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. 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)

10. Role of Long-Range Chromosome Interactions in Obesity Single-nucleotide changes in an intron of the FTO gene have a strong association with obesity Expression of IRX3 correlates with body weight An enhancer in the FTO intron interacts with the IRX3 promoter from Gorkin and Ren, Nature507, 309 (2014) Sequence changes in the FTO enhancer alters IRX3 expression

11. HOTAIR Represses Genes in trans HOTAIR is a lncRNA expressed by the HOXC locus HOTAIR associates with PRC2 and LSD1 and recruits the complex to the HOXD locus HOTAIR acts in trans to repress the HOXD locus on a different chromosome from Kugel, Trends Biochem.Sci. 37, 144 (2012)

12. ncRNA Recruits PRC2 to Control Flowering Vernalization – Many plants flower in spring after prolonged low temperatures FLC represses genes required for flowering and is highly expressed in the fall COOLAIR is an antisense RNA that inhibits FLC transcription 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 promote H3K4me

16. Effect of Transcription on Epigenetic Modifications Transcription factor binding leads to histone modifications that promotes expression of neighboring genes from Furey and Sethupathy, Science 342, 705 (2013)

17. 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)

18. 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)

19. 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)

20. Epigenetic Inheritance in Mammals? There are several examples of nongenetic germline transmission of traits resulting from pesticides, metabolic state, and behavior The majority of sperm DNA is repackaged by protamines DNA is demethylated in the single-celled embryo DNA methylation is gradually reestablished in the early embryo A second round of DNA demethylation occurs in the developing germline from Hughes, Nature507, 22 (2014)

21. The Link Between Intrauterine Growth Retardation and T2D Infants born during the Dutch Hunger Winter had lower birth rates, but had impaired glucose tolerance later in life

22. 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)

23. Parental Experiences Impact the Behavior of the Offspring from D’Urso and Brickner, Trends Genet. 30, 230 (2014) Stress reduces maternal care. Pups are more sensitive to stress and display reduced maternal care, even in the absence of stress The altered gene expression of target genes (GR in the hippocampus) is mediated by DNA methylation and histone modifications Expression patterns are inherited in future generations

24. 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)

25. 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)

26. 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

27. Epigenome Modification and Interpretation Writers catalyze posttranslational modifications on DNA or proteins Erasers remove posttranslational modifications and DNA methylation Readers interpret the modifications and alter chromatin structure from Helin and Dhanak, Nature502, 480 (2013)

28. The Metabolic State is Linked to Epigenetic Modifications Most chromatin-modifying enzymes use metabolites as co-factors The metabolic status of a cell can transduce a transcriptional response from Gut and Verdin, Nature502, 489 (2013)

29. The Complete Demethylation Pathway of 5mC 5mC is oxidated iteratively by TET 5hmC is reverted to unmodified C by passive dilution during DNA replication Oxidative products are excised by thymine DNA glycosylase and repaired by BER from Kohli and Zhang, Nature502, 472 (2013)

30. DNA Methylation Dynamics During Epigenetic Reprogramming Epigenetic memory must be erased for cells to achieve pleuripotency Maternal DNA undergoes passive demethylation in pre-implantation embryos Paternal genome is actively demethylated by TET3 DNA methylation patterns are re-established by de novo DNMTs at the blastocyst stage Primordial germ cells are demethylated through a TET-independent and a TET-mediated oxidative pathway from Kohli and Zhang, Nature502, 472 (2013)

31. DNA Methylation During Human Embryogenesis from Reik and Kelsey, Nature511, 540 (2014) DNA methylation is largely lost after fertilization, mostly from the paternal genome Demethylation of the maternal genome continues until the blastocyst stage DNA becomes remethylated upon differentiation