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Introduction to Epigenetics/Epigenomics Xiangqin Cui Department of Biostatistics University of Alabama at Birmingham Workshop on Statistical Genetics and.

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Presentation on theme: "Introduction to Epigenetics/Epigenomics Xiangqin Cui Department of Biostatistics University of Alabama at Birmingham Workshop on Statistical Genetics and."— Presentation transcript:

1 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

2 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.

3 Epigenetics Mechanisms Gene Expression RNA Interference Histone Modifications DNA Methylation

4 Hypomethylation Hypermethylation

5 Natural Roles of DNA Methylation in Mammalian System  Imprinting  X chromosome inactivation  Heterochromatin maintenance  Developmental controls  Tissue specific expression controls

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

7 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

8 Histone Modifications

9 Histone Modifications

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

11 Histone Modifications in Relation to Gene Transcription

12 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)

13 RNA Interference (RNAi)

14 siRNA Mediated Heterochromatin Maintenance

15 Technologies for Studying Epigenetics/Epigenomics DNA Methylation Irizarry et. Al. (2008) Genome Research 18(5):780 Microarray or deep sequencing

16 Bisulfite Sequencing

17

18 5’ 3’ Expression array Exon array Splicing array Promoter array Tiling array exon intron Global Interrogation of DNA Methylation using Microarrays promoter

19 Methylated/Unmethylated DNA Enrichment Methods Restriction Enzyme Based Enrichment Methods Zilberman and henikoff (2007) Development 134, 3959

20 Methylated/Unmethylated DNA Enrichment Methods Zilberman and henikoff (2007) Development 134, 3959 Immunoprecipation Based Method

21 Hybridization to microarrays Enrichment for methylated DNA Labeling Genomic DNA

22 Zilberman and henikoff (2007) Development 134, 3959

23 Technologies for Interrogating Epigenetics/Epigenomics ChIP-chip

24 Technologies for Interrogating Epigenetics/Epigenomics ChIP-chip Antibody specific to one type of histone modification Histone Modifications ChIP-seq Deep sequencing

25 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

26 Normalization The loess assumption is sometimes violated in ChIP-chip data

27 Normalization Cont. Quantile Normalization Variance Stabilizing Normalization Probe Model Based Normalization

28 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 ).

29 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.

30 Other Special Properties Cont. Map high intensity probes back to the genome Locate TF binding location Probes Chromosome ChIP-DNA Noise

31 Smoothing

32 Peak Call Identify regions that show epigenetic changes.

33 Results Visualization

34 Cisgenome Ji et al (2008) Nature Biotechnology. 26, 1293

35 Software Packages and Comparisons Johnson et al (2008) Genome Research 18: 393

36 Array Platform Comparisons Johnson et al (2008) Genome Research 18: 393


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