1. Introduction to Epigenetics/Epigenomics
Xiangqin Cui
Department of Biostatistics
University of Alabama at Birmingham
Workshop on Statistical Genetics and Genomics, Southern Regional Meeting in New Orleans, Feb 12, 2009

2. Epigenetics
Epigenetics refers to the study of changes in the regulation of gene activity and expression that are not dependent on gene DNA sequence.
While epigenetics often refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome.

3. Epigenetics Mechanisms
RNA Interference
Gene Expression
DNA Methylation
Histone Modifications

4. DNA Methylation Hypomethylation Hypermethylation

5. Natural Roles of DNA Methylation in Mammalian System
Imprinting
X chromosome inactivation
Heterochromatin maintenance
Developmental controls
Tissue specific expression controls

6. DNA Methylation and Cancer
Robertson, Nature Reviews Genetics, Vol6, 597

7. DNA Methylation and Other Human Diseases
-- Imprinting Disorder:
Beckwith-Wiedemann syndrom (BWS)
Prader-Willi syndrome (PWS)
Transient neonatal diabetes mellitus (TNDM)
-- Repeat-instability diseases
Fragile X syndrome (FRAXA)
Facioscapulohumeral muscular dystroph
-- Defects of the methylation machinery
Systemic lupus erythemtosus (SLE)
Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome

8. Histone Modifications

9. Histone Modifications

10. Li e. al. (2007) Cell 128, 707

11. Histone Modifications in Relation to Gene Transcription
Li e. al. (2007) Cell 128, 707

12. Histone Modifications and Human Diseases
Coffin-Lowry syndrome is a rare genetic disorder characterized by mental retardation and abnormalities of the head and facial and other areas. It is caused by mutations in the RSK2 gene (histone phosphorylation) and is inherited as an X-linked dominant genetic trait. Males are usually more severely affected than females.
Rubinstein-Taybi syndrome is characterized by short stature, moderate to severe intellectual disability, distinctive facial features, and broad thumbs and first toes. It is caused by mutations in CREB-binding protein (histone acetylation)

13. RNA Interference (RNAi)

14. siRNA Mediated Heterochromatin Maintenance

15. Technologies for Studying Epigenetics/Epigenomics
DNA Methylation
Microarray or deep sequencing
Irizarry et. Al. (2008) Genome Research 18(5):780

16. Bisulfite Sequencing

17. Bisulfite Sequencing

18. Global Interrogation of DNA Methylation using Microarrays
intron
promoter
exon 3’ 5’
Expression array
Exon array
Splicing array
Promoter
array
Tiling array

19. Methylated/Unmethylated DNA Enrichment Methods
Restriction Enzyme Based Enrichment Methods
Zilberman and henikoff (2007) Development 134, 3959

20. Methylated/Unmethylated DNA Enrichment Methods
Immunoprecipation Based Method
Zilberman and henikoff (2007) Development 134, 3959

21. Hybridization to microarrays
Genomic DNA
Enrichment for methylated DNA
Labeling
Labeling

22. Zilberman and henikoff (2007) Development 134, 3959

23. Technologies for Interrogating Epigenetics/Epigenomics
ChIP-chip

24. Technologies for Interrogating Epigenetics/Epigenomics
Histone Modifications
ChIP-chip
Antibody specific to one type of histone modification
ChIP-seq
Deep sequencing

25. Epigenomics Microarray Data Analyses
Major difference between data generated in epigenomics study and expression study is at the utility of the information of probe location in the genome. The adjacent probes are often correlated.
Data Analysis steps:
Data normalization
Statistical Modeling
Modeling
Peak Finding
Results Visualization along the genome

26. Normalization
The loess assumption is sometimes violated in ChIP-chip data

27. Normalization Cont. Quantile Normalization
Variance Stabilizing Normalization
Probe Model Based Normalization

28. Nomalization Based on Probe Sequences
Model the probe behavior based on probe sequence for Affymetrix arrays
Log(PM) = nucleotide + NucleotideCount2 + log(probeCopy#) + ε
Model the probe behavior based on probe GC content for long oligo arrays
For each group of probes with a give GC content, the background follows a normal distribution (µ,σ2).
Johnson et al (2006) PNAS 103, 12457; Song et al (2007)Genome Biology.8:R178

29. Other Special Properties
GC content affects antibody binding to methylated DNA--- need for normalization against GC content.
Pelizzola et al (2008) Genome Research, 18, 1652.

30. Other Special Properties Cont.
Map high intensity probes back to the genome
Locate TF binding location
ChIP-DNA
Noise
Probes
Chromosome

31. Smoothing

32. Peak Call
Identify regions that show epigenetic changes.

33. Results Visualization

34. Cisgenome http://www.biostat.jhsph.edu/~hji/cisgenome/
Ji et al (2008) Nature Biotechnology. 26, 1293

35. Software Packages and Comparisons
Johnson et al (2008) Genome Research 18: 393

36. Array Platform Comparisons
Johnson et al (2008) Genome Research 18: 393