Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each...
-
Upload
jasmin-jennings -
Category
Documents
-
view
219 -
download
2
Transcript of Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each...
![Page 1: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/1.jpg)
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
![Page 2: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/2.jpg)
Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing
![Page 3: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/3.jpg)
Using the genomeStudying expression of all genes simultaneously
1. Microarrays: “reverse Northerns”2. High-throughput sequencing• “Re-sequencing” to detect variation
![Page 4: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/4.jpg)
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
![Page 5: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/5.jpg)
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
![Page 6: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/6.jpg)
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
![Page 7: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/7.jpg)
Using the genomeStudying expression of all genes simultaneously1.Microarrays: “reverse Northerns”2.High-throughput sequencing3. Bisulfite sequencing to detect C methylation
![Page 8: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/8.jpg)
Using the genomeBisulfite sequencing to detect C methylation
![Page 9: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/9.jpg)
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
![Page 10: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/10.jpg)
Using the genome• various chromatin modifications are associated with activated & repressed genes•Acetylation, egH3K9Ac, is associated with active genes
![Page 11: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/11.jpg)
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
![Page 12: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/12.jpg)
Using the Genome•Acetylation, egH3K9Ac, is associated with active genes• Phosphorylation shows condensation• Ubiquitination of H2A and H2B shows repression & marks DNA damage
![Page 13: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/13.jpg)
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
![Page 14: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/14.jpg)
Using the GenomeMethylation is more complex:•H3K36me3 = on•H3K27me3 = off•H3K4me1 = off•H3K4me2 = primed•H3K4me3 = on
![Page 15: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/15.jpg)
Histone codeModifications tend to group together: genes with H3K4me3 also have H3K9ac
![Page 16: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/16.jpg)
Histone codeModifications tend to group together: genes with H3K4me3 also have H3K9acCytosine methylation is also associated with repressed genes
![Page 17: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/17.jpg)
Generating the histone codeHistone acetyltransferases add acetic acid
![Page 18: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/18.jpg)
Generating the histone codeHistone acetyltransferases add acetic acidMany HAT proteins: mutants are very sick!
![Page 19: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/19.jpg)
Generating the histone codeHistone acetyltransferases add acetic acidMany HAT proteins: mutants are very sick!HATs are part of many complexes
![Page 20: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/20.jpg)
Generating the histone codeBromodomains specifically bind acetylated lysines
![Page 21: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/21.jpg)
Generating the histone codeBromodomains specifically bind acetylated lysinesFound in transcriptional activators & general TFs
![Page 22: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/22.jpg)
Generating the histone codeacetylated lysinesDeacetylases “reset” by removing the acetate
![Page 23: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/23.jpg)
Generating the histone codeacetylated lysinesDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!
![Page 24: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/24.jpg)
Generating the histone codeDeacetylases “reset” by removing the acetateDeacetylase mutants are sick!Many drugs are histone deacetylase inhibitors
![Page 25: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/25.jpg)
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
![Page 26: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/26.jpg)
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+
![Page 27: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/27.jpg)
Generating the histone codeWhen coupled SAHA to PIPS (pyrrole-imidazole Polyamides) got gene-specific DNA binding & gene activation
![Page 28: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/28.jpg)
Generating the histone codeCDK8 kinases histones to repress transcription
![Page 29: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/29.jpg)
Generating the histone codeCDK8 kinases histones to repress transcriptionAppears to interact with mediator to block transcription
![Page 30: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/30.jpg)
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!
![Page 31: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/31.jpg)
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
![Page 32: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/32.jpg)
Generating the histone codeRad6 proteins ubiquitinate histone H2B to repress transcription
![Page 33: Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into.](https://reader030.fdocuments.in/reader030/viewer/2022032611/56649cd75503460f9499f71a/html5/thumbnails/33.jpg)
Generating the histone codeRad6 proteins ubiquitinate histone H2B to repress transcriptionPolycomb proteins ubiquitinate histone H2A to silence genes