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

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Mar 15, 2023 39 likes •189 views

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

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START START

FOUNDATIONS FOUNDATIONS How How-

to 1

to 1 FORMATION FORMATION How How-

to 2

to 2 SYSTEMS SYSTEMS PROBLEMS PROBLEMS Future of Future of

BIOCHEM GENETICS CELL BIO.

MOL. BIO

STEM CELLS, CLONING

REC. DNA

C E L L T Y P E 3 D

STRUCTURE

F E R T I L I

A T I O N SYSTEMS VIRUSES IMMUNE

LIFE LIFE

NERVOUS CANCER

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

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

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4 Observing gene expression in living cells www.singerlab.org

Nucleoplasm Cytoplasm

Peroxisomes

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

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

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

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

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

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

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11 What graphical model best encodes this data?

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Chromosomal Position (bp)

266000 265500 266500 267000 267500 268000 268500 269000 269500 270000

SIP4 --> ARG3 -->

GCN4 Fold Enrichment (IP/WCE) 5 10 15 20 25 30 35 ORF Location

High-resolution view of Gcn4/genome interaction

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13 CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATA GCAGTGAATTTTCGAGGGTCACGTCGTGACTCATAT GCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAA ACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCA GTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTT TGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCG GCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTA TATAAATCGACTTTTCACCTCTAAAGGCAGTTTATT CCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCA ATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAAC TTGTACACTCGTTACCATGTCAACCACAGCATCCAC GCCTTCATCTTTACGTCATTTGATTTCTATAAAAGA TCTTTCTGATGAAGAATTC Arg3 Coding Sequence GCN4 binding site

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14 73 modules 401 genes 51 TFs

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