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

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.

Epigenetics Mechanisms

Gene Expression

RNA Interference

Histone Modifications DNA Methylation

DNA Methylation

http://www.cellscience.com/reviews7/Taylor1.jpg

HypomethylationHypermethylation

Natural Roles of DNA Methylation in Mammalian System

Imprinting

X chromosome inactivation

Heterochromatin maintenance

Developmental controls

Tissue specific expression controls

DNA Methylation and Cancer

Robertson, Nature Reviews Genetics, Vol6, 597

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

Histone Modifications

http://porpax.bio.miami.edu/~cmallery/150/gene/c7.19.4.histone.mod.jpg

Histone Modifications

http://www.nature.com/nsmb/journal/v14/n11/images/nsmb1337-F1.gif

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

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

Histone Modifications in Relation to Gene Transcription

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)

RNA Interference (RNAi)

http://www.nature.com/ncpneuro/journal/v3/n7/images/ncpneuro0551-f1.jpg

siRNA Mediated Heterochromatin Maintenance

Technologies for Studying Epigenetics/Epigenomics

DNA Methylation

Irizarry et. Al. (2008) Genome Research 18(5):780

Microarray or deep sequencing

Bisulfite Sequencing

Bisulfite Sequencing

5’3’

Expression array

Exon array

Splicing array

Promoter array

Tiling array

exon intron

Global Interrogation of DNA Methylation using Microarrays

promoter

Methylated/Unmethylated DNA Enrichment Methods

Restriction Enzyme Based Enrichment Methods

Zilberman and henikoff (2007) Development 134, 3959

Methylated/Unmethylated DNA Enrichment Methods

Zilberman and henikoff (2007) Development 134, 3959

Immunoprecipation Based Method

Hybridization to microarrays

Enrichment for methylated DNA

Labeling Labeling

Genomic DNA

Zilberman and henikoff (2007) Development 134, 3959

Technologies for Interrogating Epigenetics/Epigenomics

http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg

ChIP-chip

Technologies for Interrogating Epigenetics/Epigenomics

http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg

ChIP-chip

Antibody specific to one type of histone modification

Histone Modifications

ChIP-seq

Deep sequencing

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

Normalization

• The loess assumption is sometimes violated in ChIP-chip data

Normalization Cont.

• Quantile Normalization

• Variance Stabilizing Normalization

• Probe Model Based Normalization

Nomalization Based on Probe Sequences

Johnson et al (2006) PNAS 103, 12457; Song et al (2007)Genome Biology.8:R178

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).

Other Special PropertiesGC content affects antibody binding to methylated DNA--- need for normalization against GC content.

Pelizzola et al (2008) Genome Research, 18, 1652.

Other Special Properties Cont.

• Map high intensity probes back to the genome• Locate TF binding location

Probes

Chromosome

ChIP-DNA

Noise

Smoothing

Peak Call

• Identify regions that show epigenetic changes.

Results Visualization

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

Software Packages and Comparisons

Johnson et al (2008) Genome Research 18: 393

Array Platform Comparisons

Johnson et al (2008) Genome Research 18: 393