1
|
Sheng Y, Wang Y, Yang W, Wang XQ, Lu J, Pan B, Nan B, Liu Y, Ye F, Li C, Song J, Dou Y, Gao S, Liu Y. Semiconservative transmission of DNA N 6-adenine methylation in a unicellular eukaryote. Genome Res 2024; 34:740-756. [PMID: 38744529 PMCID: PMC11216311 DOI: 10.1101/gr.277843.123] [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: 03/03/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Although DNA N 6-adenine methylation (6mA) is best known in prokaryotes, its presence in eukaryotes has recently generated great interest. Biochemical and genetic evidence supports that AMT1, an MT-A70 family methyltransferase (MTase), is crucial for 6mA deposition in unicellular eukaryotes. Nonetheless, the 6mA transmission mechanism remains to be elucidated. Taking advantage of single-molecule real-time circular consensus sequencing (SMRT CCS), here we provide definitive evidence for semiconservative transmission of 6mA in Tetrahymena thermophila In wild-type (WT) cells, 6mA occurs at the self-complementary ApT dinucleotide, mostly in full methylation (full-6mApT); after DNA replication, hemi-methylation (hemi-6mApT) is transiently present on the parental strand, opposite to the daughter strand readily labeled by 5-bromo-2'-deoxyuridine (BrdU). In ΔAMT1 cells, 6mA predominantly occurs as hemi-6mApT. Hemi-to-full conversion in WT cells is fast, robust, and processive, whereas de novo methylation in ΔAMT1 cells is slow and sporadic. In Tetrahymena, regularly spaced 6mA clusters coincide with the linker DNA of nucleosomes arrayed in the gene body. Importantly, in vitro methylation of human chromatin by the reconstituted AMT1 complex recapitulates preferential targeting of hemi-6mApT sites in linker DNA, supporting AMT1's intrinsic and autonomous role in maintenance methylation. We conclude that 6mA is transmitted by a semiconservative mechanism: full-6mApT is split by DNA replication into hemi-6mApT, which is restored to full-6mApT by AMT1-dependent maintenance methylation. Our study dissects AMT1-dependent maintenance methylation and AMT1-independent de novo methylation, reveals a 6mA transmission pathway with a striking similarity to 5-methylcytosine (5mC) transmission at the CpG dinucleotide, and establishes 6mA as a bona fide eukaryotic epigenetic mark.
Collapse
Affiliation(s)
- Yalan Sheng
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yuanyuan Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Wentao Yang
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Xue Qing Wang
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Bo Pan
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Bei Nan
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yongqiang Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Fei Ye
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Chun Li
- Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Yali Dou
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Shan Gao
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yifan Liu
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA;
| |
Collapse
|
2
|
Ghafoor H, Asim MN, Ibrahim MA, Ahmed S, Dengel A. CAPTURE: Comprehensive anti-cancer peptide predictor with a unique amino acid sequence encoder. Comput Biol Med 2024; 176:108538. [PMID: 38759585 DOI: 10.1016/j.compbiomed.2024.108538] [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: 01/08/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
Anticancer peptides (ACPs) key properties including bioactivity, high efficacy, low toxicity, and lack of drug resistance make them ideal candidates for cancer therapies. To deeply explore the potential of ACPs and accelerate development of cancer therapies, although 53 Artificial Intelligence supported computational predictors have been developed for ACPs and non ACPs classification but only one predictor has been developed for ACPs functional types annotations. Moreover, these predictors extract amino acids distribution patterns to transform peptides sequences into statistical vectors that are further fed to classifiers for discriminating peptides sequences and annotating peptides functional classes. Overall, these predictors remain fail in extracting diverse types of amino acids distribution patterns from peptide sequences. The paper in hand presents a unique CARE encoder that transforms peptides sequences into statistical vectors by extracting 4 different types of distribution patterns including correlation, distribution, composition, and transition. Across public benchmark dataset, proposed encoder potential is explored under two different evaluation settings namely; intrinsic and extrinsic. Extrinsic evaluation indicates that 12 different machine learning classifiers achieve superior performance with the proposed encoder as compared to 55 existing encoders. Furthermore, an intrinsic evaluation reveals that, unlike existing encoders, the proposed encoder generates more discriminative clusters for ACPs and non-ACPs classes. Across 8 public benchmark ACPs and non-ACPs classification datasets, proposed encoder and Adaboost classifier based CAPTURE predictor outperforms existing predictors with an average accuracy, recall and MCC score of 1%, 4%, and 2% respectively. In generalizeability evaluation case study, across 7 benchmark anti-microbial peptides classification datasets, CAPTURE surpasses existing predictors by an average AU-ROC of 2%. CAPTURE predictive pipeline along with label powerset method outperforms state-of-the-art ACPs functional types predictor by 5%, 5%, 5%, 6%, and 3% in terms of average accuracy, subset accuracy, precision, recall, and F1 respectively. CAPTURE web application is available at https://sds_genetic_analysis.opendfki.de/CAPTURE.
Collapse
Affiliation(s)
- Hina Ghafoor
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, 67663, Germany; German Research Center for Artificial Intelligence GmbH, Kaiserslautern, 67663, Germany
| | - Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, 67663, Germany.
| | - Muhammad Ali Ibrahim
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, 67663, Germany; German Research Center for Artificial Intelligence GmbH, Kaiserslautern, 67663, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, 67663, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, 67663, Germany; German Research Center for Artificial Intelligence GmbH, Kaiserslautern, 67663, Germany
| |
Collapse
|
3
|
Li D, Du J, Gao M, He C. Identification of AtALKBH1A and AtALKBH1D as DNA N 6-adenine demethylases in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112055. [PMID: 38432357 DOI: 10.1016/j.plantsci.2024.112055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
DNA N6-methyladenine (6 mA) has recently been discovered as a novel DNA modification in animals and plants. In mammals, AlkB homolog 1 (ALKBH1) has been identified as a DNA 6 mA demethylase. ALKBH1 tightly controls the DNA 6 mA methylation level of mammalian genomes and plays important role in regulating gene expression. DNA 6 mA methylation has also been reported to exist in plant genomes, however, the plant DNA 6 mA demethylases and their function remain largely unknown. Here we identify homologs of ALKBH1 as DNA 6 mA demethylases in Arabidopsis. We discover that there are four homologs of ALKBH1, AtALKBH1A, AtALKBH1B, AtALKBH1C and AtALKBH1D, in Arabidopsis. In vitro enzymatic activity studies reveal that AtALKBH1A and 1D can efficiently erase DNA 6 mA methylation. Loss of function of AtALKBH1A and AtALKBH1D causes elevated DNA 6 mA methylation levels in vivo. atalkbh1a/1d mutant displays delayed seed gemination. Based on our RNA-seq data, we find some regulators of seed gemination are dysregulated in atalkbh1a/1d, and the dysregulation is correlated with changes of DNA 6 mA methylation levels. This study identifies plant DNA 6 mA demethylases and reports the function of DNA 6 mA methylation in regulating seed germination.
Collapse
Affiliation(s)
- Donghao Li
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Juan Du
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Min Gao
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Chongsheng He
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, Hunan 410082, China.
| |
Collapse
|
4
|
Zhang L, Mu Y, Li T, Hu J, Lin H, Zhang L. Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation. Nucleic Acids Res 2024; 52:3886-3895. [PMID: 38324471 PMCID: PMC11040006 DOI: 10.1093/nar/gkae066] [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: 09/05/2023] [Revised: 11/22/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
The eukaryotic epigenetic modifications 5-methyldeoxycytosine (5mC) and N6-methyldeoxyadenine (6mA) have indispensable regulatory roles in gene expression and embryonic development. We recently identified an atypical bifunctional dioxygenase CcTet from Coprinopsis cinerea that works on both 5mC and 6mA demethylation. The nonconserved residues Gly331 and Asp337 of CcTet facilitate 6mA accommodation, while D337F unexpectedly abolishes 5mC oxidation activity without interfering 6mA demethylation, indicating a prominent distinct but unclear 5mC oxidation mechanism to the conventional Tet enzymes. Here, we assessed the molecular mechanism of CcTet in catalyzing 5mC oxidation by representing the crystal structure of CcTet-5mC-dsDNA complex. We identified the distinct mechanism by which CcTet recognizes 5mC-dsDNA compared to 6mA-dsDNA substrate. Moreover, Asp337 was found to have a central role in compensating for the loss of a critical 5mC-stablizing H-bond observed in conventional Tet enzymes, and stabilizes 5mC and subsequent intermediates through an H-bond with the N4 atom of the substrates. These findings improve our understanding of Tet enzyme functions in the dsDNA 5mC and 6mA demethylation pathways, and provide useful information for future discovery of small molecular probes targeting Tet enzymes in DNA active demethylation processes.
Collapse
Affiliation(s)
- Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tingting Li
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingyan Hu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| |
Collapse
|
5
|
Meng WY, Wang ZX, Zhang Y, Hou Y, Xue JH. Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes. J Biol Chem 2024; 300:106791. [PMID: 38403247 PMCID: PMC11065753 DOI: 10.1016/j.jbc.2024.106791] [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: 10/29/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.
Collapse
Affiliation(s)
- Wei-Ying Meng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zi-Xin Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Hou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Jian-Huang Xue
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| |
Collapse
|
6
|
Jiang T, Zhou Q, Yu KK, Chen SY, Li K. Identification and quantification of N6-methyladenosine by chemical derivatization coupled with 19F NMR spectroscopy. Org Biomol Chem 2024; 22:2566-2573. [PMID: 38465392 DOI: 10.1039/d4ob00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
N 6-Methyladenosine (6mA) is a well-known prokaryotic DNA modification that has been shown to play epigenetic roles in eukaryotic DNA. Accurate detection and quantification of 6mA are prerequisites for molecular understanding of the impact of 6mA modification on DNA. However, the existing methods have several problems, such as high false-positive rate, time-consuming and complex operating procedures. Chemical sensors for the selective detection of 6mA modification are rarely reported in the literature. Fluorinated phenylboronic acid combined with 19F NMR analysis is an effective method for determining DNA or RNA modification. In this study, we presented a simple and fast chemical method for labelling the 6th imino group of 6mA using a boric-acid-derived probe. Besides, the trifluoromethyl group of trifluoromethyl phenylboronic acid (2a) could detect 6mA modification through 19F NMR. Combined with this sensor system, 6mA modification could be detected well and quickly in 6 types of deoxynucleoside mixtures and DNA samples. Taken together, the method developed in the current study has potential for specific detection of 6mA in biological samples.
Collapse
Affiliation(s)
- Ting Jiang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Qian Zhou
- Department of Chemistry, Xihua University, Chengdu 610039, P. R. China
| | - Kang-Kang Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Shan-Yong Chen
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| |
Collapse
|
7
|
Gong Y, Wang Q, Wei L, Liang W, Wang L, Lv N, Du X, Zhang J, Shen C, Xin Y, Sun L, Xu J. Genome-wide adenine N6-methylation map reveals epigenomic regulation of lipid accumulation in Nannochloropsis. PLANT COMMUNICATIONS 2024; 5:100773. [PMID: 38007614 PMCID: PMC10943562 DOI: 10.1016/j.xplc.2023.100773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/09/2023] [Accepted: 11/23/2023] [Indexed: 11/27/2023]
Abstract
Epigenetic marks on histones and DNA, such as DNA methylation at N6-adenine (6mA), play crucial roles in gene expression and genome maintenance, but their deposition and function in microalgae remain largely uncharacterized. Here, we report a genome-wide 6mA map for the model industrial oleaginous microalga Nannochloropsis oceanica produced by single-molecule real-time sequencing. Found in 0.1% of adenines, 6mA sites are mostly enriched at the AGGYV motif, more abundant in transposons and 3' untranslated regions, and associated with active transcription. Moreover, 6mA gradually increases in abundance along the direction of gene transcription and shows special positional enrichment near splicing donor and transcription termination sites. Highly expressed genes tend to show greater 6mA abundance in the gene body than do poorly expressed genes, indicating a positive interaction between 6mA and general transcription factors. Furthermore, knockout of the putative 6mA methylase NO08G00280 by genome editing leads to changes in methylation patterns that are correlated with changes in the expression of molybdenum cofactor, sulfate transporter, glycosyl transferase, and lipase genes that underlie reductions in biomass and oil productivity. By contrast, knockout of the candidate demethylase NO06G02500 results in increased 6mA levels and reduced growth. Unraveling the epigenomic players and their roles in biomass productivity and lipid metabolism lays a foundation for epigenetic engineering of industrial microalgae.
Collapse
Affiliation(s)
- Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wensi Liang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Lianhong Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nana Lv
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xuefeng Du
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jiashun Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Luyang Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| |
Collapse
|
8
|
Yin Z, Lyu J, Zhang G, Huang X, Ma Q, Jiang J. SoftVoting6mA: An improved ensemble-based method for predicting DNA N6-methyladenine sites in cross-species genomes. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:3798-3815. [PMID: 38549308 DOI: 10.3934/mbe.2024169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The DNA N6-methyladenine (6mA) is an epigenetic modification, which plays a pivotal role in biological processes encompassing gene expression, DNA replication, repair, and recombination. Therefore, the precise identification of 6mA sites is fundamental for better understanding its function, but challenging. We proposed an improved ensemble-based method for predicting DNA N6-methyladenine sites in cross-species genomes called SoftVoting6mA. The SoftVoting6mA selected four (electron-ion-interaction pseudo potential, One-hot encoding, Kmer, and pseudo dinucleotide composition) codes from 15 types of encoding to represent DNA sequences by comparing their performances. Similarly, the SoftVoting6mA combined four learning algorithms using the soft voting strategy. The 5-fold cross-validation and the independent tests showed that SoftVoting6mA reached the state-of-the-art performance. To enhance accessibility, a user-friendly web server is provided at http://www.biolscience.cn/SoftVoting6mA/.
Collapse
Affiliation(s)
- Zhaoting Yin
- College of Information Science and Engineering, Shaoyang University, Shaoyang 422000, China
| | - Jianyi Lyu
- College of Information Science and Engineering, Shaoyang University, Shaoyang 422000, China
| | - Guiyang Zhang
- College of Information Science and Engineering, Shaoyang University, Shaoyang 422000, China
| | - Xiaohong Huang
- College of Information Science and Engineering, Shaoyang University, Shaoyang 422000, China
| | - Qinghua Ma
- College of Information Science and Engineering, Hohai University, Nanjing 210000, China
- Faculty of Information Technology, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jinyun Jiang
- College of Information Science and Engineering, Shaoyang University, Shaoyang 422000, China
| |
Collapse
|
9
|
Lin R, Liu J, Shan S, Zhang Y, Yang Y. Significant differences in the degree of genomic DNA N6-methyladenine modifications in Acidithiobacillus ferrooxidans with two different culture substrates. PLoS One 2024; 19:e0298204. [PMID: 38306373 PMCID: PMC10836689 DOI: 10.1371/journal.pone.0298204] [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: 10/25/2023] [Accepted: 01/20/2024] [Indexed: 02/04/2024] Open
Abstract
DNA N6-methyladenine (6mA) modification is widespread in organisms and plays an important functional role in the regulation of cellular processes. As a model organism in biohydrometallurgy, Acidithiobacillus ferrooxidans can obtain energy from the oxidation of ferrous iron (Fe2+) and various reduced inorganic sulfides (RISCs) under acidic conditions. To determine the linkage between genomic DNA methylation and the switching between the two oxidative metabolic pathways in A. ferrooxidans, the 6mA landscape in the genome of A. ferrooxidans cultured under different conditions was evaluated by using 6mA-IP-seq. A total of 214 and 47 high-confidence peaks of 6mA were identified under the Fe2+ and RISCs oxidizing conditions, respectively (P<10-5), suggesting that genomic methylation was greater under Fe2+ oxidizing conditions. 6mA experienced a decline at the transcription start site (TSS) and occurs frequently in gene bodies under both oxidizing conditions. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that 7 KEGG pathways were mapped into and most of the differentially methylated genes were enriched in oxidative phosphorylation and metabolic pathways. Fourteen genes were selected for studying the effect of differences in methylation on mRNA expression. Thirteen genes, excluding petA-1, demonstrated a decrease in mRNA expression as methylation levels increased. Overall, the 6mA methylation enrichment patterns are similar under two conditions but show differences in the enriched pathways. The phenomenon of upregulated gene methylation levels coupled with downregulated expression suggests a potential association between the regulation mechanisms of 6mA and the Fe2+ and RISCs oxidation pathways.
Collapse
Affiliation(s)
- RuTao Lin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
| | - JingQi Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
| | - Si Shan
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yu Zhang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of the Ministry of Education, Central South University, Changsha, Hunan, China
| | - Yu Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
| |
Collapse
|
10
|
Ramakrishnan M, Rajan KS, Mullasseri S, Ahmad Z, Zhou M, Sharma A, Ramasamy S, Wei Q. Exploring N6-methyladenosine (m 6A) modification in tree species: opportunities and challenges. HORTICULTURE RESEARCH 2024; 11:uhad284. [PMID: 38371641 PMCID: PMC10871907 DOI: 10.1093/hr/uhad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/17/2023] [Indexed: 02/20/2024]
Abstract
N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.
Collapse
Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - K Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi 682018, Kerala, India
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Subbiah Ramasamy
- Cardiac Metabolic Disease Laboratory, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamilnadu, India
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| |
Collapse
|
11
|
Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
Collapse
Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
| |
Collapse
|
12
|
Cai L, Ma A, Lei J, He C. METTL4-mediated N 6-methyladenine DNA modification regulates thermotolerance in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111916. [PMID: 37944704 DOI: 10.1016/j.plantsci.2023.111916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/18/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
DNA N6-methyladenine (6 mA) is an evolutionarily conserved DNA modification in procaryotes and eukaryotes. The DNA 6 mA methylation is tightly controlled by 6 mA regulatory proteins. DNA N6-adenine methyltransferase 1 (DAMT-1) has been identified as a DNA 6 mA methyltransferase in animals. In plants, DNA 6 mA methylation has been found, however, the DNA 6 mA methyltransferases and their function in plants are largely unknown. In our study, we find METTL4 is a DNA 6 mA methyltransferase in Arabidopsis thaliana. Both in vitro and in vivo evidences support the DNA 6 mA methyltransferase activity of METTL4. mettl4 mutant is hypersensitive to heat stress, suggesting DNA 6 mA methylation plays important role in heat stress adaption. RNA-seq and 6 mA IP-qPCR analysis show that METTL4 participates in heat stress tolerance by regulating expression of heat responsive genes. Our study find METTL4 is a plant DNA 6 mA methyltransferase and illustrates its function in regulating heat stress response.
Collapse
Affiliation(s)
- Linjun Cai
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082 Hunan, China
| | - Ancheng Ma
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082 Hunan, China
| | - Jiao Lei
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082 Hunan, China
| | - Chongsheng He
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082 Hunan, China.
| |
Collapse
|
13
|
Liu Z, Li Y, Zhang X. DNA methylation on C5-Cytosine and N6-Adenine in the Bursaphelenchus xylophilus genome. BMC Genomics 2023; 24:671. [PMID: 37936063 PMCID: PMC10631105 DOI: 10.1186/s12864-023-09783-7] [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: 12/30/2022] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND The pinewood nematode is the causal agent of the pine wilt disease, which causes severe ecological and economic losses in coniferous forests. The invasion of pine wood nematode has undergone various rapid adaptations to a wide range of temperatures and to new hosts and vector insects. DNA methylation may play crucial roles in the rapid adaptation of PWN during invasion. However, whether the PWN genome contins functional DNA modifications remains elusive. RESULTS Here, we detected the extensive presence of 5-methylcytosine (5mC) and N6-methyladenine (6mA) in the B. xylophilus genome, with low methylation levels at most positions. Cytosines were methylated in the CpG, CHG. and CHH sequence contexts, with the lowest methylation levels at CpG sites. The methylation levels of CpG and 6mA in gene regions showed opposite trends. The changes in the abundance of 5mC and 6mA showed the same trends in response to temperature change, but opposite trends during development. Sequence and phylogenetic analyses showed that the proteins BxDAMT and BxNMAD have typical characteristics of a methylase and demethylase, respectively, and are conserved among species. CONCLUSIONS These findings shed light on the epigenetic modifications present in the genome of PWN, and will improve our understanding of its invasiveness and evolution.
Collapse
Affiliation(s)
- Zhenkai Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, PR China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, PR China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, PR China.
| | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, PR China
| |
Collapse
|
14
|
Sinha D, Dasmandal T, Paul K, Yeasin M, Bhattacharjee S, Murmu S, Mishra DC, Pal S, Rai A, Archak S. MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1256186. [PMID: 37877081 PMCID: PMC10591185 DOI: 10.3389/fpls.2023.1256186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/01/2023] [Indexed: 10/26/2023]
Abstract
The Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulates gene expression, through predicting methylation sites of their promoters particularly in major crop species. In this study, we developed a user-friendly prediction server for accurate prediction of 6mA sites by incorporating a robust feature set, viz., Binary Encoding of Mono-nucleotide DNA. Our model,MethSemble-6mA, outperformed other state-of-the-art tools in terms of accuracy (93.12%). Furthermore, we investigated the pattern of probable 6mA sites at the upstream promoter regions of the LBD-containing genes in Triticum aestivum and its allied species using the developed tool. On average, each selected species had four 6mA sites, and it was found that with speciation and due course of evolution in wheat, the frequency of methylation have reduced, and a few sites remain conserved. This obviously cues gene birth and gene expression alteration through methylation over time in a species and reflects functional conservation throughout evolution. Since DNA methylation is a vital event in almost all plant developmental processes (e.g., genomic imprinting and gametogenesis) along with other life processes, our findings on epigenetic regulation of LBD-containing genes have dynamic implications in basic and applied research. Additionally, MethSemble-6mA (http://cabgrid.res.in:5799/) will serve as a useful resource for a plant breeders who are interested to pursue epigenetic-based crop improvement research.
Collapse
Affiliation(s)
- Dipro Sinha
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
| | - Tanwy Dasmandal
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Krishnayan Paul
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Institute for Plant Biotechnology, Delhi, India
| | - Md Yeasin
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | - Sougata Bhattacharjee
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Institute for Plant Biotechnology, Delhi, India
- ICAR-Indian Agricultural Research Institute, Hazaribagh, Jharkhand, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | | | - Soumen Pal
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | - Anil Rai
- Indian Council of Agricultural Research, Delhi, India
| | - Sunil Archak
- ICAR-National Bureau of Plant Genetic Resources, Delhi, India
| |
Collapse
|
15
|
Ma CJ, Li G, Shao WX, Min YH, Wang P, Ding JH, Xie NB, Wang M, Tang F, Feng YQ, Ci W, Wang Y, Yuan BF. Single-Nucleotide Resolution Mapping of N6-Methyladenine in Genomic DNA. ACS CENTRAL SCIENCE 2023; 9:1799-1809. [PMID: 37780356 PMCID: PMC10540296 DOI: 10.1021/acscentsci.3c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/03/2023]
Abstract
N6-Methyladenine (6mA) is a naturally occurring DNA modification in both prokaryotes and eukaryotes. Herein, we developed a deaminase-mediated sequencing (DM-seq) method for genome-wide mapping of 6mA at single-nucleotide resolution. The method capitalizes on the selective deamination of adenine, but not 6mA, in DNA mediated by an evolved adenine deaminase, ABE8e. By employing this method, we achieved genome-wide mapping of 6mA in Escherichia coli and in mammalian mitochondrial DNA (mtDNA) at single-nucleotide resolution. We found that the 6mA sites are mainly located in the GATC motif in the E. coli genome. We also identified 17 6mA sites in mtDNA of HepG2 cells, where all of the 6mA sites are distributed in the heavy strand of mtDNA. We envision that DM-seq will be a valuable tool for uncovering new functions of 6mA in DNA and for exploring its potential roles in mitochondria-related human diseases.
Collapse
Affiliation(s)
- Cheng-Jie Ma
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Gaojie Li
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Xuan Shao
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yi-Hao Min
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Ping Wang
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang-Hui Ding
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Min Wang
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Feng Tang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Yu-Qi Feng
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Weimin Ci
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinsheng Wang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Bi-Feng Yuan
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| |
Collapse
|
16
|
Jia Q, Zhang X, Liu Q, Li J, Wang W, Ma X, Zhu B, Li S, Gong S, Tian J, Yuan M, Zhao Y, Zhou DX. A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature. Genome Biol 2023; 24:198. [PMID: 37649077 PMCID: PMC10469495 DOI: 10.1186/s13059-023-03042-4] [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: 02/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The Fe (II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. RESULTS Here, we find that loss-of-function of the rice ALKBH1 gene leads to increased 6mA in the R-loop regions of the genome but has a limited effect on the overall 6mA level. However, in the context of mixed tissues, rather than on individual loci, the ALKBH1 mutation or overexpression mainly affects the expression of genes with a specific combination of chromatin modifications in the body region marked with H3K4me3 and H3K27me3 but depleted of DNA CG methylation. In the similar context of mixed tissues, further analysis reveals that the ALKBH1 protein preferentially binds to genes marked by the chromatin signature and has a function to maintain a high H3K4me3/H3K27me3 ratio by impairing the binding of Polycomb repressive complex 2 (PRC2) to the targets, which is required for both the basal and stress-induced expression of the genes. CONCLUSION Our findings unravel a function of ALKBH1 to control the balance between the antagonistic histone methylations for gene activity and provide insight into the regulatory mechanism of PRC2-mediated H3K27me3 deposition within the gene body region.
Collapse
Affiliation(s)
- Qingxiao Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinran Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wentao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shicheng Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, 91405, Orsay, France.
| |
Collapse
|
17
|
Chen S, Lai W, Li Y, Liu Y, Jiang J, Li X, Jiang G, Wang H. Aberrant DNA N 6 -methyladenine incorporation via adenylate kinase 1 is suppressed by ADAL deaminase-dependent 2'-deoxynucleotide pool sanitation. EMBO J 2023; 42:e113684. [PMID: 37366109 PMCID: PMC10390868 DOI: 10.15252/embj.2023113684] [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: 02/03/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Intracellular decay of N6 -methyladenine (m6A)-containing RNA potentially induces aberrant N6 -methyl-2'-adenine (6mdA) misincorporation into DNA. Biophysically, misincorporated 6mdA may destabilize the DNA duplex in a manner similar to bona fide methylated 6mdA DNA, thereby affecting DNA replication and transcription. Utilizing heavy stable isotope labeling and ultrasensitive UHPLC-MS/MS assay, we demonstrate that intracellular m6A-RNA decay does not generate free 6mdA species, nor lead to any misincorporated DNA 6mdA in most mammalian cell lines tested, unveiling the existence of a sanitation mechanism that prevents 6mdA misincorporation. Depletion of deaminase ADAL increases the levels of free 6mdA species, concomitant with the presence of DNA-misincorporated 6mdA resulting from intracellular RNA m6A decay, suggesting that ADAL catabolizes 6mdAMP in vivo. Furthermore, we show that the overexpression of adenylate kinase 1 (AK1) promotes 6mdA misincorporation, while AK1 knockdown diminishes 6mdA incorporation, in ADAL-deficient cells. We conclude that ADAL together with other factors (such as MTH1) contributes to 2'-deoxynucleotide pool sanitation in most cells but compromised sanitation (e.g., in NIH3T3 cells) and increased AK1 expression may facilitate aberrant 6mdA incorporation. This sanitation mechanism may provide a framework for the maintenance of the epigenetic 6mdA landscape.
Collapse
Affiliation(s)
- Shaokun Chen
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Yanan Li
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
| | - Yan Liu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Jie Jiang
- Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Xiangjun Li
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Guibin Jiang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
| |
Collapse
|
18
|
Mao F, Xie H, Shi Y, Jiang S, Wang S, Wu Y. The Global Changes of N6-methyldeoxyadenosine in Response to Low Temperature in Arabidopsis thaliana and Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2373. [PMID: 37375998 DOI: 10.3390/plants12122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
N6-methyldeoxyadenosine (6mA) is a recently discovered DNA modification involved in regulating plant adaptation to abiotic stresses. However, the mechanisms and changes of 6mA under cold stress in plants are not yet fully understood. Here, we conducted a genome-wide analysis of 6mA and observed that 6mA peaks were predominantly present within the gene body regions under both normal and cold conditions. In addition, the global level of 6mA increased both in Arabidopsis and rice after the cold treatment. The genes that exhibited an up-methylation showed enrichment in various biological processes, whereas there was no significant enrichment observed among the down-methylated genes. The association analysis revealed a positive correlation between the 6mA level and the gene expression level. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice unraveled that fluctuations in 6mA levels caused by cold exposure were not correlated to changes in transcript levels. Furthermore, we discovered that orthologous genes modified by 6mA showed high expression levels; however, only a minor amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice under low-temperature conditions. In conclusion, our study provides information on the role of 6mA in response to cold stress and reveals its potential for regulating the expression of stress-related genes.
Collapse
Affiliation(s)
- Fei Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hairong Xie
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yucheng Shi
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shasha Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
19
|
Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
Collapse
Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
20
|
Li B, Zhang M, Sun W, Yue D, Ma Y, Zhang B, Duan L, Wang M, Lindsey K, Nie X, Zhang X, Yang X. N6-methyladenosine RNA modification regulates cotton drought response in a Ca 2+ and ABA-dependent manner. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1270-1285. [PMID: 36949572 DOI: 10.1111/pbi.14036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 05/27/2023]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m6 A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m6 A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m6 A methylation in cotton response to drought stress. The results reveal that m6 A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m6 A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m6 A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m6 A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca2+ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca2+ -related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m6 A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m6 A methylation on targeted transcripts in the ABA and Ca2+ signalling transduction pathways.
Collapse
Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mengmeng Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Boyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingfeng Duan
- College of Engineering, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Xinjiang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| |
Collapse
|
21
|
Lyu C, Wang HD, Lai W, Wang H. Identification and quantification of DNA N 6-methyladenine modification in mammals: A challenge to modern analytical technologies. Curr Opin Chem Biol 2023; 73:102259. [PMID: 36652775 DOI: 10.1016/j.cbpa.2022.102259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/18/2023]
Abstract
DNA N6-methyladenine modification (6mA) is a predominant epigenetic mark in prokaryotes but rarely present in multicellular metazoa. The analytical technologies have been developed for sensitive detection of 6mA, including ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-MS/MS) and single molecule real-time sequencing (SMRTseq). However, it remains challenging to detect 6mA at global level and/or in the context of sequence in multicellular metazoa (including mammals). This mini-review brings insights into current dilemma and potential solutions for the identification and quantifications of 6mA in mammals.
Collapse
Affiliation(s)
- Cong Lyu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui-Dong Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
22
|
Özdilek AS, Atakan A, Özsarı G, Acar A, Atalay MV, Doğan T, Rifaioğlu AS. ProFAB-open protein functional annotation benchmark. Brief Bioinform 2023; 24:7025464. [PMID: 36736370 DOI: 10.1093/bib/bbac627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/12/2022] [Accepted: 12/25/2022] [Indexed: 02/05/2023] Open
Abstract
As the number of protein sequences increases in biological databases, computational methods are required to provide accurate functional annotation with high coverage. Although several machine learning methods have been proposed for this purpose, there are still two main issues: (i) construction of reliable positive and negative training and validation datasets, and (ii) fair evaluation of their performances based on predefined experimental settings. To address these issues, we have developed ProFAB: Open Protein Functional Annotation Benchmark, which is a platform providing an infrastructure for a fair comparison of protein function prediction methods. ProFAB provides filtered and preprocessed protein annotation datasets and enables the training and evaluation of function prediction methods via several options. We believe that ProFAB will be useful for both computational and experimental researchers by enabling the utilization of ready-to-use datasets and machine learning algorithms for protein function prediction based on Gene Ontology terms and Enzyme Commission numbers. ProFAB is available at https://github.com/kansil/ProFAB and https://profab.kansil.org.
Collapse
Affiliation(s)
- A Samet Özdilek
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Ahmet Atakan
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
- Department of Computer Engineering, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Gökhan Özsarı
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
- Department of Computer Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Aybar Acar
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - M Volkan Atalay
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Tunca Doğan
- Department of Computer Engineering and Artificial Intelligence Engineering, Hacettepe University, Ankara, Turkey
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Ahmet S Rifaioğlu
- Department of Electrical-Electronics Engineering, İskenderun Technical University, Hatay, Turkey
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
23
|
Cadavid IC, Balbinott N, Margis R. Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress. Genet Mol Biol 2023; 46:e20220166. [PMID: 36706026 PMCID: PMC9881580 DOI: 10.1590/1678-4685-gmb-2022-0166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/18/2022] [Indexed: 01/28/2023] Open
Abstract
Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.
Collapse
Affiliation(s)
- Isabel Cristina Cadavid
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, Porto Alegre, Brazil
| |
Collapse
|
24
|
Han K, Wang J, Wang Y, Zhang L, Yu M, Xie F, Zheng D, Xu Y, Ding Y, Wan J. A review of methods for predicting DNA N6-methyladenine sites. Brief Bioinform 2023; 24:6887111. [PMID: 36502371 DOI: 10.1093/bib/bbac514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.
Collapse
Affiliation(s)
- Ke Han
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China.,College of Pharmacy, Harbin University of Commerce, Harbin, 150076, China
| | - Jianchun Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yu Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Lei Zhang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Mengyao Yu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Fang Xie
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Dequan Zheng
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yaoqun Xu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Jie Wan
- Laboratory for Space Environment and Physical Sciences, Harbin Institute of Technology, Harbin, 150001, China
| |
Collapse
|
25
|
Eprintsev AT, Fedorin DN, Igamberdiev AU. Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize ( Zea mays L.) Leaves. Int J Mol Sci 2022; 23:13495. [PMID: 36362281 PMCID: PMC9653993 DOI: 10.3390/ijms232113495] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 09/29/2023] Open
Abstract
Limited methyl-specific restriction of genomic DNA by endonuclease MAL1 revealed the changes in its methyl status caused by adenine modification in maize (Zea mays L.) leaves under different light conditions (dark, light, irradiation by red and far-red light). Incubation in the light and irradiation by red light exhibited an activating effect on DNA adenine methylase activity, which was reflected in an increase in the number of methylated adenines in GATC sites. Far-red light and darkness exhibited an opposite effect. The use of nitrite conversion of DNA followed by methyladenine-dependent restriction by MboI nuclease revealed a phytochrome B-dependent mechanism of regulation of the methyl status of adenine in the GATC sites in the promoter of the gene encoding the mitochondrial isoform of citrate synthase. Irradiation of plants with red light caused changes in the adenine methyl status of the analyzed amplicon, as evidenced by the presence of restriction products of 290, 254, and 121 nucleotides. Adenine methylation occurred at all three GATC sites in the analyzed DNA sequence. It is concluded that adenylate methylation is controlled by phytochrome B via the transcription factor PIF4 and represents an important mechanism for the tricarboxylic acid cycle regulation by light.
Collapse
Affiliation(s)
- Alexander T. Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Dmitry N. Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| |
Collapse
|
26
|
Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
Collapse
Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
27
|
Rehman MU, Tayara H, Zou Q, Chong KT. i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites. Bioinformatics 2022; 38:3885-3891. [PMID: 35771648 DOI: 10.1093/bioinformatics/btac434] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION DNA N6-methyladenine (6mA) has been demonstrated to have an essential function in epigenetic modification in eukaryotic species in recent research. 6mA has been linked to various biological processes. It's critical to create a new algorithm that can rapidly and reliably detect 6mA sites in genomes to investigate their biological roles. The identification of 6mA marks in the genome is the first and most important step in understanding the underlying molecular processes, as well as their regulatory functions. RESULTS In this article, we proposed a novel computational tool called i6mA-Caps which CapsuleNet based a framework for identifying the DNA N6-methyladenine sites. The proposed framework uses a single encoding scheme for numerical representation of the DNA sequence. The numerical data is then used by the set of convolution layers to extract low-level features. These features are then used by the capsule network to extract intermediate-level and later high-level features to classify the 6mA sites. The proposed network is evaluated on three datasets belonging to three genomes which are Rosaceae, Rice and Arabidopsis thaliana. Proposed method has attained an accuracy of 96.71%, 94% and 86.83% for independent Rosaceae dataset, Rice dataset and A.thaliana dataset respectively. The proposed framework has exhibited improved results when compared with the existing top-of-the-line methods. AVAILABILITY AND IMPLEMENTATION A user-friendly web-server is made available for the biological experts which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/i6mA-Caps/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
| |
Collapse
|
28
|
Feng Y, Luo Z, Huang R, Yang X, Cheng X, Zhang W. Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2022; 23:ijms23158404. [PMID: 35955535 PMCID: PMC9368837 DOI: 10.3390/ijms23158404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K+ and Na+ affect G4 formation genome-wide is still unclear in plants. Here, we conducted BG4-DNA-IP-seq, DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing, under K+ and Na+ + PEG conditions in vitro. We found that K+-specific IP-G4s had a longer peak size, more GC and PQS content, and distinct AT and GC skews compared to Na+-specific IP-G4s. Moreover, K+- and Na+-specific IP-G4s exhibited differential subgenomic enrichment and distinct putative functional motifs for the binding of certain trans-factors. More importantly, we found that K+-specific IP-G4s were more associated with active marks, such as active histone marks, and low DNA methylation levels, as compared to Na+-specific IP-G4s; thus, K+-specific IP-G4s in combination with active chromatin features facilitate the expression of overlapping genes. In addition, K+- and Na+-specific IP-G4 overlapping genes exhibited differential GO (gene ontology) terms, suggesting they may have distinct biological relevance in rice. Thus, our study, for the first time, explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.
Collapse
Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Ranran Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Xueming Yang
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (Y.F.); (Z.L.); (R.H.); (X.C.)
- Correspondence: ; Tel.: +86-25-84396610; Fax: +86-25-84396302
| |
Collapse
|
29
|
Villagómez-Aranda AL, Feregrino-Pérez AA, García-Ortega LF, González-Chavira MM, Torres-Pacheco I, Guevara-González RG. Activating stress memory: eustressors as potential tools for plant breeding. PLANT CELL REPORTS 2022; 41:1481-1498. [PMID: 35305133 PMCID: PMC8933762 DOI: 10.1007/s00299-022-02858-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/26/2022] [Indexed: 05/08/2023]
Abstract
Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.
Collapse
Affiliation(s)
- A L Villagómez-Aranda
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - A A Feregrino-Pérez
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - L F García-Ortega
- Laboratory of Learning and Research in Biological Computing, Centre for Research and Advanced Studies, National Polytechnic Institute (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - M M González-Chavira
- Molecular Markers Laboratory, Bajío Experimental Field, National Institute for Forestry, Agriculture and Livestock Research (INIFAP), Celaya-San Miguel de Allende, Celaya, Guanajuato, Mexico
| | - I Torres-Pacheco
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - R G Guevara-González
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico.
| |
Collapse
|
30
|
Miao Z, Wang G, Shen H, Wang X, Gabriel DW, Liang W. BcMettl4-Mediated DNA Adenine N6-Methylation Is Critical for Virulence of Botrytis cinerea. Front Microbiol 2022; 13:925868. [PMID: 35847085 PMCID: PMC9279130 DOI: 10.3389/fmicb.2022.925868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
DNA adenine N6-methylation (6mA) plays a critical role in various biological functions, but its occurrence and functions in filamentous plant pathogens are largely unexplored. Botrytis cinerea is an important pathogenic fungus worldwide. A systematic analysis of 6mA in B. cinerea was performed in this study, revealing that 6mA is widely distributed in the genome of this fungus. The 2 kb regions flanking many genes, particularly the upstream promoter regions, were susceptible to methylation. The role of BcMettl4, a 6mA methyltransferase, in the virulence of B. cinerea was investigated. BcMETTL4 disruption and point mutations of its catalytic motif “DPPW” both resulted in significant 6mA reduction in the genomic DNA and in reduced virulence of B. cinerea. RNA-Seq analysis revealed a total of 13 downregulated genes in the disruption mutant ΔBcMettl4 in which methylation occurred at the promoter sites. These were involved in oxidoreduction, secretory pathways, autophagy and carbohydrate metabolism. Two of these genes, BcFDH and BcMFS2, were independently disrupted. Knockout of BcFDH led to reduced sclerotium formation, while disruption of BcMFS2 resulted in dramatically decreased conidium formation and pathogenicity. These observations indicated that 6mA provides potential epigenetic markers in B. cinerea and that BcMettl4 regulates virulence in this important plant pathogen.
Collapse
Affiliation(s)
- Zhengang Miao
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Guangyuan Wang
- College of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Heng Shen
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Xue Wang
- Yantai Agricultural Technology Extension Center, Yantai, China
| | - Dean W. Gabriel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Wenxing Liang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Wenxing Liang,
| |
Collapse
|
31
|
Li H, Zhang N, Wang Y, Xia S, Zhu Y, Xing C, Tian X, Du Y. DNA N6-Methyladenine Modification in Eukaryotic Genome. Front Genet 2022; 13:914404. [PMID: 35812743 PMCID: PMC9263368 DOI: 10.3389/fgene.2022.914404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is treated as an important epigenetic mark in various biological activities. In the past, a large number of articles focused on 5 mC while lacking attention to N6-methyladenine (6 mA). The presence of 6 mA modification was previously discovered only in prokaryotes. Recently, with the development of detection technologies, 6 mA has been found in several eukaryotes, including protozoans, metazoans, plants, and fungi. The importance of 6 mA in prokaryotes and single-celled eukaryotes has been widely accepted. However, due to the incredibly low density of 6 mA and restrictions on detection technologies, the prevalence of 6 mA and its role in biological processes in eukaryotic organisms are highly debated. In this review, we first summarize the advantages and disadvantages of 6 mA detection methods. Then, we conclude existing reports on the prevalence of 6 mA in eukaryotic organisms. Next, we highlight possible methyltransferases, demethylases, and the recognition proteins of 6 mA. In addition, we summarize the functions of 6 mA in eukaryotes. Last but not least, we summarize our point of view and put forward the problems that need further research.
Collapse
Affiliation(s)
- Hao Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ning Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuechen Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Siyuan Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yating Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Chen Xing
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xuefeng Tian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Yinan Du,
| |
Collapse
|
32
|
Jiménez-Ramírez IA, Pijeira-Fernández G, Moreno-Cálix DM, De-la-Peña C. Same modification, different location: the mythical role of N 6-adenine methylation in plant genomes. PLANTA 2022; 256:9. [PMID: 35696004 DOI: 10.1007/s00425-022-03926-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The present review summarizes recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics, discusses its importance in plant genomes, and highlights its chemical nature and functions. Adenine methylation is an epigenetic modification present in DNA (6mA) and RNA (m6A) that has a regulatory function in many cellular processes. This modification occurs through a reversible reaction that covalently binds a methyl group, usually at the N6 position of the purine ring. This modification carries biophysical properties that affect the stability of nucleic acids as well as their binding affinity with other molecules. DNA 6mA has been related to genome stability, gene expression, DNA replication, and repair mechanisms. Recent advances have shown that 6mA in plant genomes is related to development and stress response. In this review, we present recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics. We discuss the key elements of this modification, focusing mainly on its importance in plant genomes. Furthermore, we highlight its chemical nature and the regulatory effects that it exerts on gene expression and plant development. Finally, we emphasize the functions of 6mA in photosynthesis, stress, and flowering.
Collapse
Affiliation(s)
- Irma A Jiménez-Ramírez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Gema Pijeira-Fernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Delia M Moreno-Cálix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
| |
Collapse
|
33
|
Zhang G, Diao S, Song Y, He C, Zhang J. Genome-wide DNA N6-adenine methylation in sea buckthorn (Hippophae rhamnoides L.) fruit development. TREE PHYSIOLOGY 2022; 42:1286-1295. [PMID: 34986489 DOI: 10.1093/treephys/tpab177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
As a new epigenetic mark, DNA N6-adenine (6mA) methylation plays an important role in various biological processes and has been reported in many prokaryotic organisms in recent years. However, the distribution patterns and functions of DNA 6mA modification have been poorly studied in non-model crops. In this study, we observed that the methylation ratio of 6mA was about 0.016% in the sea buckthorn (Hippophae rhamnoides L.) genome using mass spectrometry. We first constructed a comprehensive 6mA landscape in sea buckthorn genome using nanopore sequencing at single-base resolution. Distribution analysis suggested that 6mA methylated sites were widely distributed in the sea buckthorn chromosomes, which were similar to those in Arabidopsis and rice. Furthermore, reduced 6mA DNA methylation is associated with different expression of genes related to the fruit-ripening process in sea buckthorn. Our results revealed that 6mA DNA modification could be considered an important epigenomic mark and contributes to the fruit ripening process in plants.
Collapse
Affiliation(s)
- Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, xiangshan street, haidian district, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, xiangshan street, haidian district, China
| | - Yating Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, xiangshan street, haidian district, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, xiangshan street, haidian district, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, xiangshan street, haidian district, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, longpan street, xuanwu district, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
34
|
Chen J, Hu R, Chen Y, Lin X, Xiang W, Chen H, Yao C, Liu L. Structural basis for MTA1c-mediated DNA N6-adenine methylation. Nat Commun 2022; 13:3257. [PMID: 35672411 PMCID: PMC9174199 DOI: 10.1038/s41467-022-31060-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/26/2022] [Indexed: 11/09/2022] Open
Abstract
DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.
Collapse
Affiliation(s)
- Jiyun Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Rong Hu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ying Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xiaofeng Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Wenwen Xiang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Canglin Yao
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Liang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| |
Collapse
|
35
|
A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA. Nat Chem Biol 2022; 18:733-741. [PMID: 35654845 DOI: 10.1038/s41589-022-01041-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
N6-methyladenosine (6mA) is a DNA modification that has recently been found to play regulatory roles during mammalian early embryo development and mitochondrial transcription. We found that a dioxygenase CcTet from the fungus Coprinopsis cinerea is also a dsDNA 6mA demethylase. It oxidizes 6mA to the intermediate N6-hydroxymethyladenosine (6hmA) with robust activity of 6mA-containing duplex DNA (dsDNA) as well as isolated genomics DNA. Structural characterization revealed that CcTet utilizes three flexible loop regions and two key residues-D337 and G331-in the active pocket to preferentially recognize substrates on dsDNA. A CcTet D337F mutant protein retained the catalytic activity on 6mA but lost activity on 5-methylcytosine. Our findings uncovered a 6mA demethylase that works on dsDNA, suggesting potential 6mA demethylation in fungi and elucidating 6mA recognition and the catalytic mechanism of CcTet. The CcTet D337F mutant protein also provides a chemical biology tool for future functional manipulation of DNA 6mA in vivo.
Collapse
|
36
|
Li X, Guo S, Cui Y, Zhang Z, Luo X, Angelova MT, Landweber LF, Wang Y, Wu TP. NT-seq: a chemical-based sequencing method for genomic methylome profiling. Genome Biol 2022; 23:122. [PMID: 35637459 PMCID: PMC9150344 DOI: 10.1186/s13059-022-02689-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 12/15/2022] Open
Abstract
DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although many sequencing methods have been developed to sequence specific types of methylation, few technologies can be used for efficiently mapping multiple types of methylation. Here, we present NT-seq for mapping all three types of methylation simultaneously. NT-seq reliably detects all known methylation motifs in two bacterial genomes and can be used for identifying de novo methylation motifs. NT-seq provides a simple and efficient solution for detecting multiple types of DNA methylation.
Collapse
Affiliation(s)
- Xuwen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shiyuan Guo
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California Riverside, Riverside, CA, USA
| | - Yan Cui
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zijian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinlong Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margarita T Angelova
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, USA
| | - Laura F Landweber
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, USA
| | - Yinsheng Wang
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California Riverside, Riverside, CA, USA.,Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Tao P Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
37
|
Chen D, Li Y. PredMHC: An Effective Predictor of Major Histocompatibility Complex Using Mixed Features. Front Genet 2022; 13:875112. [PMID: 35547252 PMCID: PMC9081368 DOI: 10.3389/fgene.2022.875112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 12/03/2022] Open
Abstract
The major histocompatibility complex (MHC) is a large locus on vertebrate DNA that contains a tightly linked set of polymorphic genes encoding cell surface proteins essential for the adaptive immune system. The groups of proteins encoded in the MHC play an important role in the adaptive immune system. Therefore, the accurate identification of the MHC is necessary to understand its role in the adaptive immune system. An effective predictor called PredMHC is established in this study to identify the MHC from protein sequences. Firstly, PredMHC encoded a protein sequence with mixed features including 188D, APAAC, KSCTriad, CKSAAGP, and PAAC. Secondly, three classifiers including SGD, SMO, and random forest were trained on the mixed features of the protein sequence. Finally, the prediction result was obtained by the voting of the three classifiers. The experimental results of the 10-fold cross-validation test in the training dataset showed that PredMHC can obtain 91.69% accuracy. Experimental results on comparison with other features, classifiers, and existing methods showed the effectiveness of PredMHC in predicting the MHC.
Collapse
Affiliation(s)
- Dong Chen
- College of Electrical and Information Engineering, Quzhou University, Quzhou, China
| | - Yanjuan Li
- College of Electrical and Information Engineering, Quzhou University, Quzhou, China
| |
Collapse
|
38
|
Shen C, Wang K, Deng X, Chen J. DNA N 6-methyldeoxyadenosine in mammals and human disease. Trends Genet 2022; 38:454-467. [PMID: 34991904 PMCID: PMC9007851 DOI: 10.1016/j.tig.2021.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023]
Abstract
N6-methyladenine (6mA) is the most prevalent DNA modification in prokaryotes. However, its presence and significance in eukaryotes remain elusive. Recently, with methodology advances in detection and sequencing of 6mA in eukaryotes, 6mA is back in the spotlight. Although multiple studies have reported that 6mA is an important epigenetic mark in eukaryotes and plays a regulatory role in DNA transcription, transposon activation, stress response, and other bioprocesses, there are some discrepancies in the current literature. We review the recent advances in 6mA research in eukaryotes, especially in mammals. In particular, we describe the abundance/distribution of 6mA, its potential role in regulating gene expression, identified regulators, and pathological roles in human diseases, especially in cancer. The limitations faced by the field and future perspectives in 6mA research are also discussed.
Collapse
Affiliation(s)
- Chao Shen
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Kitty Wang
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Xiaolan Deng
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| | - Jianjun Chen
- Department of Systems Biology, City of Hope, Monrovia 91007, USA
| |
Collapse
|
39
|
Sheng Y, Zhou M, You C, Dai X. Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
40
|
Tang X, Zheng P, Li X, Wu H, Wei DQ, Liu Y, Huang G. Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species. Methods 2022; 204:142-150. [PMID: 35477057 DOI: 10.1016/j.ymeth.2022.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
DNA N6-methyladenine (6mA) is a key DNA modification, which plays versatile roles in the cellular processes, including regulation of gene expression, DNA repair, and DNA replication. DNA 6mA is closely associated with many diseases in the mammals and with growth as well as development of plants. Precisely detecting DNA 6mA sites is of great importance to exploration of 6mA functions. Although many computational methods have been presented for DNA 6mA prediction, there is still a wide gap in the practical application. We presented a convolution neural network (CNN) and bi-directional long-short term memory (Bi-LSTM)-based deep learning method (Deep6mAPred) for predicting DNA 6mA sites across plant species. The Deep6mAPred stacked the CNNs and the Bi-LSTMs in a paralleling manner instead of a series-connection manner. The Deep6mAPred also employed the attention mechanism for improving the representations of sequences. The Deep6mAPred reached an accuracy of 0.9556 over the independent rice dataset, far outperforming the state-of-the-art methods. The tests across plant species showed that the Deep6mAPred is of a remarkable advantage over the state of the art methods. We developed a user-friendly web application for DNA 6mA prediction, which is freely available at http://106.13.196.152:7001/ for all the scientific researchers. The Deep6mAPred would enrich tools to predict DNA 6mA sites and speed up the exploration of DNA modification.
Collapse
Affiliation(s)
- Xingyu Tang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Xueyong Li
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Hongyan Wu
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dong-Qing Wei
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha, Hunan 410081, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China.
| |
Collapse
|
41
|
Takahashi Y, Shoura M, Fire A, Morishita S. Context-dependent DNA polymerization effects can masquerade as DNA modification signals. BMC Genomics 2022; 23:249. [PMID: 35361121 PMCID: PMC8973881 DOI: 10.1186/s12864-022-08471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 03/15/2022] [Indexed: 11/23/2022] Open
Abstract
Background Single molecule measurements of DNA polymerization kinetics provide a sensitive means to detect both secondary structures in DNA and deviations from primary chemical structure as a result of modified bases. In one approach to such analysis, deviations can be inferred by monitoring the behavior of DNA polymerase using single-molecule, real-time sequencing with zero-mode waveguide. This approach uses a Single Molecule Real Time (SMRT)-sequencing measurement of time between fluorescence pulse signals from consecutive nucleosides incorporated during DNA replication, called the interpulse duration (IPD). Results In this paper we present an analysis of loci with high IPDs in two genomes, a bacterial genome (E. coli) and a eukaryotic genome (C. elegans). To distinguish the potential effects of DNA modification on DNA polymerization speed, we paired an analysis of native genomic DNA with whole-genome amplified (WGA) material in which DNA modifications were effectively removed. Adenine modification sites for E. coli are known and we observed the expected IPD shifts at these sites in the native but not WGA samples. For C. elegans, such differences were not observed. Instead, we found a number of novel sequence contexts where IPDs were raised relative to the average IPDs for each of the four nucleotides, but for which the raised IPD was present in both native and WGA samples. Conclusion The latter results argue strongly against DNA modification as the underlying driver for high IPD segments for C. elegans, and provide a framework for separating effects of DNA modification from context-dependent DNA polymerase kinetic patterns inherent in underlying DNA sequence for a complex eukaryotic genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08471-2.
Collapse
Affiliation(s)
- Yusuke Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Massa Shoura
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Andrew Fire
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
42
|
Liu M, Sun ZL, Zeng Z, Lam KM. MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block. Brief Bioinform 2022; 23:6553606. [PMID: 35325050 DOI: 10.1093/bib/bbac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.
Collapse
Affiliation(s)
- Mengya Liu
- School of Computer Science and Technology, Anhui University, Hefei, 230601, China
| | - Zhan-Li Sun
- School of Artificial Intelligence, Anhui University, Hefei, 230601, China
| | - Zhigang Zeng
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kin-Man Lam
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| |
Collapse
|
43
|
Zhang L, Rong W, Ma J, Li H, Tang X, Xu S, Wang L, Wan L, Zhu Q, Jiang B, Su F, Cui H. Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:827391. [PMID: 35321246 PMCID: PMC8937020 DOI: 10.3389/fcell.2022.827391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a widespread epigenetic signal in human genome. With Nanopore technology, differential methylation modifications including 5-methylcytosine (5mC) and 6-methyladenine (6mA) can be identified. 5mC is the most important modification in mammals, although 6mA may also function in growth and development as well as in pathogenesis. While the role of 5mC at CpG islands in promoter regions associated with transcriptional regulation has been well studied, but the relationship between 6mA and transcription is still unclear. Thus, we collected two pairs of tumor tissues and adjacent normal tissues from hepatocellular carcinoma (HCC) surgical samples for Nanopore sequencing and transcriptome sequencing. It was found that 2,373 genes had both 5mC and 6mA, along with up- and down-regulated methylation sites. These genes were regarded as unstable methylation genes. Compared with 6mA, 5mC had more inclined distribution of unstable methylation sites. Chi-square test showed that the levels of 5mC were consistent with both up- and down-regulated genes, but 6mA was not significant. Moreover, the top three unstable methylation genes, TBC1D3H, CSMD1, and ROBO2, were all related to cancer. Transcriptome and survival analyses revealed four potential tumor suppressor genes including KCNIP4, CACNA1C, PACRG, and ST6GALNAC3. In this study, we firstly proposed to combine 5mC and 6mA methylation sites to explore functional genes, and further research found top of these unstable methylation genes might be functional and some of them could serve as potential tumor suppressor genes. Our study provided a new solution for epigenetic regulation research and therapy of HCC.
Collapse
Affiliation(s)
- Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Luyao Wang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qing Zhu
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
| | - Boyue Jiang
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongyuan Cui
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
- *Correspondence: Hongyuan Cui,
| |
Collapse
|
44
|
Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W. Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription. PLANT PHYSIOLOGY 2022; 188:1632-1648. [PMID: 34893906 PMCID: PMC8896617 DOI: 10.1093/plphys/kiab566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 06/01/2023]
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
Collapse
Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Francesco Rota Sperti
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| |
Collapse
|
45
|
SMOC: a smart model for open chromatin region prediction in rice genomes. J Genet Genomics 2022; 49:514-517. [DOI: 10.1016/j.jgg.2022.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 01/24/2023]
|
46
|
Wang S, Xie H, Mao F, Wang H, Wang S, Chen Z, Zhang Y, Xu Z, Xing J, Cui Z, Gao X, Jin H, Hua J, Xiong B, Wu Y. N 4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana. Genome Biol 2022; 23:5. [PMID: 34980211 PMCID: PMC8722123 DOI: 10.1186/s13059-021-02578-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6-methyladenosine (m6A)/N6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored. RESULTS Here, we demonstrate the existence of N4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry. CONCLUSIONS Our findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.
Collapse
Affiliation(s)
- Shuai Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hairong Xie
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Shu Wang
- Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd., Nanjing, China
| | - Zhenglin Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yuxia Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhihui Xu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Jinming Xing
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhaokang Cui
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hongmei Jin
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jian Hua
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, USA
| | - Bo Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
47
|
Le NQK, Ho QT. Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes. Methods 2021; 204:199-206. [PMID: 34915158 DOI: 10.1016/j.ymeth.2021.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
As one of the most common post-transcriptional epigenetic modifications, N6-methyladenine (6 mA), plays an essential role in various cellular processes and disease pathogenesis. Therefore, accurately identifying 6 mA modifications is necessary for a deep understanding of cellular processes and other possible functional mechanisms. Although a few computational methods have been proposed, their respective models were developed with small training datasets. Hence, their practical application is quite limited in genome-wide detection. To overcome the existing limitations, we present a novel model based on transformer architecture and deep learning to identify DNA 6 mA sites from the cross-species genome. The model is constructed on a benchmark dataset and explored a feature derived from pre-trained transformer word embedding approaches. Subsequently, a convolutional neural network was employed to learn the generated features and generate the prediction outcomes. As a result, our predictor achieved excellent performance during independent test with the accuracy and Matthews correlation coefficient (MCC) of 79.3% and 0.58, respectively. Overall, its performance achieved better accuracy than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, our model is expected to assist biologists in accurately identifying 6mAs and formulate the novel testable biological hypothesis. We also release source codes and datasets freely at https://github.com/khanhlee/bert-dna for front-end users.
Collapse
Affiliation(s)
- Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan.
| | - Quang-Thai Ho
- College of Information & Communication Technology, Can Tho University, Viet Nam; Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan
| |
Collapse
|
48
|
RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat Biotechnol 2021; 39:1581-1588. [PMID: 34294912 DOI: 10.1038/s41587-021-00982-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
RNA N6-methyladenosine (m6A) modifications are essential in plants. Here, we show that transgenic expression of the human RNA demethylase FTO in rice caused a more than threefold increase in grain yield under greenhouse conditions. In field trials, transgenic expression of FTO in rice and potato caused ~50% increases in yield and biomass. We demonstrate that the presence of FTO stimulates root meristem cell proliferation and tiller bud formation and promotes photosynthetic efficiency and drought tolerance but has no effect on mature cell size, shoot meristem cell proliferation, root diameter, plant height or ploidy. FTO mediates substantial m6A demethylation (around 7% of demethylation in poly(A) RNA and around 35% decrease of m6A in non-ribosomal nuclear RNA) in plant RNA, inducing chromatin openness and transcriptional activation. Therefore, modulation of plant RNA m6A methylation is a promising strategy to dramatically improve plant growth and crop yield.
Collapse
|
49
|
Nguyen TTD, Trinh VN, Le NQK, Ou YY. Using k-mer embeddings learned from a Skip-gram based neural network for building a cross-species DNA N6-methyladenine site prediction model. PLANT MOLECULAR BIOLOGY 2021; 107:533-542. [PMID: 34843033 DOI: 10.1007/s11103-021-01204-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
This study used k-mer embeddings as effective feature to identify DNA N6-Methyladenine sites in plant genomes and obtained improved performance without substantial effort in feature extraction, combination and selection. Identification of DNA N6-methyladenine sites has been a very active topic of computational biology due to the unavailability of suitable methods to identify them accurately, especially in plants. Substantial results were obtained with a great effort put in extracting, heuristic searching, or fusing a diverse types of features, not to mention a feature selection step. In this study, we regarded DNA sequences as textual information and employed natural language processing techniques to decipher hidden biological meanings from those sequences. In other words, we considered DNA, the human life book, as a book corpus for training DNA language models. K-mer embeddings then were generated from these language models to be used in machine learning prediction models. Skip-gram neural networks were the base of the language models and ensemble tree-based algorithms were the machine learning algorithms for prediction models. We trained the prediction model on Rosaceae genome dataset and performed a comprehensive test on 3 plant genome datasets. Our proposed method shows promising performance with AUC performance approaching an ideal value on Rosaceae dataset (0.99), a high score on Rice dataset (0.95) and improved performance on Rice dataset while enjoying an elegant, yet efficient feature extraction process.
Collapse
Affiliation(s)
| | - Van Ngu Trinh
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, 31151, South Korea
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei City, 106, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei City, 106, Taiwan
| | - Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 32003, Taiwan.
| |
Collapse
|
50
|
Hou Q, Wan X. Epigenome and Epitranscriptome: Potential Resources for Crop Improvement. Int J Mol Sci 2021; 22:12912. [PMID: 34884725 PMCID: PMC8658206 DOI: 10.3390/ijms222312912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/26/2022] Open
Abstract
Crop breeding faces the challenge of increasing food demand, especially under climatic changes. Conventional breeding has relied on genetic diversity by combining alleles to obtain desired traits. In recent years, research on epigenetics and epitranscriptomics has shown that epigenetic and epitranscriptomic diversity provides additional sources for crop breeding and harnessing epigenetic and epitranscriptomic regulation through biotechnologies has great potential for crop improvement. Here, we review epigenome and epitranscriptome variations during plant development and in response to environmental stress as well as the available sources for epiallele formation. We also discuss the possible strategies for applying epialleles and epitranscriptome engineering in crop breeding.
Collapse
Affiliation(s)
- Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| |
Collapse
|