Establishment of Cell Identity in Drosophila Embryos

1. Establishment of Cell Identity in Drosophila Embryos Segment identity is established by sequential spatially-localized expression of specific genes Regulatory genes are expressed transiently Transcriptional memory is maintained throughout development from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-24

2. Misexpression of Homeotic Genes Lead to Morphological Abominations from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-25

3. Polycomb and Trithorax Complexes Prevents changes in cell identity by preserving transcription patterns Chromatin is altered in a heritable manner Polycomb-group Proteins Maintains a silenced state Prevents chromatin remodelling Trithorax-group Proteins Maintains an active state Counteracts the action of PcG proteins Memory system composed of PcG and trxG complexes is linked to the histone code

4. Polycomb Group Complexes on Chromatin in Drosophila PcG proteins are recruited to Polycomb response elements E(z) of PRC2 trimethylates H3K27 Pc of PRC1 is recruited to H3K27me3 dRING on PRC1 ubiquitylates H2AK119 H3K27me3 is segregated to both daughter chromosomes to maintain repression from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)

5. Recruitment of PRC2 to Chromatin in Mammals PRC2 can be recruited to a PRE by transcription factors or long ncRNAs from Morey and Helin, Trends Biochem.Sci. 35, 323 (2010)

6. PRC1 and PRC2 Promote Chromatin Compaction from Bantignies and Cavalli, Trends Genet. 27, 454 (2011) Chromatin compaction reinforces PcG silencing and maintains repressive domains

7. Co-suppression Increase in gene copy number results in decreased expression Dependent on PcG genes PcG complexes interact in trans from Pirrotta, Cell93, 333 (1998)

8. Formation of a Repressive Chromatin Hub PREs and promoters make contact and form chromatin loops CTCF and cohesin stabilize loops Chromatin loops are enriched in visible PcG bodies Loops could reinforce the memory of the silenced state from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)

9. Chromosome Kissing PcG proteins mediate long- range chromatin contacts Distant complexes of chromosome loops can interact with eath other from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)

10. Segment-specific Localization of Genes in PcG Bodies PcG genes maintain the regional identity of segments by repressing Hox genes in specific regions Hox genes are organized in two clusters in Drosophila PcG bodies are subdomains of the nucleus that correlate with gene repression Antp and AbdB genes are silenced in the head (B) Antp and Ubx are silenced in the posterior (C) from Hodgson and Brock, Cell144, 170 (2011)

11. HOTAIR Represses Genes in trans HOTAIR is a ncRNA expressed by the HOXC locus HOTAIR associates with PRC2 and recruits the complex to the HOXD locus HOTAIR acts in trans to repress the HOXD locus on a different chromosome

12. ncRNA Recruits PRC2 to Control Flowering Vernalization – Many plants flower in spring after prolonged low temperatures FLC2 represses genes required for flowering COLDAIR is a ncRNA that is induced by prolonged low temperatures COLDAIR acts in cis and recruits PRC2, promotes H3K27me3, and stably represses FLC from Heo and Sung, Epigenetics6, 433 (2011)

13. Propagation of H3K27 Methylation EED2 (ESC) binds H3K27me3 and enhances methylation activity of EZH2 [E(Z)] on a separate histone EZH2 [E(Z)] methylates H3K27 on adjoining nucleosomes and newly replicated chromatin from Richly et al., BioEssays32, 669 (2010)

14. Demethylation of H3K27me3 Promotes Gene Activation PRC2 is recruited to H3K27me3 to mediate gene repression UTX and JMJD3 are recruited to Hox promoters and reverse repression Change in cell fate is mediated by H3K27 demethylation and H3K4 methylation, whose activities are present in the same complex from Rivenbark and Strahl, Science318, 403 (2007)

15. Trithorax-group Protein Mechanism of Action TrxG proteins maintain an active transcriptional state TrxG proteins modify histones, remodel chromatin, and oppose PcG-mediated gene silencing

16. The Viable Yellow Agouti Locus Agouti promotes yellow pigment formation on black hair shaft Wild-type mice have brown fur due to Agouti expression from hair cell-specific promoter Avy contains an IAP insertion that contains a promoter expressed in all cells from Dolinoy, Nutr.Rev. 22(Suppl. 1),S7 (2008)

17. Avy is a Metastable Epiallele Avy can be modified in a variable and reversible manner Methylation status of IAP determines the activity of the ectopic promoter Ectopic Agouti expression causes yellow fur, obesity, diabetes and tumorigenesis Avy can be used as an epigenetic biosensor to study the nutritional and environmental influences on the fetal epigenome from Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)

18. Maternal Nutrition Alters Gene Expression by Epigenetic Modification Feeding of pregnant Avy/a mice with methyl-rich supplements repress the ectopic Avy promoter Offspring of diet-supplemented mice have brown coat color and methylated IAP from Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)

19. Progression of Epigenetic Changes in IUGR Rats Pdx1 is a transcription factor necessary for b-cell function Intrauterine growth restriction recruits histone deacetylases that prevents USF-1 binding Altered histone methylation reinforces Pdx1 repression Recruitment of DNMT3A locks Pdx1 in a silent state The result is defective glucose homeostasis from Pinney and Simmons, Trends Endocrinol.Metab. 21, 223 (2009)

20. Somatic Cell Reprogramming Pleuripotency genes in somatic cells have methylated CpG islands Epigenetic marks must be reset to generate induced pleuripotent stem (iPS) cells Repressive histone methylation marks must be removed, followed by removal of DNA methylation which activates the gene from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009)

21. Epigenetics and Heart Failure Brg1, a SWI/SNF component, is activated by cardiac stress Brg1 suppresses expression of a CKI to promote myocyte proliferation Brg1 promotes reprogramming to an embryonic state of transcription Brg1 forms a complex with HDAC and PARP and triggers a shift from a-myosin heavy chain expression to b-myosin heavy chain expression from Hang et al., Nature 466, 62 (2010)

22. Epigenetic Modifications May Drive Cognitive Decline Chromatin remodeling in the hippocampus is necessary for stabilizing long term memories Aged mice have lower H4K12 acetylation HDAC inhibitor restores H4K12 acetylation and improved memory function from Sweatt, Science328, 701 (2010)

23. Prion Epigenetics Prions template conformational conversion of other molecules of the same protein Prions are formed through an oligomeric nucleus, and the elongating polymer is severed by protein remodeling factors Prions are disseminated to daughter cells during cell division from Halfmann and Lindquist, Science330, 629 (2010)

24. Stress Accelerates Prion Appearance Abrupt changes have consequences for protein folding Prion-free cells are adapted to environment 1, but poorly adapted to environment 2 Prion formation and disappearance provide fitness advantages in different environments from Halfmann and Lindquist, Science330, 629 (2010) Prions connect environmental conditions to acquisition and inheritance of new traits