Epigenetics and Gene Regulation
This new module jointly concerns statistical genetic principles around epigenetics and gene regulation. Lectures and practical sessions will introduce students to the methodology for studying both germline and somatic epigenetic processes, with particular attention to methylation profiling. Additional topics will include methylation QTL analysis, epigenome-wide association studies, and methylation risk scores, and aging effects.
The second half of the course focuses on methods for predicting gene expression and its consequences for trait variation. We will cover TWAS, regulatory motif discovery, and machine learning approaches to inference of non-coding DNA function. Related research in single cell genomics and network inference are introduced, though these are covered in more detail in Modules 14 and 18 respectively.
Learning Objectives: After attending this module, participants will be able to:
- Understand the difference between germline and somatic epigenetic phenomena.
- Know the major modes of epigenetic profiling, including methylation, chromatin accessibility, histone modification, and chromatin contacts.
- Perform a methylation profiling analysis, as well as compute mQTL and methylation risk scores.
- Understand the theory of transcription factor binding site (TFBS) identification.
- Be able to predict gene expression from raw or summary data and perform TWAS
- Evaluate tools for enhancer activity prediction such as Deep-SEA, LINSIGHT and ChromHMM.
Course Dates
- Wed June 5, 1:30 p.m. – 5:00 p.m. EST
- Thu June 6, 8:30 a.m. – 5:00 p.m. EST
- Fri June 7, 8:30 a.m. – 5:00 p.m. EST
Instructors
- Karen Conneely
- Jingjing Yang
Suggested Course Pairings
Integrative Genomics Stream
- Module 2: Genetics and Genomics
- Module 7: Quantitative Genetics
- Module 14: Gene Expression
- Module 18: Gene Networks and Pathways
Course Materials
Visit the Box here
About the Instructors
Karen Conneely is an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. She is particularly interested in the role of DNA methylation as mediator between genetic variation, environment and phenotype. Ongoing work in her lab uses computational approaches to understand the relationship between multiple epigenetic mechanisms, gene expression, and human aging. Access Karen’s publications here.
Jingjing Yang is also an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. The Yang Lab is developing statistical and computational methods and tools for quantitative genomics data analysis and biomedical data analysis. Her TIGAR and OTTERS software supports Transcriptome-wide Association Studies. Learn more about Jingjing’s work here.