Download Introduction to Epigenetics/Epigenomics

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
RNA Interference
Gene Expression
Histone Modifications
DNA Methylation
DNA Methylation
Hypomethylation
Hypermethylation
http://www.cellscience.com/reviews7/Taylor1.jpg
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
Histone Modifications in Relation to Gene Transcription
Li e. al. (2007)
Cell 128, 707
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 Xlinked 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
Microarray or deep sequencing
Irizarry et. Al. (2008) Genome Research 18(5):780
Bisulfite Sequencing
Bisulfite Sequencing
Global Interrogation of DNA
Methylation using Microarrays
5’
promoter
Expression
array
Exon array
Splicing array
Promoter
array
Tiling array
exon
intron
3’
Methylated/Unmethylated DNA
Enrichment Methods
Restriction Enzyme Based Enrichment Methods
Zilberman and henikoff (2007) Development 134, 3959
Methylated/Unmethylated DNA
Enrichment Methods
Immunoprecipation Based Method
Zilberman and henikoff (2007) Development 134, 3959
Hybridization to microarrays
Genomic DNA
Enrichment for methylated DNA
Labeling
Labeling
Zilberman and henikoff (2007) Development 134, 3959
Technologies for Interrogating
Epigenetics/Epigenomics
ChIP-chip
http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg
Technologies for Interrogating
Epigenetics/Epigenomics
Histone Modifications
ChIP-chip
Antibody specific
to one type of
histone
modification
ChIP-seq
Deep sequencing
http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg
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
 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
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.
Other Special Properties Cont.
• Map high intensity probes back to the genome
• Locate TF binding location
ChIP-DNA
Noise
Probes
Chromosome
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