1. Introduction to the Tsinghua University ENCODE Journal Club Monica C. Sleumer ( 苏漠 ) 2012-09-24

2. Tsinghua ENCODE Journal Club Objectives Read and discuss all 31 ENCODE papers Discuss the 13 “Threads” in the ENCODE explorer Discuss the overall meaning of the ENCODE project – Media reactions Understand how to apply ENCODE findings to our own research Generate a long-term repository for our findings on our journal club website: bioinfo.au.tsinghua.edu.cn/encode/

3. Human Genome 3,101,804,739 base pairs 22 chromosomes plus X and Y 21,224 protein-coding genes 15,952 ncRNA genes 3–8% of bases are under selection – From comparative genomic studies Question: What is the genome doing?

4. ENCODE Project Objectives Find all functional elements – Bound by specific proteins – Transcribed – Histone modifications – DNA methylation Use this information to annotate functional regions – Genes (coding and non-coding) – Promoters – Enhancers – Specific transcription factor binding sites – Silencers – Insulators – Chromatin states Cross-reference data from other studies – Comparative genomics – 1000 Genomes Project – Genome-wide association studies (GWAS) Different combination in each cell type

5. ENCODE projects ENCODE pilot project: 1% of the genome 2003-2007 modENCODE: Drosophila and C. elegans Mouse ENCODE in progress? ENCODE main project 2007-2012 – 1649 dataset-generating experiments – 147 cell types – 235 antibodies and assay protocols – 450 authors – 32 institutes 31 publications 2012-09-06 – 6 in Nature – all discussed on 2012-09-19 – 18 in Genome Research – 6 in Genome Biology – one of these discussed today – 1 in BMC Genetics www.nature.com/encode/category/research-papers

6. Materials 147 types of human cell lines, 3 priority levels Tier 1 cell lines: top priority for all experiments Tier 2 cell lines to be done after Tier 1 (next slide) Tier 3: any other cell lines NameDescriptionLineageTissueKaryotype GM12878 B-lymphocyte, lymphoblastoid, Epstein-Barr Virus, 1000 Genomes Project mesodermbloodnormal H1-hESCembryonic stem cells inner cell mass embryonic stem cellnormal K562 leukemia, 53-year-old female with chronic myelogenous leukemia mesodermbloodcancer

7. Tier 2 Cell Lines http://encodeproject.org/ENCODE/cellTypes.html

8. Methods RNA-SeqDifferent fractions of RNA -> sequencing CAGE5’ Capped RNA sequencing RNA-PETSequencing 5’ Cap plus poly-A tail ChIP-seqChromatin immunoprecipitation of a DNA binding protein -> sequencing DNase-seqCut exposed DNA with DNase I -> sequencing FAIRE-seqNucleosome-depleted DNA -> sequencing RRBSBisulphite treatment: unmethylated C->U -> sequencing 3C,5C, ChIA-PET Chromatin interactions -> sequencing Wu Dingming 2012-09-19 Ma Xiaopeng 2012-09-19 Guo Weilong He Chao 2012-09-19 Li Yanjian 2012-09-19 All methods (DNA or RNA sequencing) can be traced back to a genomic location Findings vary between cell types

9. Primary Findings 80.4% of the human genome is doing at least one of the following: – Bound by a transcription factor – Transcribed – Modified histone 99% is within 1.7 kb of at least one of the biochemical events 95% within 8 kb of a DNA–protein interaction or DNase I footprint 7 chromatin states: – 399,124 enhancer-like regions – 70,292 promoter-like regions Correlation between transcription, chromatin marks, and TF binding Functional regions contain lots of SNPs – Disease-associated SNPs in non-coding regions tend to be in functional elements

10. Applications Visible as genome tracks in UCSC Gene or pathway of interest Mutation from – Cancer sequencing – Genome-wide association studies – Find out what that part of the genome is doing Compare with your cancer data (RNA-seq) Comparative genome analysis

11. Online Resources Interactive app on Nature ENCODE main page Journal club website: bioinfo.au.tsinghua.edu.cn/encode/ www.nature.com/encode/

12. bioinfo.au.tsinghua.edu.cn/encode/

13. Next ENCODE Journal Club Meeting Suggested meeting day: Thursday ( 周四 ) 2012-10-11 LIANG Zhengyu? One more volunteer speaker needed