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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.

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Introduction to Epigenetics/Epigenomics

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  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 RNA Interference Gene Expression DNA Methylation Histone Modifications

  4. DNA Methylation Hypomethylation Hypermethylation http://www.cellscience.com/reviews7/Taylor1.jpg

  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 http://porpax.bio.miami.edu/~cmallery/150/gene/c7.19.4.histone.mod.jpg

  9. Histone Modifications http://www.nature.com/nsmb/journal/v14/n11/images/nsmb1337-F1.gif

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

  11. Histone Modifications in Relation to Gene Transcription Li e. al. (2007) Cell 128, 707

  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) http://www.nature.com/ncpneuro/journal/v3/n7/images/ncpneuro0551-f1.jpg

  14. siRNA Mediated Heterochromatin Maintenance

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

  16. Bisulfite Sequencing

  17. Bisulfite Sequencing

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

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

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

  21. Hybridization to microarrays Genomic DNA Enrichment for methylated DNA Labeling Labeling

  22. Zilberman and henikoff (2007) Development 134, 3959

  23. Technologies for Interrogating Epigenetics/Epigenomics ChIP-chip http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg

  24. 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

  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 • 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

  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 ChIP-DNA Noise Probes Chromosome

  31. Smoothing

  32. Peak Call • Identify regions that show epigenetic changes.

  33. Results Visualization

  34. Cisgenome http://www.biostat.jhsph.edu/~hji/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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