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Nanopore-Based Microbial Epigenomics


Epigenetic modifications play important roles in gene expression and regulation, and are involved in numerous cellular processes such as development, cell differentiation and tumorigenesis. Our Nanopore-based microbial epigenomics analysis can provide new insights into some exciting fields of epigenetics research, including simultaneous detection of DNA/RNA base modifications and nucleotide sequences, the complete characterization of long non-coding RNA (lncRNA), and comprehensive elucidation of chromatin capture.

Our Advantages:
  • Nanopore-based epigenomics analysis can directly sequence the native strand of interest without amplification or optics amplification.
  • Rapid insight into samples, on-demand sequencing and custom workflows by real-time streaming of sequence data.
  • Provide comprehensive and reliable genome-wide information regarding DNA methylation.
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Introduction to our nanopore-based epigenomics analysis

DNA is methylated by the MTase enzymes, which transfer a methyl group from S-adenosyl-l-methionine (SAM) to the appropriate positions of target bases. MTases function either alongside a cognate restriction enzyme as part of a RM (restriction-modification) system or as ‘orphans’ that lack a cognate restriction enzyme. Nanopore sequencing instruments rely on engineered biological nanopores embedded in a lipid membrane to sequence single-stranded DNA (ssDNA). A voltage is applied across the membrane, and ssDNA is ratcheted through a biological nanopore by a molecular motor protein bound to the DNA library molecule. The ionic current flowing through the nanopore depends on the set of nucleotides occupying the constriction point. The methylated nucleotides introduce distinct current patterns which can be detected. Nanopore-based epigenomics allows for simultaneous detection of DNA or RNA sequence, base modifications, and more comprehensive chromatin capture studies. And we use metaepigenomics, a powerful approach, to identify a vast unexplored variety of microbial DNA methylation systems.

Compared to SMRT-based epigenomic sequencing, nanopore-based epigenomics analysis can detect more types of DNA modifications, such as N6-methyladenine (m6A), 5-methylcytosine (m5C), and N4-methylcytosine (m4C) motifs. Nanopore-based epigenomics analysis can be used to understand the roles of methylation in the regulation of gene expression, virulence, and pathogen-host interactions. As sets of methylated motifs and MTases can vary widely, even between closely related microbial strains, nanopore-based epigenomics analysis is expected to enable differential methylation analyses between microbial populations.

Nanopore-based epigenomics analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes data generation, alignment and assembly, methylation analysis, and other custom analyses to help you understand the microbial epigenomics.


Pipeline Content
Data generation Exportation of sequence data and data processing such as adapter trimming
Alignment and assembly Genome assembly and polishing using NGS data
Methylation analysis Methylation calling from different basecalling groups using tools such as nanopolish
Custom analysis Structural variant detection, SNP detection, etc.

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 sequencing data (FASTQ), trimmed and stitched sequences, quality-control dashboard, statistic data, and your designated bioinformatics report.

References

  1. John Beaulaurier, et al. Deciphering bacterial epigenomes using modern sequencing technologies. Nature Reviews Genetic. 2019, 20:157–172.
  2. Minsoung Rhee and Mark A. Burns. Nanopore sequencing technology: research trends and applications. Trend in Biotechnology. 2006, 24(12):580-586.
  3. Satoshi Hiraoka, et al. Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature Communications. 2019, 10:159.

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