1
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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2
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Liu J, Zhang Y, Zhou N, He J, Xu J, Cai Z, Yang L, Liu Y. Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects. IMETA 2024; 3:e186. [PMID: 38898993 PMCID: PMC11183182 DOI: 10.1002/imt2.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 06/21/2024]
Abstract
DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes, particularly through transcriptional regulation. With the rapid implementation of third-generation sequencing technology, we are currently experiencing a golden age of bacterial epigenomics. However, there has been a lack of comprehensive research exploring the versatility and consequential impact of bacterial DNA methylome on cellular and physiological functions. There is a critical need for a user-friendly bioinformatics tool that can effectively characterize DNA methylation modification features and predict the regulation patterns. To address this gap, the current study introduces Bacmethy, an innovative tool that utilizes SMRT-seq data and offers a range of analytical modules. First, the tool classifies methylation sites in the genome, highlighting the distinct regulations present under varying modification fractions and location enrichment. Furthermore, this tool enables us to identify regulatory region methylation and potential cis and trans interactions between methylation sites and regulatory effectors. Using benchmark data sets and our data, we show that our tool facilitates the understanding of the distinctive traits of DNA methylation modifications and predicts transcriptional regulation effects on important physiological and pathological functions. Bacmethy code is freely available, and the Docker image is downloadable. Bacmethy has been made available as a user-friendly web server interface at https://bacmethy.med.sustech.edu.cn.
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Affiliation(s)
- Ji‐Hong Liu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Yizhou Zhang
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Ning Zhou
- Clinical LaboratorySouthern University of Science and Technology HospitalShenzhenChina
| | - Jiale He
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Jing Xu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
| | - Zhao Cai
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Liang Yang
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Third People's Hospital, The Second Affiliated Hospital of Southern University of Science and TechnologyNational Clinical Research Center for Infectious DiseaseShenzhenChina
| | - Yang Liu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
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3
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Dennis AF, Xu Z, Clark DJ. Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline. Nucleic Acids Res 2024; 52:e45. [PMID: 38634798 PMCID: PMC11109960 DOI: 10.1093/nar/gkae288] [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: 01/22/2024] [Revised: 03/23/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Theoretically, nucleosome footprints and nucleosome-depleted regions can be identified using M.EcoGII, which methylates adenines in any sequence context, providing a high-resolution map of accessible regions in each DNA molecule. Here, we report PacBio long-read sequence data for budding yeast nuclei treated with M.EcoGII and a bioinformatic pipeline which corrects for three key challenges undermining this promising method. First, detection of m6A in individual DNA molecules by the PacBio software is inefficient, resulting in false footprints predicted by random gaps of seemingly unmethylated adenines. Second, there is a strong bias against m6A base calling as AT content increases. Third, occasional methylation occurs within nucleosomes, breaking up their footprints. After correcting for these issues, our pipeline calculates a correlation coefficient-based score indicating the extent of chromatin heterogeneity within the cell population for every gene. Although the population average is consistent with that derived using other techniques, we observe a wide range of heterogeneity in nucleosome positions at the single-molecule level, probably reflecting cellular chromatin dynamics.
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Affiliation(s)
- Allison F Dennis
- Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhuwei Xu
- Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [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: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- 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
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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5
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Feng X, Cui X, Zhang LS, Ye C, Wang P, Zhong Y, Wu T, Zheng Z, He C. Sequencing of N 6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. Mol Cell 2024; 84:596-610.e6. [PMID: 38215754 PMCID: PMC10872247 DOI: 10.1016/j.molcel.2023.12.021] [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: 10/17/2022] [Revised: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Although DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method, to measure 6mA at base resolution. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through the successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is generally low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution for a comprehensive understanding of DNA 6mA in eukaryotes.
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Affiliation(s)
- Xinran Feng
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA; Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chang Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Pingluan Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuhao Zhong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhong Zheng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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6
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Dennis AF, Xu Z, Clark DJ. Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m 6A detection efficiency and calling bias correcting pipeline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569045. [PMID: 38076871 PMCID: PMC10705563 DOI: 10.1101/2023.11.28.569045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Theoretically, nucleosome footprints and nucleosome-depleted regions can be identified using M.EcoGII, which methylates adenines in any sequence context, providing a high-resolution map of accessible regions in each DNA molecule. Here we report PacBio long-read sequence data for budding yeast nuclei treated with M.EcoGII and a bioinformatic pipeline which corrects for three key challenges undermining this promising method. First, detection of m6A in individual DNA molecules by the PacBio software is inefficient, resulting in false footprints predicted by random gaps of seemingly unmethylated adenines. Second, there is a strong bias against m6A base calling as AT content increases. Third, occasional methylation occurs within nucleosomes, breaking up their footprints. After correcting for these issues, our pipeline calculates a correlation coefficient-based score indicating the extent of chromatin heterogeneity within the cell population for every gene. Although the population average is consistent with that derived using other techniques, we observe a wide range of heterogeneity in nucleosome positions at the single-molecule level, probably reflecting cellular chromatin dynamics.
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Affiliation(s)
| | | | - David J. Clark
- Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
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7
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Konanov DN, Babenko VV, Belova AM, Madan AG, Boldyreva DI, Glushenko OE, Butenko IO, Fedorov DE, Manolov AI, Krivonos DV, Lazarev VN, Govorun VM, Ilina EN. Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads. Bioinformatics 2023; 39:btad702. [PMID: 37982752 PMCID: PMC10689673 DOI: 10.1093/bioinformatics/btad702] [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: 04/24/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023] Open
Abstract
MOTIVATION The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco. RESULTS We present Snapper, a new highly sensitive approach, to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H.pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H.pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase. AVAILABILITY AND IMPLEMENTATION Snapper is implemented using Python and is freely available as a pip package named "snapper-ont." Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).
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Affiliation(s)
- Dmitry N Konanov
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Vladislav V Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Aleksandra M Belova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Arina G Madan
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology, State University, Dolgoprudny 141700, Russia
| | - Daria I Boldyreva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Oksana E Glushenko
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Ivan O Butenko
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Dmitry E Fedorov
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | | | - Danil V Krivonos
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology, State University, Dolgoprudny 141700, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Vadim M Govorun
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Elena N Ilina
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
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8
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Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
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Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Yang J, Son Y, Kang M, Park W. AamA-mediated epigenetic control of genome-wide gene expression and phenotypic traits in Acinetobacter baumannii ATCC 17978. Microb Genom 2023; 9:mgen001093. [PMID: 37589545 PMCID: PMC10483419 DOI: 10.1099/mgen.0.001093] [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: 12/04/2022] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the aamA (encoding AcinetobacterAdenine Methylase A) mutant of A. baumannii strain ATCC 17978. Our single-molecule real-time sequencing-based methylome analysis revealed multiple AamA-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the trmD operon (rpsP, rimM, trmD, and rplS) were identified through our methylome and transcriptome analyses. AamA methylation also appeared to control the expression of many genes linked to membrane functions (lolAB, lpxO), replication (dnaA) and protein synthesis (trmD operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the aamA gene, and the complementation of aamA gene restored the wild-type phenotypes. Other tested phenotypic traits such as outer-membrane vesicle production, biofilm formation and virulence were also affected in the aamA mutant. Collectively, our data indicated that epigenetic regulation through AamA-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in A. baumannii ATCC 17978.
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Affiliation(s)
- Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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10
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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.
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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.
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11
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Breckell GL, Silander OK. Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli. G3 (BETHESDA, MD.) 2022; 13:6858946. [PMID: 36454087 PMCID: PMC9911048 DOI: 10.1093/g3journal/jkac310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
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Affiliation(s)
- Georgia L Breckell
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
| | - Olin K Silander
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
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12
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Kong Y, Cao L, Deikus G, Fan Y, Mead EA, Lai W, Zhang Y, Yong R, Sebra R, Wang H, Zhang XS, Fang G. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 2022; 375:515-522. [PMID: 35113693 PMCID: PMC9382770 DOI: 10.1126/science.abe7489] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors that challenge the prevalence of 6mA in eukaryotes. We developed a metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination. Applying this method, we observed high-resolution 6mA deposition in two protozoa. We found that commensal or soil bacteria explained the vast majority of 6mA in insect and plant samples. We found no evidence of high abundance of 6mA in Drosophila, Arabidopsis, or humans. Plasmids used for genetic manipulation, even those from Dam methyltransferase mutant Escherichia coli, could carry abundant 6mA, confounding the evaluation of candidate 6mA methyltransferases and demethylases. On the basis of this work, we advocate for a reassessment of 6mA in eukaryotes.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Lei Cao
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Edward A. Mead
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences; Beijing 100085, China
| | - Yizhou Zhang
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York; NY 10029, USA
| | - Raymund Yong
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York; NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
- Sema4, a Mount Sinai venture; Stamford, CT, 06902, USA
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences; Beijing 100085, China
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University; New Brunswick, NJ, 08854, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
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13
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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15
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Délot EC, Vilain E. Towards improved genetic diagnosis of human differences of sex development. Nat Rev Genet 2021; 22:588-602. [PMID: 34083777 PMCID: PMC10598994 DOI: 10.1038/s41576-021-00365-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/05/2023]
Abstract
Despite being collectively among the most frequent congenital developmental conditions worldwide, differences of sex development (DSD) lack recognition and research funding. As a result, what constitutes optimal management remains uncertain. Identification of the individual conditions under the DSD umbrella is challenging and molecular genetic diagnosis is frequently not achieved, which has psychosocial and health-related repercussions for patients and their families. New genomic approaches have the potential to resolve this impasse through better detection of protein-coding variants and ascertainment of under-recognized aetiology, such as mosaic, structural, non-coding or epigenetic variants. Ultimately, it is hoped that better outcomes data, improved understanding of the molecular causes and greater public awareness will bring an end to the stigma often associated with DSD.
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Affiliation(s)
- Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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16
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Abstract
Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological relevance of methylation. Indeed, as the number of mapped bacterial methylomes recently surpassed 4,000, increasing evidence supports roles for methylation in gene expression regulation, virulence, and host colonization, among others. In this paper, I summarize lessons taken from high-dimensional methylome data analyses and recent efforts that we and others are developing to leverage such findings into meaningful biological insights and overarching frameworks. Ultimately, I highlight anticipated research avenues and technological developments likely to unfold in the coming years.
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Affiliation(s)
- Pedro H. Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
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17
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Chaturvedi A, Cruz Corella J, Robbins C, Loha A, Menin L, Gasilova N, Masclaux FG, Lee SJ, Sanders IR. The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya. Commun Biol 2021; 4:901. [PMID: 34294866 PMCID: PMC8298701 DOI: 10.1038/s42003-021-02414-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis. Anurag Chaturvedi et al. use long-read PacBio sequencing and LC-MS to profile 5mC and 6mA DNA methylation in the model arbuscular mycorrhizal fungus, Rhizophagus irregularis. Their results suggest that R. irregularis shows methylation profiles distinct from other early-diverging fungi, and Dikarya and provide further insight into how these fungi may have adapted to form symbiotic relationships with important plant species.
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Affiliation(s)
- Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Environmental Genomics Group, School of Biosciences, The University of Birmingham, Birmingham, UK
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chanz Robbins
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Anita Loha
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Natalia Gasilova
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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18
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Comparative Pathogenomics of Escherichia coli: Polyvalent Vaccine Target Identification through Virulome Analysis. Infect Immun 2021; 89:e0011521. [PMID: 33941580 PMCID: PMC8281228 DOI: 10.1128/iai.00115-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics of bacterial pathogens has been useful for revealing potential virulence factors. Escherichia coli is a significant cause of human morbidity and mortality worldwide but can also exist as a commensal in the human gastrointestinal tract. With many sequenced genomes, it has served as a model organism for comparative genomic studies to understand the link between genetic content and potential for virulence. To date, however, no comprehensive analysis of its complete “virulome” has been performed for the purpose of identifying universal or pathotype-specific targets for vaccine development. Here, we describe the construction of a pathotype database of 107 well-characterized completely sequenced pathogenic and nonpathogenic E. coli strains, which we annotated for major virulence factors (VFs). The data are cross referenced for patterns against pathotype, phylogroup, and sequence type, and the results were verified against all 1,348 complete E. coli chromosomes in the NCBI RefSeq database. Our results demonstrate that phylogroup drives many of the “pathotype-associated” VFs, and ExPEC-associated VFs are found predominantly within the B2/D/F/G phylogenetic clade, suggesting that these phylogroups are better adapted to infect human hosts. Finally, we used this information to propose polyvalent vaccine targets with specificity toward extraintestinal strains, targeting key invasive strategies, including immune evasion (group 2 capsule), iron acquisition (FyuA, IutA, and Sit), adherence (SinH, Afa, Pap, Sfa, and Iha), and toxins (Usp, Sat, Vat, Cdt, Cnf1, and HlyA). While many of these targets have been proposed before, this work is the first to examine their pathotype and phylogroup distribution and how they may be targeted together to prevent disease.
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19
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Fu S, Zhang T, Jiang H, Xu Y, Chen J, Zhang L, Su X. DNA nanotechnology enhanced single-molecule biosensing and imaging. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116267] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Payelleville A, Brillard J. Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. Front Microbiol 2021; 12:685670. [PMID: 34054792 PMCID: PMC8160106 DOI: 10.3389/fmicb.2021.685670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.
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Affiliation(s)
- Amaury Payelleville
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France.,Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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21
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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22
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Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat Methods 2021; 18:491-498. [PMID: 33820988 PMCID: PMC8107137 DOI: 10.1038/s41592-021-01109-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/03/2021] [Indexed: 01/09/2023]
Abstract
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco ( https://github.com/fanglab/nanodisco ), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.
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23
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Spadar A, Perdigão J, Phelan J, Charleston J, Modesto A, Elias R, de Sessions PF, Hibberd ML, Campino S, Duarte A, Clark TG. Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Sci Rep 2021; 11:6491. [PMID: 33753763 PMCID: PMC7985491 DOI: 10.1038/s41598-021-85724-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction-Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | | | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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24
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Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
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Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
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25
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He X, Lu T, Zhou X. Whole genome sequencing and comparative genomics analysis of Pectobacterium carotovorum identifies key pathogenic genes. Mol Phylogenet Evol 2021; 162:107114. [PMID: 33744402 DOI: 10.1016/j.ympev.2021.107114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 12/29/2022]
Abstract
Based on Single moleculereal time(SMRT)sequencing technology, the high-quality whole genome sequence of Pectobacterium carotovorum (PC1) was obtained by the PacBio RS II sequencer. The genome is a single circular chromosome of 5.3 Mb in size, containing three kinds of m6A methylation modification by SMRT Portal analysis. Genome annotation showed that 575 virulence factor genes, 304 drug resistance genes, 774 pathogen genes, 7 secretory systems and 22 pairs of two-component regulatory system could be relevant to bacterial pathogenicity. In addition, the average nucleotide identities (ANI) analysisshowed that the PC1 exhibited the highest homology with the Pectobacteriumcarotovorumsubsp.carotovorumstrain BP201601.1 (NZ_CP034236). There are 28 unique gene families to PC1 using cluster analysis of gene families. According to the analysis of key pathogenic genes, we have obtained three kinds of highly conserved genes related to cell wall degrading enzymes, including 19 pectinase genes, 25 cellulase genes and 22 protease genes. Our studies have provided a theoretical basis for investigation of bacterial soft rot and biological specific bactercides of PC1.
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Affiliation(s)
- Xiaoliang He
- School of Biological Science and Engineering, Hebei University of Science and Technology, Shijiazhang, Hebei, China
| | - Tianhua Lu
- School of Biological Science and Engineering, Hebei University of Science and Technology, Shijiazhang, Hebei, China
| | - Xiaohui Zhou
- School of Biological Science and Engineering, Hebei University of Science and Technology, Shijiazhang, Hebei, China.
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26
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Puchtler TJ, Johnson K, Palmer RN, Talbot EL, Ibbotson LA, Powalowska PK, Knox R, Shibahara A, M S Cunha P, Newell OJ, Wu M, Chana J, Athanasopoulou EN, Waeber AM, Stolarek M, Silva AL, Mordaka JM, Haggis-Powell M, Xyrafaki C, Bush J, Topkaya IS, Sosna M, Ingham RJ, Huckvale T, Negrea A, Breiner B, Šlikas J, Kelly DJ, Dunning AJ, Bell NM, Dethlefsen M, Love DM, Dear PH, Kuleshova J, Podd GJ, Isaac TH, Balmforth BW, Frayling CA. Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets. Nucleic Acids Res 2021; 48:e132. [PMID: 33152076 PMCID: PMC7736801 DOI: 10.1093/nar/gkaa987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 11/12/2022] Open
Abstract
Despite remarkable progress in DNA sequencing technologies there remains a trade-off between short-read platforms, having limited ability to sequence homopolymers, repeated motifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or throughput. Moreover, current methods do not allow direct readout of epigenetic modifications from a single read. With the aim of addressing these limitations, we have developed an optical electrowetting sequencing platform that uses step-wise nucleotide triphosphate (dNTP) release, capture and detection in microdroplets from single DNA molecules. Each microdroplet serves as a reaction vessel that identifies an individual dNTP based on a robust fluorescence signal, with the detection chemistry extended to enable detection of 5-methylcytosine. Our platform uses small reagent volumes and inexpensive equipment, paving the way to cost-effective single-molecule DNA sequencing, capable of handling widely varying GC-bias, and demonstrating direct detection of epigenetic modifications.
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Affiliation(s)
- Tim J Puchtler
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Kerr Johnson
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Rebecca N Palmer
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Emma L Talbot
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Lindsey A Ibbotson
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Paulina K Powalowska
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Rachel Knox
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aya Shibahara
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Pedro M S Cunha
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Oliver J Newell
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mei Wu
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jasmin Chana
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | | | - Andreas M Waeber
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Magdalena Stolarek
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Ana-Luisa Silva
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Justyna M Mordaka
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | | | - Christina Xyrafaki
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - James Bush
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Ibrahim S Topkaya
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Maciej Sosna
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Richard J Ingham
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Thomas Huckvale
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aurel Negrea
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Boris Breiner
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Justinas Šlikas
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Douglas J Kelly
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Alexander J Dunning
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Neil M Bell
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mark Dethlefsen
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - David M Love
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Paul H Dear
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jekaterina Kuleshova
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Gareth J Podd
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Tom H Isaac
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Barnaby W Balmforth
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Cameron A Frayling
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
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27
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Liu J, Wang J, Xiao X, Lai X, Dai D, Zhang X, Zhu X, Zhao Z, Wang J, Li Z. A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model. BMC Genomics 2020; 21:753. [PMID: 33208104 PMCID: PMC7677778 DOI: 10.1186/s12864-020-07008-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the biological research. However, the third generation sequencing data has a high level of the sequencing error rates, which inevitably affects the downstream analysis. Although the issue of sequencing error has been improving these years, large amounts of data were produced at high sequencing errors, and huge waste will be caused if they are discarded. Thus, the error correction for the third generation sequencing data is especially important. The existing error correction methods have poor performances at heterozygous sites, which are ubiquitous in diploid and polyploidy organisms. Therefore, it is a lack of error correction algorithms for the heterozygous loci, especially at low coverages. Results In this article, we propose a error correction method, named QIHC. QIHC is a hybrid correction method, which needs both the next generation and third generation sequencing data. QIHC greatly enhances the sensitivity of identifying the heterozygous sites from sequencing errors, which leads to a high accuracy on error correction. To achieve this, QIHC established a set of probabilistic models based on Bayesian classifier, to estimate the heterozygosity of a site and makes a judgment by calculating the posterior probabilities. The proposed method is consisted of three modules, which respectively generates a pseudo reference sequence, obtains the read alignments, estimates the heterozygosity the sites and corrects the read harboring them. The last module is the core module of QIHC, which is designed to fit for the calculations of multiple cases at a heterozygous site. The other two modules enable the reads mapping to the pseudo reference sequence which somehow overcomes the inefficiency of multiple mappings that adopt by the existing error correction methods. Conclusions To verify the performance of our method, we selected Canu and Jabba to compare with QIHC in several aspects. As a hybrid correction method, we first conducted a groups of experiments under different coverages of the next-generation sequencing data. QIHC is far ahead of Jabba on accuracy. Meanwhile, we varied the coverages of the third generation sequencing data and compared performances again among Canu, Jabba and QIHC. QIHC outperforms the other two methods on accuracy of both correcting the sequencing errors and identifying the heterozygous sites, especially at low coverage. We carried out a comparison analysis between Canu and QIHC on the different error rates of the third generation sequencing data. QIHC still performs better. Therefore, QIHC is superior to the existing error correction methods when heterozygous sites exist.
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Affiliation(s)
- Jiaqi Liu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China. .,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.
| | - Xiao Xiao
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xin Lai
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Daocheng Dai
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Zhongmeng Zhao
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Juan Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Annoroad Gene Institute, Beijing, 100176, China
| | - Zhimin Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China. .,Annoroad Gene Institute, Beijing, 100176, China.
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28
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Modlin SJ, Conkle-Gutierrez D, Kim C, Mitchell SN, Morrissey C, Weinrick BC, Jacobs WR, Ramirez-Busby SM, Hoffner SE, Valafar F. Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife 2020; 9:58542. [PMID: 33107429 PMCID: PMC7591249 DOI: 10.7554/elife.58542] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
This study assembles DNA adenine methylomes for 93 Mycobacterium tuberculosis complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling. Second, heterogeneity analysis of partially active methyltransferase alleles revealed that intracellular stochastic methylation generates a mosaic of methylomes within isogenic cultures, which we formalize as ‘intercellular mosaic methylation’ (IMM). Mutation-driven IMM was nearly ubiquitous in the globally prominent Beijing sublineage. Third, promoter methylation is widespread and associated with differential expression in the ΔhsdM transcriptome, suggesting promoter HsdM-methylation directly influences transcription. Finally, comparative and functional analyses identified 351 sites hypervariable across isolates and numerous putative regulatory interactions. This multi-omic integration revealed features of methylomic variability in clinical isolates and provides a rational basis for hypothesizing the functions of DNA adenine methylation in MTBC physiology and adaptive evolution.
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Affiliation(s)
- Samuel J Modlin
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Derek Conkle-Gutierrez
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Calvin Kim
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Scott N Mitchell
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Christopher Morrissey
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | | | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Sarah M Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Sven E Hoffner
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States.,Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
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29
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Nye TM, Fernandez NL, Simmons LA. A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria. Crit Rev Biochem Mol Biol 2020; 55:576-591. [PMID: 33059472 DOI: 10.1080/10409238.2020.1828257] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The presence of post-replicative DNA methylation is pervasive among both prokaryotic and eukaryotic organisms. In bacteria, the study of DNA methylation has largely been in the context of restriction-modification systems, where DNA methylation serves to safeguard the chromosome against restriction endonuclease cleavage intended for invading DNA. There has been a growing recognition that the methyltransferase component of restriction-modification systems can also regulate gene expression, with important contributions to virulence factor gene expression in bacterial pathogens. Outside of restriction-modification systems, DNA methylation from orphan methyltransferases, which lack cognate restriction endonucleases, has been shown to regulate important processes, including DNA replication, DNA mismatch repair, and the regulation of gene expression. The majority of research and review articles have been focused on DNA methylation in the context of Gram-negative bacteria, with emphasis toward Escherichia coli, Caulobacter crescentus, and related Proteobacteria. Here we summarize the epigenetic functions of DNA methylation outside of host defense in Gram-positive bacteria, with a focus on the regulatory effects of both phase variable methyltransferases and DNA methyltransferases from traditional restriction-modification systems.
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Affiliation(s)
- Taylor M Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas L Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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30
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Peedicayil J. Pharmacoepigenetics and Pharmacoepigenomics: An Overview. Curr Drug Discov Technol 2020; 16:392-399. [PMID: 29676232 DOI: 10.2174/1570163815666180419154633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND The rapid and major advances being made in epigenetics are impacting pharmacology, giving rise to new sub-disciplines in pharmacology, pharmacoepigenetics, the study of the epigenetic basis of variation in response to drugs; and pharmacoepigenomics, the application of pharmacoepigenetics on a genome-wide scale. METHODS This article highlights the following aspects of pharmacoepigenetics and pharmacoepigenomics: epigenetic therapy, the role of epigenetics in pharmacokinetics, the relevance of epigenetics to adverse drug reactions, personalized medicine, drug addiction, and drug resistance, and the use of epigenetic biomarkers in drug therapy. RESULTS Epigenetics is having an increasing impact on several areas of pharmacology. CONCLUSION Pharmacoepigenetics and pharmacoepigenomics are new sub-disciplines in pharmacology and are likely to have an increasing impact on the use of drugs in clinical practice.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology & Clinical Pharmacology, Christian Medical College, Vellore, India
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31
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Li Y. Modern epigenetics methods in biological research. Methods 2020; 187:104-113. [PMID: 32645449 DOI: 10.1016/j.ymeth.2020.06.022] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 01/09/2023] Open
Abstract
The definition of epigenetics refers that molecular modifications on DNA that can regulate gene activity are independent of DNA sequence and mitotically stable. Notably, epigenetics studies have grown exponentially in the past few years. Recent progresses that lead to exciting discoveries and groundbreaking nature of this area demand thorough methodologies and advanced technologies to move epigenetics to the forefront of molecular biology. The most recognized epigenetic regulations are DNA methylation, histone modifications, and non-coding RNAs (ncRNAs). This review will discuss the modern techniques that are available to detect locus-specific and genome-wide changes for all epigenetic codes. Furthermore, updated analysis of technologies, newly developed methods, recent breakthroughs and bioinformatics pipelines in epigenetic analysis will be presented. These methods, as well as many others presented in this specific issue, provide comprehensive guidelines in the area of epigenetics that facilitate further developments in this promising and rapidly developing field.
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Affiliation(s)
- Yuanyuan Li
- Department of Obstetrics, Gynecology & Women's Heath, University of Missouri, Columbia, MO 65212, USA; Department of Surgery, University of Missouri, Columbia, MO 65212, USA.
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32
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Coy SR, Gann ER, Papoulis SE, Holder ME, Ajami NJ, Petrosino JF, Zinser ER, Van Etten JL, Wilhelm SW. SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems. Front Microbiol 2020; 11:887. [PMID: 32508769 PMCID: PMC7248222 DOI: 10.3389/fmicb.2020.00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives.
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Affiliation(s)
- Samantha R. Coy
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- BioSciences at Rice, Rice University, Houston, TX, United States
| | - Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Spiridon E. Papoulis
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael E. Holder
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Erik R. Zinser
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James L. Van Etten
- Department of Plant Pathology and the Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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33
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Morovic W, Budinoff CR. Epigenetics: A New Frontier in Probiotic Research. Trends Microbiol 2020; 29:117-126. [PMID: 32409146 DOI: 10.1016/j.tim.2020.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
Research into the benefits of probiotics has progressed beyond interventional studies to identifying the underlying molecular mechanisms. Health-promoting effector molecules produced by probiotics are well documented and have been linked to specific genes and even individual nucleotides. However, the factors controlling the expression of these molecules are poorly understood and we argue that epigenetic influences likely play an important role in mediating the health-promoting attributes of probiotics. Here, we review established epigenetic regulation of important microbial genetic systems involved in health promotion, safety, and industrialization to provide evidence that the same regulation occurs in probiotic organisms. We advocate for studies combining genomic and meta-epigenomic data to better understand the mode of action of probiotics, their associated microbiomes, and their effects on consumers.
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34
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Liu Y, Cheng J, Siejka-Zielińska P, Weldon C, Roberts H, Lopopolo M, Magri A, D'Arienzo V, Harris JM, McKeating JA, Song CX. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS. Genome Biol 2020; 21:54. [PMID: 32127008 PMCID: PMC7053107 DOI: 10.1186/s13059-020-01969-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compatible with both Oxford Nanopore and PacBio Single-Molecule Real-Time (SMRT) sequencing, lrTAPS detects methylation with accuracy comparable to short-read Illumina sequencing but with long-range epigenetic phasing. We applied lrTAPS to sequence difficult-to-map regions in mouse embryonic stem cells and to identify distinct methylation events in the integrated hepatitis B virus genome.
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Affiliation(s)
- Yibin Liu
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Jingfei Cheng
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Paulina Siejka-Zielińska
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Carika Weldon
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hannah Roberts
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Maria Lopopolo
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrea Magri
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Valentina D'Arienzo
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - James M Harris
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Jane A McKeating
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK.
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35
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Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Opportunities and challenges in long-read sequencing data analysis. Genome Biol 2020; 21:30. [PMID: 32033565 PMCID: PMC7006217 DOI: 10.1186/s13059-020-1935-5] [Citation(s) in RCA: 737] [Impact Index Per Article: 184.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.
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Affiliation(s)
- Shanika L. Amarasinghe
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Xueyi Dong
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Luke Zappia
- Bioinformatics, Murdoch Children’s Research Institute, Parkville, 3052 Australia
- School of Biosciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Australia
| | - Matthew E. Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
- School of Mathematics and StatisticsThe University of Melbourne, Parkville, 3010 Australia
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
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36
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Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. Antimicrob Agents Chemother 2020; 64:AAC.02225-19. [PMID: 31740560 DOI: 10.1128/aac.02225-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
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37
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Gouil Q, Keniry A. Latest techniques to study DNA methylation. Essays Biochem 2019; 63:639-648. [PMID: 31755932 PMCID: PMC6923321 DOI: 10.1042/ebc20190027] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022]
Abstract
Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and animals. Meanwhile, research on other base modifications, including 6-methyladenine and 4-methylcytosine that are frequent in prokaryotes, has been impeded by the lack of a comparable technique. Bisulfite sequencing also suffers from a number of drawbacks that are difficult to surmount, among which DNA degradation, lack of specificity, or short reads with low sequence diversity. In this review, we explore the recent refinements to bisulfite sequencing protocols that enable targeting genomic regions of interest, detecting derivatives of 5-methylcytosine, and mapping single-cell methylomes. We then present the unique advantage of long-read sequencing in detecting base modifications in native DNA and highlight the respective strengths and weaknesses of PacBio and Nanopore sequencing for this application. Although analysing epigenetic data from long-read platforms remains challenging, the ability to detect various modified bases from a universal sample preparation, in addition to the mapping and phasing advantages of the longer read lengths, provide long-read sequencing with a decisive edge over short-read bisulfite sequencing for an expanding number of applications across kingdoms.
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Affiliation(s)
- Quentin Gouil
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Andrew Keniry
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
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38
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Harhay GP, Harhay DM, Bono JL, Capik SF, DeDonder KD, Apley MD, Lubbers BV, White BJ, Larson RL, Smith TPL. A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats. Sci Rep 2019; 9:18087. [PMID: 31792233 PMCID: PMC6889271 DOI: 10.1038/s41598-019-53866-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 11/04/2019] [Indexed: 01/17/2023] Open
Abstract
The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation is based on minor changes in genome sequence, as small as a few base pairs, within segments of genome called simple sequence repeats (SSRs) that consist of multiple copies of a short sequence (from one to several nucleotides), repeated in series. SSRs are found in eukaryotes as well as prokaryotes, and length variation in them occurs at frequencies up to a million-fold higher than bacterial point mutations through the process of slipped strand mispairing (SSM) by DNA polymerase during replication. The characterization of SSR length by standard sequencing methods is complicated by the appearance of length variation introduced during the sequencing process that obscures the lower abundance repeat number variants in a population. Here we report a computational approach to correct for sequencing process-induced artifacts, validated for tetranucleotide repeats by use of synthetic constructs of fixed, known length. We apply this method to a laboratory culture of Histophilus somni, prepared from a single colony, and demonstrate that the culture consists of populations of distinct sequence phase and length variants at individual tetranucleotide SSR loci.
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Affiliation(s)
- Gregory P Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States.
| | - Dayna M Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - James L Bono
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Sarah F Capik
- Texas A&M AgriLife Research, Amarillo, TX and the College of Veterinary Medicine & Biomedical Sciences, Texas A&M University System, College Station, TX, United States
| | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, United States
| | - Michael D Apley
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Brian V Lubbers
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Bradley J White
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Robert L Larson
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Timothy P L Smith
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
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39
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Deng C, Naler LB, Lu C. Microfluidic epigenomic mapping technologies for precision medicine. LAB ON A CHIP 2019; 19:2630-2650. [PMID: 31338502 PMCID: PMC6697104 DOI: 10.1039/c9lc00407f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
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Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
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40
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Jensen TØ, Tellgren-Roth C, Redl S, Maury J, Jacobsen SAB, Pedersen LE, Nielsen AT. Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nat Commun 2019; 10:3311. [PMID: 31427571 PMCID: PMC6700114 DOI: 10.1038/s41467-019-11179-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/27/2019] [Indexed: 01/25/2023] Open
Abstract
Genome-wide analysis of DNA methylation patterns using single molecule real-time DNA sequencing has boosted the number of publicly available methylomes. However, there is a lack of tools coupling methylation patterns and the corresponding methyltransferase genes. Here we demonstrate a high-throughput method for coupling methyltransferases with their respective motifs, using automated cloning and analysing the methyltransferases in vectors carrying a strain-specific cassette containing all potential target sites. To validate the method, we analyse the genomes of the thermophile Moorella thermoacetica and the mesophile Acetobacterium woodii, two acetogenic bacteria having substantially modified genomes with 12 methylation motifs and a total of 23 methyltransferase genes. Using our method, we characterize the 23 methyltransferases, assign motifs to the respective enzymes and verify activity for 11 of the 12 motifs. Single molecule real-time DNA sequencing allows genome-wide identification of DNA methylation patterns. Here, Jensen et al. present a high-throughput method that allows rapid coupling of DNA methylation patterns with their corresponding methyltransferase genes in bacteria.
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Affiliation(s)
- Torbjørn Ølshøj Jensen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Christian Tellgren-Roth
- Uppsala Genome Center, National Genomics Infrastructure, SciLifeLab, SE-751 08, Uppsala, Sweden
| | - Stephanie Redl
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jérôme Maury
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | | | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.
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41
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Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat Commun 2019; 10:2449. [PMID: 31164644 PMCID: PMC6547721 DOI: 10.1038/s41467-019-10168-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. We sequence a human genome HX1 and a Chlamydomonas reinhardtii genome using Nanopore sequencing, and then evaluate DeepMod on three types of genomes (Escherichia coli, Chlamydomonas reinhardtii and human genomes). For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species. DNA modification generates unique electric signals in Oxford Nanopore sequencing data but the signals can be complicated to decipher. Here, the authors develop a deep learning framework, DeepMod, to detect DNA base modifications including 5mC and 6mA using Nanopore sequencing data
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42
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Phillips ZN, Husna AU, Jennings MP, Seib KL, Atack JM. Phasevarions of bacterial pathogens - phase-variable epigenetic regulators evolving from restriction-modification systems. MICROBIOLOGY-SGM 2019; 165:917-928. [PMID: 30994440 DOI: 10.1099/mic.0.000805] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phase-variable DNA methyltransferases control the expression of multiple genes via epigenetic mechanisms in a wide variety of bacterial species. These systems are called phasevarions, for phase-variable regulons. Phasevarions regulate genes involved in pathogenesis, host adaptation and antibiotic resistance. Many human-adapted bacterial pathogens contain phasevarions. These include leading causes of morbidity and mortality worldwide, such as non-typeable Haemophilus influenzae, Streptococcus pneumoniae and Neisseria spp. Phase-variable methyltransferases and phasevarions have also been discovered in environmental organisms and veterinary pathogens. The existence of many different examples suggests that phasevarions have evolved multiple times as a contingency strategy in the bacterial domain, controlling phenotypes that are important in adapting to environmental change. Many of the organisms that contain phasevarions have existing or emerging drug resistance. Vaccines may therefore represent the best and most cost-effective tool to prevent disease caused by these organisms. However, many phasevarions also control the expression of current and putative vaccine candidates; variable expression of antigens could lead to immune evasion, meaning that vaccines designed using these targets become ineffective. It is therefore essential to characterize phasevarions in order to determine an organism's stably expressed antigenic repertoire, and rationally design broadly effective vaccines.
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Affiliation(s)
- Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Asma-Ul Husna
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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43
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Li J, Chen Y, Zheng T, Kong L, Zhu S, Sun Y, Deng Z, Yang L, You D. Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency. PLoS Genet 2019; 15:e1008026. [PMID: 30933976 PMCID: PMC6459556 DOI: 10.1371/journal.pgen.1008026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/11/2019] [Accepted: 02/17/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphorothioate (PT) modifications of the DNA backbone, widespread in prokaryotes, are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago. However, methods for high resolution mapping of PT modification level are still lacking. Here, we developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq we foud that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, we developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. Our study has demonstrated the heterogeneity of PT modification in the bacterial population and we also established general tools for rigorous mapping and characterization of PT modification events at whole genome level. We describe to our knowledge the first genome-wide quantitative characterization of PT landscape and provides appropriate strategies for further functional studies of PT modification.
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Affiliation(s)
- Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sucheng Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yihua Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
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44
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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45
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Liu Q, Georgieva DC, Egli D, Wang K. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics 2019; 20:78. [PMID: 30712508 PMCID: PMC6360650 DOI: 10.1186/s12864-018-5372-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides. METHODS To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases ("neighborhood effects"). RESULTS We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications. CONCLUSIONS In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will facilitate large-scale functional genomics experiments that use modified nucleotides.
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Daniela C. Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032 USA
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY 10032 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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46
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Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [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: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
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Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
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47
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Mouammine A, Collier J. The impact of DNA methylation in Alphaproteobacteria. Mol Microbiol 2018; 110:1-10. [PMID: 29995343 DOI: 10.1111/mmi.14079] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2018] [Indexed: 02/02/2023]
Abstract
Alphaproteobacteria include bacteria with very different modes of life, from free-living to host-associated and pathogenic bacteria. Their genomes vary in size and organization from single circular chromosomes to multipartite genomes and are often methylated by one or more adenine or cytosine methyltransferases (MTases). These include MTases that are part of restriction/modification systems and so-called orphan MTases. The development of novel technologies accelerated the analysis of methylomes and revealed the existence of epigenetic patterns in several Alphaproteobacteria. This review describes the known functions of DNA methylation in Alphaproteobacteria and also discusses its potential drawbacks through the accidental deamination of methylated cytosines. Particular emphasis is given to the strong connection between the cell cycle-regulated orphan MTase CcrM and the complex network that controls gene expression and cell cycle progression in Alphaproteobacteria.
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Affiliation(s)
- Annabelle Mouammine
- Faculty of Biology and Medicine, Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH 1015, Switzerland
| | - Justine Collier
- Faculty of Biology and Medicine, Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH 1015, Switzerland
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48
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Abstract
The causes and consequences of spatiotemporal variation in mutation rates remain to be explored in nearly all organisms. Here we examine relationships between local mutation rates and replication timing in three bacterial species whose genomes have multiple chromosomes: Vibrio fischeri, Vibrio cholerae, and Burkholderia cenocepacia. Following five mutation accumulation experiments with these bacteria conducted in the near absence of natural selection, the genomes of clones from each lineage were sequenced and analyzed to identify variation in mutation rates and spectra. In lineages lacking mismatch repair, base substitution mutation rates vary in a mirrored wave-like pattern on opposing replichores of the large chromosomes of V. fischeri and V. cholerae, where concurrently replicated regions experience similar base substitution mutation rates. The base substitution mutation rates on the small chromosome are less variable in both species but occur at similar rates to those in the concurrently replicated regions of the large chromosome. Neither nucleotide composition nor frequency of nucleotide motifs differed among regions experiencing high and low base substitution rates, which along with the inferred ~800-kb wave period suggests that the source of the periodicity is not sequence specific but rather a systematic process related to the cell cycle. These results support the notion that base substitution mutation rates are likely to vary systematically across many bacterial genomes, which exposes certain genes to elevated deleterious mutational load. That mutation rates vary within bacterial genomes is well known, but the detailed study of these biases has been made possible only recently with contemporary sequencing methods. We applied these methods to understand how bacterial genomes with multiple chromosomes, like those of Vibrio and Burkholderia, might experience heterogeneous mutation rates because of their unusual replication and the greater genetic diversity found on smaller chromosomes. This study captured thousands of mutations and revealed wave-like rate variation that is synchronized with replication timing and not explained by sequence context. The scale of this rate variation over hundreds of kilobases of DNA strongly suggests that a temporally regulated cellular process may generate wave-like variation in mutation risk. These findings add to our understanding of how mutation risk is distributed across bacterial and likely also eukaryotic genomes, owing to their highly conserved replication and repair machinery.
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49
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Atack JM, Tan A, Bakaletz LO, Jennings MP, Seib KL. Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies. Trends Microbiol 2018; 26:715-726. [PMID: 29452952 PMCID: PMC6054543 DOI: 10.1016/j.tim.2018.01.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/06/2018] [Accepted: 01/26/2018] [Indexed: 01/04/2023]
Abstract
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features. The study of DNA methyltransferase specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with whole-transcriptome/proteome analysis to comprehensively characterize these systems in a number of important bacterial pathogens.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
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50
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Liu L, Zhang Y, Jiang D, Du S, Deng Z, Wang L, Chen S. Recent Advances in the Genomic Profiling of Bacterial Epigenetic Modifications. Biotechnol J 2018; 14:e1800001. [PMID: 29878585 DOI: 10.1002/biot.201800001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/03/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Liqiong Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan 442000 Hubei China
| | - Yizhou Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
| | - Dongxu Jiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan 442000 Hubei China
| | - Shiming Du
- Taihe Hospital; Hubei University of Medicine; Shiyan 442000 Hubei China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education; School of Pharmaceutical Sciences; Zhongnan Hospital; Wuhan University; Wuhan 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan 442000 Hubei China
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