LIFE LIFE STEM Future of Future of CELLS, CLONING How- -to 2 - PowerPoint PPT Presentation

LIFE LIFE STEM Future of Future of CELLS, CLONING How- -to 2 to 2 How SYSTEMS 3 D PROBLEMS PROBLEMS STRUCTURE CANCER NERVOUS FORMATION FORMATION VIRUSES C E L L SYSTEMS SYSTEMS T Y P E How- -to 1 to 1 How REC. DNA IMMUNE F E R T I L I - Z A T I O N BIOCHEM GENETICS MOL. BIO CELL BIO. START START FOUNDATIONS FOUNDATIONS 1

CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATA GCAGTGAATTTTCGAGGGTCACGTCGTGACTCATAT GCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAA ACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCA GTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTT TGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCG GCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTA TATAAATCGACTTTTCACCTCTAAAGGCAGTTTATT CCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCA ATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAAC TTGTACACTCGTTACCATGTCAACCACAGCATCCAC GCCTTCATCTTTACGTCATTTGATTTCTATAAAAGA TCTTTCTGATGAAGAATTC 2

CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATA GCAGTGAATTTTCGAGGGTCACGTCGTGACTCATAT GCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAA ACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCA GTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTT TGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCG GCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTA TATAAATCGACTTTTCACCTCTAAAGGCAGTTTATT CCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCA ATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAAC TTGTACACTCGTTACC ATGTCAACCACAGCATCCAC GCCTTCATCTTTACGTCATTTGATTTCTATAAAAGA TCTTTCTGATGAAGAATTC Arg3 Genomic DNA (beginning) 3

Observing gene expression in living cells www.singerlab.org Peroxisomes Nucleoplasm Cytoplasm 4

Imaged every 2.5 minutes for 4 hrs Cyan FP-laci Cyan FP-peroxisomes Yellow FP-MS2 5 DNA Protein RNA

CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATA GCAGTGAATTTTCGAGGGTCACGTCGTGACTCATAT GCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAA ACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCA GTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTT TGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCG GCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTA TATAAATCGACTTTTCACCTCTAAAGGCAGTTTATT CCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCA ATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAAC TTGTACACTCGTTACC ATGTCAACCACAGCATCCAC GCCTTCATCTTTACGTCATTTGATTTCTATAAAAGA TCTTTCTGATGAAGAATTC Arg3 Genomic DNA (beginning) 6

Clustering data reveals patterns Rows are genes Columns are expression values at time points 1 – 30 (synthetic data) Input 7

Clustering data reveals patterns Rows are genes Columns are expression values at time points 1 – 30 (synthetic data) Input 8

Clustering data reveals patterns Rows are genes Columns are expression values at time points 1 – 30 (synthetic data) Clustered Input 9

time 1 - 24 Clustering expression gene 1 data from . synchronized cells . reveals cell cycle . dependant genes . . . Red - gene up . . Green - gene down . . . . . . gene 800 10

What graphical model best encodes this data? 11

High-resolution view of Gcn4/genome interaction 35 30 25 20 GCN4 Fold Enrichment (IP/WCE) 15 10 5 Chromosomal Position (bp) 265500 266000 266500 267000 267500 268000 268500 269000 269500 270000 SIP4 --> ARG3 --> ORF Location 12

GCN4 binding site CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATA GCAGTGAATTTTCGAGGGTCACGTCG TGACTCA TAT GCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAA ACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCA GTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTT TGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCG GCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTA TATAAATCGACTTTTCACCTCTAAAGGCAGTTTATT CCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCA ATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAAC TTGTACACTCGTTACC ATGTCAACCACAGCATCCAC GCCTTCATCTTTACGTCATTTGATTTCTATAAAAGA TCTTTCTGATGAAGAATTC Arg3 Coding Sequence 13

73 modules 401 genes 51 TFs 14

15 http://www.sciencemag.org./cgi/reprint/295/5560/1669.pdf?ck=nck