Sequencing Genomes1) Map the genome2) Prepare an AC library3) Order the library

4) Subdivide each AC into lambda contigs

5) Subdivide each lambda into plasmids

6) sequence the plasmids

Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing

Using the genomeStudying expression of all genes simultaneously

1. Microarrays: “reverse Northerns”2. High-throughput sequencing• “Re-sequencing” to detect variation

Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing•“Re-sequencing” to detect variation•Sequencing all mRNA to quantitate gene expression

Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing•“Re-sequencing” to detect variation•Sequencing all mRNA to quantitate gene expression•Sequencing all mRNA to identify and quantitate splicing variants

Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing•“Re-sequencing” to detect variation•Sequencing all mRNA to quantitate gene expression•Sequencing all mRNA to identify and quantitate splicing variants•Sequencing all RNA to identify and quantitate ncRNA

Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing3. Bisulfite sequencing to detect C methylation

Using the genomeBisulfite sequencing to detect C methylation

Using the genomeBisulfite sequencing to detect C methylationChIP-chip or ChIP-seq to detect chromatin modifications: 17 mods are associated with active genes in CD-4 T cells

Using the genome• various chromatin modifications are associated with activated & repressed genes•Acetylation, egH3K9Ac, is associated with active genes

Using the Genome•various chromatin modifications are associated with activated & repressed genes •Acetylation, egH3K9Ac, is associated with active genes• Phosphorylation of H2aS1, H2aT119, H3T3, H3S10 & H3S28 shows condensation

Using the Genome•Acetylation, egH3K9Ac, is associated with active genes• Phosphorylation shows condensation• Ubiquitination of H2A and H2B shows repression & marks DNA damage

Using the Genome•Acetylation, egH3K9Ac, is associated with active genes• Phosphorylation shows condensation• Ubiquitination of H2A and H2B shows repression• Methylation is more complex: H3K36me3 = on•H3K27me3 = off

Using the GenomeMethylation is more complex:•H3K36me3 = on•H3K27me3 = off•H3K4me1 = off•H3K4me2 = primed•H3K4me3 = on

Histone codeModifications tend to group together: genes with H3K4me3 also have H3K9ac

Histone codeModifications tend to group together: genes with H3K4me3 also have H3K9acCytosine methylation is also associated with repressed genes

Generating the histone codeHistone acetyltransferases add acetic acid

Generating the histone codeHistone acetyltransferases add acetic acidMany HAT proteins: mutants are very sick!

Generating the histone codeHistone acetyltransferases add acetic acidMany HAT proteins: mutants are very sick!HATs are part of many complexes

Generating the histone codeBromodomains specifically bind acetylated lysines

Generating the histone codeBromodomains specifically bind acetylated lysinesFound in transcriptional activators & general TFs

Generating the histone codeacetylated lysinesDeacetylases “reset” by removing the acetate

Generating the histone codeacetylated lysinesDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!

Generating the histone codeDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!Many drugs are histone deacetylase inhibitors

Generating the histone codeDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!Many drugs are histone deacetylase inhibitorsSAHA = suberanilohydroxamic acid = vorinostatMerck calls it Zolinza, treats cutaneous T cell lymphoma

Generating the histone codeDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!Many drugs are histone deacetylase inhibitorsSAHA = suberanilohydroxamic acid = vorinostatMerck calls it Zolinza, treats cutaneous T cell lymphomaBinds HDAC active site & chelates Zn2+

Generating the histone codeWhen coupled SAHA to PIPS (pyrrole-imidazole Polyamides) got gene-specific DNA binding & gene activation

Generating the histone codeCDK8 kinases histones to repress transcription

Generating the histone codeCDK8 kinases histones to repress transcriptionAppears to interact with mediator to block transcription

Generating the histone codeCDK8 kinases histones to repress transcriptionAppears to interact with mediator to block transcriptionPhosphorylation of Histone H3 correlates with activation of heat shock genes!

Generating the histone codeCDK8 kinases histones to repress transcriptionAppears to interact with mediator to block transcriptionPhosphorylation of Histone H3 correlates with activation of heat shock genes!Phosphatases reset the genes

Generating the histone codeRad6 proteins ubiquitinate histone H2B to repress transcription

Generating the histone codeRad6 proteins ubiquitinate histone H2B to repress transcriptionPolycomb proteins ubiquitinate histone H2A to silence genes