Genome-wide Association Studies (GWAS) Pasieka, Science Photo Library
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1 Lecture 5
2 Genome-wide Association Studies (GWAS) Pasieka, Science Photo Library
3 Chi-squared test to evaluate whether the odds ratio is different from 1. Corrected for multiple testing Source: wikipedia.org Need to watch out for potential bias such as population stratification
4 An example of GWAS report risk SNPs associated with systemic sclerosis Radstake et al., Nature Genetics 42, (2010)
5 Source:
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8 Most risk SNPs are associated with low odds ratios
9 Most risk associated SNPs are outside of coding regions Total: 531 SNP-disease associations Hindorff et al., PNAS 2009 vol. 106 (23) pp
10 Hypothesis These non-coding risk associated SNPs may affect transcriptional regulatory processes
11 Transcription in Eukaryotes Takes place in the nucleus The lower strand is used as template RNA is made from 5 to 3 direction Multiple steps Class II genes are transcribed by RNAP2 and requires posttranscriptional processing
12 Transcription al initiation RNAPII loading to promoters requires general transcription factors (GTF)
13
14 cis-regulatory elements in the genome Insulator (Barrier) Promoter Enhancer Insulator (Enhancer blocking) Insulator (Barrier) Silencing element
15 Promoters Promoters are where transcription initiates Many promoter elements have been found TATA box was discovered in 1979 by comparison of a number of mrna start sites
16 How to Locate promoters in the human genome? Determine the full length transcripts and align to the genome Cap Analysis of Gene Expression
17 How to Locate promoters in the human genome? Determine the full length transcripts and align to the genome Locate promoters based on binding sites of the pre-initiation complex
18 Locate promoters in the human genome Locate promoters based on binding sites of the pre-initiation complex ChIP-chip analysis is a general approach for mapping transcription factor binding sites ChIP-seq provides a more cost-effective, genome-wide approach
19 cis-regulatory elements in the genome Insulator (Barrier) Promoter Enhancer Insulator (Enhancer blocking) Insulator (Barrier) Silencing element
20 Model of enhancer function Coactivators RNAP RNAP
21 Transcription Factors in Eukaryotic Genomes Source: * Riechmann et al., Science (2000) ** BioBASE (TRANSFAC database) *** Tupler et al. Nature (2001)
22 Transcription factor classification
23 Separate DNA binding and activating regions of Gal4p DNA binding Dimerization Activation domains Gal80-interacting domain
24 Separate DNA binding and activating regions of Gal4p - domain swap experiments
25 p300 is a transcriptional co-activator -- MoBio/Free/Ch4G2.htm
26 Locating enhancers by mapping the p300 binding sites Visel et al., Nature 2009
27 Chromatin signature of promoters and enhancers Enhancers are marked by H3K4me1 but NOT H3K4me3 Promoters are marked by H3K4me3 and a depletion of H3K4me1 Heintzman et al., Nature Genetics, 2007
28 Chromatin-based predictions of promoters and enhancers Promoter Enhancer H3K4me1 H3K4me3 P1 P2 P3 H3K4me1 H3K4me3 E1 E2 E3 Heintzman et al., Nature Genetics, 2007
29 cis-regulatory elements in the genome Insulator (Barrier) Promoter Enhancer Insulator (Enhancer blocking) Insulator (Barrier) Silencing element
30 Barrier Elements Gaszner and Felsenfeld Nature Reviews Genetics advance online publication; published online 15 August 2006 doi: /nrg1925
31 Gaszner and Felsenfeld Nature Reviews Genetics advance online publication; published online 15 August 2006 doi: /nrg1925
32 Gaszner and Felsenfeld Nature Reviews Genetics advance online publication; published online 15 August 2006 doi: /nrg1925
33 Cohesins and CTCF colocalize on insulators
34
35 Hypothesis These non-coding risk associated SNPs may affect transcriptional regulatory processes
36 Risk associated SNPs are enriched at promoter regions
37
38 Disease associated SNPs are enriched at enhancers identified in specific cell types Ernst et al., Nature 2011
39 Summary Much of the non-coding sequences in the human genome are likely involved in transcriptional regulation Sequence variations within these sites could contribute to a variety of human diseases and phenotypic variations A major challenge is to link the sequence variations within the distal regulatory sequences to variations in expression of target genes
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