Epigenetics and Methylation Analysis

BEA offers solutions for studies of gene regulation on the epigenetic level with the most commonly used platform for epigenetic studies, namely the Illumina Infinium Human Methylation BeadChips. For analysis of transcription factor binding or analysis of chromatin modifications we offer ChIP sequencing which is a powerful method for identifying genome wide binding and differential histone modification sites.

Illumina Methylation Analysis

Methylation profiling with Bead array technology allows researchers to analyze the effects of aberrant methylation (either hyper- or hypomethylation) for a variety of applications. Illumina has developed a robust methylation profiling platform that provides quantitative methylation measurement at the single-CpG-site level, providing the highest resolution for understanding epigenetic changes.



Illumina Infinium MethylationEPIC bead chip
The Infinium MethylationEPIC bead chip is the successor of the popular Infinium Methylation450K bead chip. It covers >90% of CpGs found on Infinium Methylation450K plus an additional 350,000 CpGs in enhancer regions. These enhancer regions, identified by ENCODE and FANTOM5, have been shown to be critical sites for differential methylation.

There are no major changes upon the succession, apart from bead chip sample format, where Infinium MethylationEPIC bead chip is in 8-sample format and Infinium Methylation450K bead chip is in 12-sample format. It uses the same robust chemistry and workflow as in Infinium Methylation450K.


≥500 ng gDNA of good quality in 45 ul is recommended to use as input. Quantitative measurement should be performed by using a spectrofluorometer. Qualitative measurement is performed by using Agilent Tapestation genomic tapescreen.


Reduced representation bisulfite sequencing (RRBS)

RRBS reduce the scale and cost of whole genome bisulfite sequencing by only sequencing a reduced, representative sample of the whole genome. DNA is first digested with a restriction enzyme such as MspI which is methylation sensitive and cuts at CCGG sites. The CpG-rich regions of the genome is thereby enriched. The DNA ends are then filled in and adapters are ligated. The DNA-fragments are then size selected, bisulfite converted, and sequenced. This simple approach captures 85% of CpG islands and 60% of promoters and requires very little input sample. The reduction in DNA also means that fewer reads are needed for accurate sequencing, reducing cost drastically. One disadvantage of RRBS is that the assay does not capture all CpG islands or promoters. RRBS has become popular when high-throughput, low cost methylation analysis is needed such as in clinical applications. Currently BEA is using Diagenode's Premium RRBS kit .


ChIP-Sequencing

By combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. ChIP-Seq enables thorough examination of the interactions between proteins and nucleic acids on a genome-wide scale. Sequence analysis of bound DNA targets for transcription factors or histone modifications across the entire genome of any organism can reveal gene regulatory networks in combination with RNA sequencing and methylation analysis.

We construct ChIP sequencing libraries using the NEBNext ChIP-Seq library reagent set for Illumina for standard input ( 5-10 ng DNA) or the Rubicon Thruplex DNA-seq kit for low input (<2ng DNA). For higher eukaryotes a minimum of 10-20 million mapped reads per sample are recommended for performing a whole genome ChIP analysis.