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Genomes

Genomes. http://www.ornl.gov. Each cell within an organism contains a complete genome, but only deploys a fraction of the genes. Positive: selective activation of a gene at a particular place and time to produce a gene product

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Genomes

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  1. Genomes http://www.ornl.gov

  2. Each cell within an organism contains a complete genome, but only deploys a fraction of the genes Positive: selective activation of a gene at a particular place and time to produce a gene product Negative: selective silencing of a gene or removal of a gene product at a particular place and time

  3. Gene expression regulation at the level of DNA Sequence-dependent cis-acting factors: promoters/regulatory sequences of genes trans-acting factors: proteins and RNAs that bind cis-elements and promote or repress gene expression DNA methylation: methylation of CpG islands promotes silencing Range: Usually functions at level of single gene, or at most a local group of genes

  4. Regulatory network from early sea urchin development Levine and Davidson, PNAS, 2005

  5. DNA is embedded in chromatin

  6. Regulation of gene expression at the level of chromatin Sequence-independent linker histones: control DNA compaction and accessibility to trans-acting factors post-translational modifications of histone tails: control compaction of DNA and serve as docking sites for trans-acting factors Range: Can act at the level of a single gene, often acts over groups of genes and over larger domains (20-200kb), and can affect gene expression over an entire chromosome

  7. Regulation of gene expression at the level of RNA mRNA Stability/decay: length of poly A tail, binding of proteins and RNAs that either protect or degrade transcripts Subcellular localization: sequestration by proteins, ribosome stalling

  8. RNA also acts as a regulator of gene expression miRNA siRNA

  9. DNA is silenced at the level of histone modifications through an RNAi-like mechanism centromere repeats

  10. Genomics Technologies systematic gene mutation/RNAi screens sequence analyses Functional Networks global protein analysis genome-wide expression profiling genotyping nucleic acid/ protein interactions

  11. Genome organization is non-random with respect to gene expression in multiple organisms local chromatin chromosome

  12. Germ cells act to maintain the species somatic cells somatic cells gametes embryo gametes embryo

  13. C. elegans hermaphrodite germ line stem cells meiosis embryos sperm oocytes

  14. germline formation during larval development L1 L2 L3 L3/L4 late L4 meiosis stem cells young adult oocytes sperm somatic gonad

  15. Levels of gene regulation in the germline Chromosome: silencing of the X Large domain: clustering of germline-expressed genes Local domain: operon formation stem cells meiosis embryos sperm oocytes

  16. C. elegans DNA microarrays ~20,000 genes in the worm genome ~18,000 genes on the array

  17. Germline mutant comparisons spermonly (fem-3gf) oocytesonly (fem-1lf) vs. wild type no germ line (glp-4) vs.

  18. C. elegans hermaphrodite germ line oogenic germline 3003 genes sperm 1380 genes

  19. Sperm genes are different from oogenic germline genes

  20. Large-scale in situ hybridization distal distal+ proximal proximal NextDB: Nematode EXpression paTtern DataBase Kohara lab Japan 98% of all genes in oogenic germline category show germline expression by in situ distal proximal

  21. Why?

  22. The oogenesis genes on the X chromosome express at lower levels than those on the autosomes A B

  23. The hermaphrodite paired X does not stain with antibodies against transcriptionally active chromatin conformation α DNA Merge -H3methylK4 diplotene stem cells diakinesis pachytene

  24. A B Transgene 1 2 5 6 3 4 C D Hermaphrodite X is silenced early in meiotic prophase but not late diakinesis diplotene inactive transgene diakinesis diakinesis active transgene  -H3methylK4

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