Presentation on theme: "Introduction to Epigenetics/Epigenomics Xiangqin Cui Department of Biostatistics University of Alabama at Birmingham Workshop on Statistical Genetics and."— Presentation transcript:
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 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
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)
siRNA Mediated Heterochromatin Maintenance
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
Hybridization to microarrays Enrichment for methylated DNA Labeling Genomic DNA
Zilberman and henikoff (2007) Development 134, 3959
Technologies for Interrogating Epigenetics/Epigenomics ChIP-chip
Technologies for Interrogating Epigenetics/Epigenomics 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 + NucleotideCount 2 + 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,σ 2 ).
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 Probes Chromosome ChIP-DNA Noise
Peak Call Identify regions that show epigenetic changes.
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