Current Topics in Genomics and Epigenomics
Course Introduction
The rapid progress of the next-generation sequencing technology significantly advances
the studies in human genome structures and functions. At the same time, we have much
deeper understandings of the mechanisms and functions of the epigenome (DNA
methlyation, histone modification, chromatin structure, etc.). This course will introduce
the current frontiers in genomics and epigenomics, including the new concepts in the
related fields and the new computational and experimental techniques.
Course Structure
This short course will comprise of both lecture and paper discussion, focusing on seven
related topic areas. During the first half of the class meeting, a general introduction will
be given to a particular topic. This is followed by a student-led paper discussion in the
second half. This course employs problem-based learning as a teaching tool.
Topics
Apr 15, 10:00-12:00 A decade of genome sequencing
Apr 17, 10:00-12:00 Transcriptional control elements in the genome
Paper discussion: Thurman et al., Nature 2012 (Student Group
#1)
Apr 19, 10:00-12:00 Chromatin modifications and dynamics
Paper discussion: Zhu et al., Cell 2013 (Student Group #2)
Apr 22, 10:00-12:00 Transcriptional landscape and Non-coding RNAs in the genome
Paper discussion: Djebali et al. Nature 2012 (Student Group
#3)
Apr 24, 10:00-12:00 DNA methylation analysis
Paper discussion: Stadler et al., Nature 2011 (Student Group #4)
Apr 26, 10:00-12:00 Analysis of higher order chromatin structure
Paper discussion: Nora et al. Nature 2012 (Student Group #5)
Apr 29, 10:00-12:00 Genomic Analysis of Stem Cell Pluripotency
Paper discussion: Chen et al., Cell 2008 (Student Group #6)
Apr 30, 10:00-12:00 PBL presentations
Problem Based Learning Exercise
Overview: Small groups (four - five students each) will be assigned to work on a project.
Students within each group will work together to learn about their assigned subject (see
below) and decide on a specific aspect to develop into a group presentation. At the end
of the course, each group will give a 5-minute ‘mini-talk’ as part of an integrated group
presentation, with a total of no more than 25 minutes. The goals of this exercise will be
to promote self-directed study, collaborative interactions and oral presentation skills.
Tasks:
The humans and mice diverged from their common ancestors over 70 million years ago.
During this period, much of the genome sequences have diverged, with nucleotide
sequences at many functional sequences exhibiting considerable degree of
conservation. Now, the ENCODE consortium has generated comprehensive maps of
transcription, histone modifications, chromatin accessibility and transcription factor
binding in both human and mouse genomes (http://genome.ucsc.edu/ENCODE/).
Comparative analysis of these maps of biochemical activities between the two species
should reveal both conserved biological processes and pathways that undergo rapid
evolution. The goal of this problem based learning exercise is to learn more about the
functional sequences in each mammalian genome via comparative analysis.
1. Each group will be assembled around one of the following aspects:
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Sequence comparison
Transcription profiles and transcriptome landscape
Cis regulatory landscapes
Chromatin accessibility maps
Epigenomic profiles
Chromatin architecture
2. Each group should propose to ask some questions, such as:
 What are the datasets available for a specific biochemical assay from each
species?
 What are the similarities and differences in the two species for a specific
biochemical activity?
 Are there biological explanation for the similarities and differences?
 What mechanisms could be driving the similarities or differences?
3. Based on the initial collection of information, the group should decide on a specific
aspect to explore. The group should then divide up this topic into specific components
for ‘minitalks’. The group will then organize the talks to present to the class as a whole.
The first speaker for each group will give a general overview and outline of the talks.
Evaluation:
At the end of this course, each student will be given an evaluation score (“good”,
“excellent” and “outstanding”) based on the following criteria Contents: need to be up to date and accurate;
 Questions: appropriateness and creativeness will receive high scores;
 Presentation: needs to be logic, clear, and on time.