1. Organism Estimated size (in bases) Estimated gene # Average gene density/base Diploid chromosome # Human2.9 x 10 9 ~30,0001/100,00046 Rat2.8 x 10 9 ~30,0001/100,00042 Mouse2.5 x 10 9 ~30,0001/100,00040 Drosophila1.8 x 10 8 13,6001/9,0008 Arabidopsis1.2 x 10 8 25,5001/4,00010 C. elegans9.7 x 10 7 19,1001/5,00012 S. cerevisiae1.2 x 10 7 6,3001/2,00032 E. coli4.7 x 10 6 3,2001/14001 H. influenzae1.8 x 10 6 1,7001/10001 Genomes http://www.ornl.gov

2. 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 Each cell within an organism contains a complete genome, but only deploys a fraction of the genes

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

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

6. DNA is embedded in chromatin

7. 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

8. 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

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

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

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

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

13. embryogametes embryo gametes Germ cells act to maintain the species somatic cells

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

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

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

17. ~20,000 genes in the worm genome ~18,000 genes on the array C. elegans DNA microarrays

18. wild type no germ line (glp-4) Germline mutant comparisons vs. sperm only (fem-3gf) oocytes only (fem-1lf) vs.

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

20. Sperm genes are different from oogenic germline genes

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

22. Why?

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

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

25. Hermaphrodite X is silenced early in meiotic prophase but not late Transgene 1 3 4 25 6 BA C D diplotene inactive transgene active transgene diakinesis -H3methylK4 