels, which co-localized with heterochromatic histone modifications, predominantly H3K9me3. N6-mA levels were dynamically regulated by the DNA demethylase ALKBH1, depletion of which led to transcriptional silencing of oncogenic pathways through decreasing chromatin accessibility. Targeting the N6-mA regulator ALKBH1 in patient-derived human glioblastoma models inhibited tumor cell proliferation and extended the survival of tumor-bearing mice, supporting this novel DNA modification as a potential therapeutic target for glioblastoma. Collectively, our results uncover a novel epigenetic node in cancer through the DNA modification N6-mA.
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Affiliation(s)
- Qi Xie
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA
| | - Tao P. Wu
- Department of Genetics and Yale Stem Cell Center, Yale
School of Medicine, New Haven CT 06520, USA,Present address: Department of Molecular and Human
Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Ryan C. Gimple
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA,Department of Pathology, Case Western Reserve University,
Cleveland, OH 44120, USA
| | - Zheng Li
- Department of Genetics and Yale Stem Cell Center, Yale
School of Medicine, New Haven CT 06520, USA
| | - Briana C. Prager
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA,Department of Pathology, Case Western Reserve University,
Cleveland, OH 44120, USA,Cleveland Clinic Lerner College of Medicine, Case Western
Reserve University, Cleveland OH 44195, USA
| | - Qiulian Wu
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA
| | - Yang Yu
- Department of Chemistry, University of California,
Riverside CA 92521, USA
| | - Pengcheng Wang
- Department of Chemistry, University of California,
Riverside CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California,
Riverside CA 92521, USA
| | - David U. Gorkin
- Center for Epigenomics, Department of Cellular and
Molecular Medicine, University of California, San Diego, La Jolla CA 92037,
USA
| | - Cheng Zhang
- Center for Epigenomics, Department of Cellular and
Molecular Medicine, University of California, San Diego, La Jolla CA 92037,
USA
| | - Alexis V. Dowiak
- Center for Epigenomics, Department of Cellular and
Molecular Medicine, University of California, San Diego, La Jolla CA 92037,
USA
| | - Kaixuan Lin
- Department of Genetics and Yale Stem Cell Center, Yale
School of Medicine, New Haven CT 06520, USA
| | - Chun Zeng
- Departments of Pediatrics and Cellular and Molecular
Medicine, Pediatric Diabetes Research Center, University of California, San Diego,
La Jolla CA 92093, USA
| | - Yinghui Sui
- Departments of Pediatrics and Cellular and Molecular
Medicine, Pediatric Diabetes Research Center, University of California, San Diego,
La Jolla CA 92093, USA
| | - Leo J. Y. Kim
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA,Department of Pathology, Case Western Reserve University,
Cleveland, OH 44120, USA
| | - Tyler E. Miller
- Department of Pathology, Case Western Reserve University,
Cleveland, OH 44120, USA
| | - Li Jiang
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA
| | | | - Zhi Huang
- Department of Stem Cell Biology and Regenerative
Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland OH 44195, USA
| | - Xiaoguang Fang
- Department of Stem Cell Biology and Regenerative
Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland OH 44195, USA
| | - Kui Zhai
- Department of Stem Cell Biology and Regenerative
Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland OH 44195, USA
| | - Stephen C. Mack
- Department of Pediatrics, Division of Hematology and
Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston TX,
77030, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular and Molecular
Medicine, Pediatric Diabetes Research Center, University of California, San Diego,
La Jolla CA 92093, USA
| | - Shideng Bao
- Department of Stem Cell Biology and Regenerative
Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland OH 44195, USA
| | - Amber E. Kerstetter-Fogle
- Case Comprehensive Cancer Center, Case Western Reserve
University School of Medicine, Cleveland OH, 44106, USA,Department of Neurological Surgery, University
Hospitals-Cleveland Medical Center, Cleveland OH, 44106, USA
| | - Andrew E. Sloan
- Case Comprehensive Cancer Center, Case Western Reserve
University School of Medicine, Cleveland OH, 44106, USA,Department of Neurological Surgery, University
Hospitals-Cleveland Medical Center, Cleveland OH, 44106, USA
| | - Andrew Z. Xiao
- Department of Genetics and Yale Stem Cell Center, Yale
School of Medicine, New Haven CT 06520, USA,Correspondence to: Jeremy N. Rich
() and Andrew Z. Xiao
()
| | - Jeremy N. Rich
- Department of Medicine, Division of Regenerative Medicine,
University of California, San Diego, La Jolla CA 92037, USA,Department of Neurosciences, University of California,
San Diego, School of Medicine, La Jolla CA 92037, USA,Lead Contact,Correspondence to: Jeremy N. Rich
() and Andrew Z. Xiao
()
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