DNA methylation and methylome analysis with NGS - February 2015
Section outline
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DNA methylation and methylome analysis with NGS
Fribourg, 10-11 February 2015
Overview
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.
Objectives
Learn about DNA methylation and other chromatin modifications.
Learn the tools and databases available to study the methylome.
Requirements
Requirements: a portable computer with WIFI and 4Gb RAM. Basic knowledge of the R package.
Application
Application on the StarOmics page.
Deadline for registration and cancellation is set to Jan 31, 2015.
Location
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Université de Fribourg
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Building Pérolles PER21, room C130
Additional information
The course will be taught by Philipp Bucher, Christoph Schmid and Michael Stadler.
For administrative questions, please contact staromics@cuso.ch
For technical and scientific questions, please contact laurent.falquet@unifr.ch -
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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
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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
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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
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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 biology15:15 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?