Topic outline

  • General

    DNA methylation and methylome analysis with NGS

    Fribourg, 10-11 February 2015


    Methylations of the DNA are important modifications that affect the DNA of bacteria and higher eucaryotes. The DNA can be modified on different bases (6mA, 4mC, 5mC) and these modifications have various effects, e.g., on gene expression or protection against foreign DNA. These modifications can be transmitted from generation to generation, they are called epigenetics modifications. Current next generation sequencing technologies allow for the detection of those modifications at the genome level introducing the « methylome ». In addition Histone modifications are also part of the epigenomics modifications that can influence gene expression. These modification can be analyzed by NGS methods. In this workshop we will study the methods used to produce and to analyze this NGS data.


    Learn about DNA methylation and other chromatin modifications.

    Learn the tools and databases available to study the methylome.


    Requirements: a portable computer with WIFI and 4Gb RAM. Basic knowledge of the R package.


    Application on the StarOmics page

    Deadline for registration and cancellation is set to Jan 31, 2015.


    Additional information

    The course will be taught by Philipp Bucher, Christoph Schmid and Michael Stadler.

    For administrative questions, please contact
    For technical and scientific questions, please contact

  • Feb 10 morning: Introduction and R reminder

    9:15 Welcome address

    9:20 Introduction to the biological problem and to the methods.

    10:30 Coffee break

    11:00 Little R reminder

    12:30 Lunch break

  • Feb 10 afternoon: DNA methylation in Eukaryotes

    In this session, we will discuss DNA methylation in eukaryotes, with a focus on mammalian 5mC methylation of cytosines in CpG context.

    13:30 The first part (theory, around 1 hour) will present the topics:

    • Introduction and  role of DNA-methylation in mammals
    • How is DNA-methylation experimentally measured (technology)
    • Typical methylation patterns found in mammals (PMDs, LMRs, UMRs/CGI) and their biological interpretation
    • Outline of a typical analysis workflow and tools

    In the second part (exercises, rest of the session), we will use R/Bioconductor on small sample datasets to:

    • go from raw bis-seq reads to cytosine methylation values
    • identify hypomethylated regions (methylome segmentation)
    • visualize and interpret the results

    For the second part (exercises) please install the required R packages as shown in the exercises handout in section 1 "Install required software".

    15:15 Coffee break

  • Feb 11 morning: Other chromatin epigenetic modifications (histones, etc.)

    9:15 Theoretical part (60-90 min)

    Principles of ChIP-Seq data analysis will be explained with examples. The most important tools of the ChIP-seq and Signal Search Analysis (SSA) servers will be introduced.

    10:30 Coffee break

    11:00 Practical (web-based)

    Chromatin and genomic context analysis of unmethylated and lowly methylated regions using tools from the ChIP-Seq and SSA servers.

    12:30 Lunch break

  • Feb 11 afternoon: DNA methylation in Prokaryotes

    13:30: Theoretical part (60-90 min):

    intro Prokaryotic epigenetics
    - differences to eukaryotes: more diverse modifications, defined target sequence motifs, RM-systems, ...
    - SMRT sequencing technology, data analysis workflow,
    - brief review of recent literature: applications of SMRT sequencing & findings on biology

    15:15 Coffee break

    15:45 practical session (RStudio, web server, 120 min.)

    - What is the positional resolution of SMRT sequencing, determination of modified bases within specific target motif sequences?
    - How sensitive is SMRT sequencing, compute the fractions of motif instances with modifications detectable by SMRT in bacterial genomes?
    - Are the detected modifications associated with positions of specific genomic features?