introduction to epigenetics/epigenomics xiangqin cui department of biostatistics university of...
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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
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.
Natural Roles of DNA Methylation in Mammalian System
Imprinting
X chromosome inactivation
Heterochromatin maintenance
Developmental controls
Tissue specific expression controls
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 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)
Technologies for Studying Epigenetics/Epigenomics
DNA Methylation
Irizarry et. Al. (2008) Genome Research 18(5):780
Microarray or deep 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
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 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
Cisgenome http://www.biostat.jhsph.edu/~hji/cisgenome/ Ji et al (2008) Nature Biotechnology. 26, 1293