Introduction to Epigenetics/Epigenomics

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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
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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.

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Epigenetics Mechanisms
RNA Interference
Gene Expression
DNA Methylation
Histone Modifications
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DNA Methylation
Hypomethylation Hypermethylation
http//www.cellscience.com/reviews7/Taylor1.jpg
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Natural Roles of DNA Methylation in Mammalian
System

• Imprinting
• X chromosome inactivation
• Heterochromatin maintenance
• Developmental controls
• Tissue specific expression controls

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

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Histone Modifications
http//porpax.bio.miami.edu/cmallery/150/gene/c7.
19.4.histone.mod.jpg
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Histone Modifications
http//www.nature.com/nsmb/journal/v14/n11/images/
nsmb1337-F1.gif
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Li e. al. (2007) Cell 128, 707
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Histone Modifications in Relation to Gene
Transcription
Li e. al. (2007) Cell 128, 707
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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)
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RNA Interference (RNAi)
http//www.nature.com/ncpneuro/journal/v3/n7/image
s/ncpneuro0551-f1.jpg
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siRNA Mediated Heterochromatin Maintenance
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Technologies for Studying Epigenetics/Epigenomics
DNA Methylation
Microarray or deep sequencing
Irizarry et. Al. (2008) Genome Research 18(5)780
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Bisulfite Sequencing
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Bisulfite Sequencing
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Global Interrogation of DNA Methylation using
Microarrays
intron
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exon
promoter
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Expression array
Exon array
Splicing array
Promoter array
Tiling array
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Methylated/Unmethylated DNA Enrichment Methods
Restriction Enzyme Based Enrichment Methods
Zilberman and henikoff (2007) Development 134,
3959
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Methylated/Unmethylated DNA Enrichment Methods
Immunoprecipation Based Method
Zilberman and henikoff (2007) Development 134,
3959
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Hybridization to microarrays
Genomic DNA
Enrichment for methylated DNA
Labeling
Labeling
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Zilberman and henikoff (2007) Development 134,
3959
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Technologies for Interrogating Epigenetics/Epigeno
mics
ChIP-chip
http//www.nature.com/jid/journal/v125/n2/extref/5
603467x1.jpg
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Technologies for Interrogating Epigenetics/Epigeno
mics
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/5
603467x1.jpg
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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

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Normalization

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

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Normalization Cont.

• Quantile Normalization
• Variance Stabilizing Normalization
• Probe Model Based Normalization

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Nomalization Based on Probe Sequences

• Model the probe behavior based on probe
  sequence for Affymetrix arrays

Log(PM) nucleotide NucleotideCount2
log(probeCopy) e

• 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,s2).
Johnson et al (2006) PNAS 103, 12457 Song et al
(2007)Genome Biology.8R178
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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.
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Other Special Properties Cont.

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

ChIP-DNA
Noise
Probes Chromosome
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Smoothing
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Peak Call

• Identify regions that show epigenetic changes.

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Results Visualization
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Cisgenome http//www.biostat.jhsph.edu/hji/cisgen
ome/ Ji et al (2008) Nature Biotechnology. 26,
1293
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Software Packages and Comparisons
Johnson et al (2008) Genome Research 18 393
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Array Platform Comparisons
Johnson et al (2008) Genome Research 18 393