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SMRT-Based Microbial Epigenomics


Our SMRT-based microbial epigenomics is amenable to long-read lengths and enables mapping of methylation patterns within highly repetitive genomic regions. Our SMRT sequencing technology can simultaneously determine nucleotide sequence and the methylation status of each nucleotide, through real-time observation of DNA polymerase kinetics.

Our Advantages:
  • Determine the methylation status of every sequenced nucleotide.
  • Longest average read lengths and highest consensus accuracy.
  • Experienced scientists and advanced platforms.
  • Reliable bioinformatics analysis programs and pipelines.
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Introduction to our SMRT-based microbial epigenomics analysis

Microbial genomes contain a variety of base modifications, most of which are methylations occurring at adenine or cytosine residues. DNA methylation plays an important role in microbial defense against foreign DNA. During SMRT sequencing, DNA polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands. The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and enable us to detect DNA modifications including 4-methylcytosine (m4C), 6-methyladenosine (m6A), 5-hydroxymethylcytosine (5hmC), and 5-methylcytosine (m5C), by measuring the variation in the polymerase kinetics. We also provide Nanopore-based epigenomics service for microbial epigenomics studies.

In addition to the detection of DNA methylation, PacBio SMRT sequencing also allows us to reveal phase variation of restriction-modification (R-M) genes that regulate batteries of genes involved in pathogenesis, host adaption, and antibiotic resistance. R-M systems can not only drive bacterial evolution by increasing C-T mutations and double-strand breaks, but also alter the transcription of genes involved in virulence, host adaption, pathogenicity, and antibiotic resistance. SMRT-based microbial epigenomics can be used to understand the pattern and function of DNA methylation, identify targets for therapeutic treatment, and reveal phase variation of R-M genes. It has a wide range of applications, including studies of cell cycle control and DNA repair, developmental biology, cancer research, etc.

SMRT-based microbial epigenomics analysis workflow

Bioinformatics Analysis

  1. Genome-wide identification of base modifications.
  2. Functional annotation of epigenetic modifications.
  3. Systematic annotation of the MTase genes.
  4. Reveal phase variation of R-M genes that regulate genes involved in pathogenesis, host adaption, and antibiotic resistance.

Sample Requirement

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw data files in BAM format, demultiplex CCS reads in FASTQ format, quality-control dashboard, statistic data, and your designated bioinformatics analysis report.

References

  1. Yang Y, et al. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics. 350(16):2-10.
  2. Matthew Ouellette, et al. Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. Genes 2018, 129:1-23.
  3. Zhuang Miao, et al. Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. Oncotarget. 2015, 6(25): 21493–21506.

Areas of Interest

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