Genome-wide Profiling of 5fC and 5caC


If your research goal is to reveal and map the genome-wide distribution of newly discovered epigenetic markers 5fC and 5caC that may play a key role in epigenetics, or to quantify TDG-mediated excision of 5fC/5caC at high resolution, Creative BioMart currently offers methylation-assisted bisulfite sequencing (MAB-Seq) technology that allows base-resolution mapping of 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two oxidized 5-methylcytosine (5mC) bases indicative of active, and measurement of their relative abundance.

What Is MAB-Seq/caMAB-Seq?

In MAB-Seq, genomic DNA is first treated with the bacterial DNA CpG methyltransferase M.SssI that efficiently methylates cytosines (C) within CpG dinucleotides. Bisulfite conversion of M.SssI-treated DNA only deaminates 5fC and 5caC; the originally unmodified C within CpGs becomes resistant to bisulfite conversion due to its conversion to 5mC. In subsequent sequencing, only 5fC and 5caC are read as T, while C/5mC/5hmC are read as C. Based on MAB-Seq, the caMAB-Seq (5caC methylase-assisted bisulfite sequencing) is further developed to directly map 5caC at single-base resolution. In this modified version of MAB-Seq, genomic DNA is first treated with sodium borohydride (NaBH4) to reduce 5fC back to 5hmC. Owing to the combination of NaBH4 reduction with M.SssI treatment, 5caC is directly mapped as T after bisulfite conversion, while C/5mC/5hmC/5fC are read as C.

Schematic Illustration of the Principle behind methylation-assisted bisulfite sequencing (MAB-Seq)/5caC methylase-assisted bisulfite sequencing (caMAB-Seq)

Figure 1. Schematic Illustration of the Principle behind MAB-Seq/caMAB-Seq. (Wu H.; et al. 2016).

Features of MAB-Seq

  1. Can simultaneously map the genome-wide 5fC/5caC and relatively quantify their abundance in a single sequencing experiment
  2. Single-base resolution makes MAB-Seq suitable for analyzing the DNA sequence context surrounding 5fC and 5caC
  3. Amenable to both genome-scale and locus-specific analysis
  4. Complementary to caMAB-Seq (direct 5caC mapping)
  5. Compared to subtraction-based mapping methods, MAB-Seq requires less sequencing work and enables robust statistical calling of 5fC/5caC
  6. The most economical, fast and reliable method currently available for studying DNA demethylation dynamics in mammalian genomes

Advantages of Choosing Creative BioMart

  1. Tolerance of multiple sample types: we accept a wide range of biological and clinical samples, including but not limited to genomic DNA, cultured cells and fresh/frozen tissues from mammals.
  2. Experienced technical team & Advanced technology platform: our state-of-art technologies and strict quality control at every step make sure that our services and final presented data are performed and presented with reliability.
  3. Flexible & One-stop service: customers only need to provide samples, and we will complete the full experiment. We offer flexible services depending on your research objectives and budget, mapping 5fC/5caC at the scale of whole genome (WG-MAB-Seq), within specific genomic regions enriched for enhancer-marking histone modifications (ChIP-MAB-Seq), or at CpG-rich sequences such as gene promoters (RR-MAB-Seq).
  4. Professional data analysis: we have a professional bioinformatics analysis team to provide you with both standard data analyses and customized bioinformatics analyses.

Workflow of Our Service at Creative BioMart

Workflow of Genome-wide Profiling of 5fC and 5caC at Creative BioMart

Figure 2. Workflow of Genome-wide Profiling of 5fC and 5caC at Creative BioMart

With skillful experts and stringent quality control, genome-wide profiling of 5fC and 5caC service provided by Creative BioMart is ready for any customer demands with optimal customization. If you have any questions about this service, please don’t hesitate to contact us.

References
1. Neri F.; et al. Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis. Nature Protocols. 2016, 11(7): 1191-1205.
2. Wu H.; et al. Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq. Nature protocols. 2016, 11(6): 1081-1100.

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