1. Heterochromatin Darkly stained and condensed Transcriptionally silent and silences adjacent genes Present at centromeres and telomeres HP1 interacts with H3 only when K9 is methylated Repressive structure can be propagated Euchromatic gene placed in heterochromatin is repressed from Lodish et al., Molecular Cell Biology, 6 th ed. Fig 6-33

2. Histone Modifications Associated with Heterochromatin and Euchromatin from Lodish et al., Molecular Cell Biology, 6 th ed. Fig 6-33

3. Initiation of Heterochromatin Assembly from Grewal and Gia, Nature Rev.Genet. 8, 35 (2007) Transcription factors and RNAi machinery bind to specific sequences or repetitive elements to recruit histone modifying enzymes Boundary elements prevent further heterochromatin spread HP1 recruits histone modifying enzymes to facilitate heterochromatin spread Modified histones recruit HP1

4. Propagation of Heterochromatin from Maison and Almounzi, Nature Rev.Mol.Cell Biol. 5, 296 (2004) Passage of the replication fork releases parental modified nucleosomes Nucleosome binding sites are created by recruitment of CAF1 by PCNA CAF1-bound HP1 recruits Suv39h, Dnmt1, and HDAC Methylated histones provide new HP1 binding sites Structural RNA associates

5. from Grewal and Gia, Nature Rev.Genet. 8, 35 (2007) Heterochromatin Functions DNA or H3 methylation recruits adaptors such as HP1 Adaptors recruit effectors that are involved in chromosome segregation, gene silencing, transcriptional activation, and histone modification

6. Role of RNAi in Heterochromatin Formation in S. pombe dsRNA is transcribed from centromeric repeats or synthetic hairpin RNAs dsRNA is processed to siRNA siRNA promotes H3 K9 methylation by Clr4 Methylated H3 K9 recruits Swi6 to form silenced chromatin Transcription of the top strand of centromeric repeats is repressed Rdp1 activity ensures continuous dsRNA synthesis Recruitment of Clr4 by Swi6 chromatin leads to spread of heterochromatin from Schramke and Allshire, Science 301, 1069 (2003)

7. Histone Acetylation Regulates SIR Complex Association with Chromatin from Grunstein, Cell 93, 325 (1998) Acetylation of histone H4 K12 facilitates binding of Sir complex if K16 is deacetylated

8. Formation of Telomeric Heterochromatin from Grunstein, Cell 93, 325 (1998) RAP1 binds to C 1-3 A repeats Recruits Sir proteins Overexpression of Sir3 causes spread of telomeric heterochromatin Silencing decreases exponentially with distance

9. Mechanism of Silencing at Telomeres Sir2 deacetylates histones Sir3,4 binds deacetylated histones and recruits additional Sir2 from Lodish et al., Molecular Cell Biology, 6 th ed. Fig 7-35

10. Insulators Prevent the Progression of Condensed Chromatin from West et al, Genes Dev. 16, 271 (2002) Insulators protect genes from inappropriate signals Insulators block the action of distal enhancers Insulators prevent the spreading of heterochromatin

11. gypsy Retrotransposon Contains an Insulator gypsy protects a transgene from position effects su(Hw) is necessary for enhancer blocking activity gypsy contains a su(Hw) binding site su(Hw) blocks the process that brings enhancer and promoter together Formation of insulator bodies at the nuclear periphery to divide the chromosome into looped domains Multiple su(Hw) binding sites can inhibit enhancer blocking activity

12. Models for Heterochromatin Barrier Formation from Donze and Kamakaka, BioEssays 24, 344 (2002) Stable block interrupts propagation of heterochromatin Active barrier recruits a complex containing chromatin remodeling activity

13. Epigenetics Heritable changes in gene function that cannot be explained by changes in gene sequences DNA methylation Polycomb and trithorax complexes

14. from Zhang, Science 320, 489 (2008) Epigenetic Modifications Within an Arabidopsis Chromosome Heterochromatin correlates with epigenetic marks

15. DNA Methylation Methylation at CpG residues Sites of methylation Inactive X Imprinted loci Transposon-derived sequences CpG islands Methylation patterns are reproduced at each round of cell division

16. from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009) Establishment of DNA Methylation Pattern Most CpGs are unmethylated before implantation RNA pol II recruits H3K4 methyltransferase DNMT3L only binds unmethylated H3K4 and recruits DNA methyltransferases

17. Mechanisms for Repression Mediated by MBD Proteins from Wade, BioEssays 23, 1131 (2001)

18. Rett Syndrome is linked to mutations in MECP2 on the X chromosome MeCP2 binds CpG residues and silences target genes such as BDNF and corticotropin-releasing hormone Neural activity triggers MeCP2 phosphorylation and target gene activation MeCP2 Regulates Gene Expression in Response to Neural Activity Hippocampal neurons grow dendrites with fewer branches when MeCP2 is blocked from Miller, Science 314, 1356 (2006) from Bienvenu and Chelly, Nature Rev.Genet. 7, 415 (2006)

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

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

21. Polycomb-group Proteins Maintains a silenced state 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 Prevents changes in cell identity by preserving transcription patterns Polycomb and Trithorax Complexes Chromatin is altered in a heritable manner Prevents chromatin remodelling

22. Model for PcG Formation and Function from Lund and van Lohuizen, Curr.Opin.Cell Biol. 16, 239 (2004) PRC2 complex methylates H3 K9 and K27 H3K27me3 recruits Polycomb and PRC1 complex H3K27me3 is segregated to both daughter DNAs to maintain repression PcG complexes are recruited to PREs

23. 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, Science 318, 403 (2007)

24. Trithorax Complex Mechanism of Action TrxC methylates H3K4 and recruits HAT and remodeling complexes Acetylated H3K9 prevents methylation, and prevents HP1 binding

25. Somatic Cell Reprogramming from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009) 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

26. Co-suppression PcG complexes interact in trans Increase in gene copy number results in decreased expression Dependent on PcG genes from Pirrotta, Cell 93, 333 (1998)

27. Imprinting Expression of only one allele of a locus Only 80 genes in mammals are imprinted Most imprinted genes are involved in growth control Imprinted genes involves allele specific methylation and is resistant to genome-wide demethylation Clusters of imprinted genes contain noncoding RNAs that are involved control allele-specific expression

28. Imprinted Expression of the H19 and Igf2 Genes from Reik and Murrell, Nature 405, 408 (2000) Maternal – H19 expression Paternal – Igf2 expression

29. Imprinting is Regulated by a Methylation-sensitive Boundary from Reik and Murrell, Nature 405, 408 (2000) ICR is methylated in the male germ line ICR is protected from methylation in the female germ line by CTCF CTCF binding to the ICR in females prevents activation of Igf2 by downstream enhancer In males, the downstream enhancer activates Igf2 and H19 expression is repressed by DNA methylation

30. from Ferguson-Smith and Surani, Science 293, 1086 (2001) Imprinting of the PWS-AS Locus The AS-ICR is required for methylation and inactivation of the PWS-ICR in females to repress nearby genes The AS-ICR is nonfunctional in males allowing the PWS-ICR to activate nearby genes The PWS-ICR promotes expression of an antisense Ube3a transcript in males

31. from Straub and Becker, Nature Rev.Genet. 8, 47 (2007) Dosage Compensation Mechanisms Genomes compensate for different numbers of sex chromosomes by adjusting gene expression levels

32. X Inactivation in Mammals X inactivation is initiated from the Xic Xist and Tsix partially overlap and are transcribed in opposite directions from the Xic from Lodish et al., Molecular Cell Biology, 6 th ed. Fig 22-7

33. Model for the Initiation of X Inactivation from Lodish et al., Molecular Cell Biology, 6 th ed. Fig 22-7 The Xic in female cells colocalize prior to X inactivation Low expression of Tsix from X i leads to Xist transcription Xist RNA coats the X i in cis The chromatin structure of X i becomes condensed

34. Stepwise Progression of X Inactivation in Differentiating ES Cells from Brockdorff, Trends Genet. 18, 352 (2002) One X chromosome is converted to facultative heterochromatin Xist transcription off the inactive X initiates chromatin modification events X inactivation is maintained epigenetically

35. Calico Cats One of the genes controlling fur color is on the X chromosome B – orange b - black Random X inactivation early in embryonic development leads to patchworks of skin cells expressing each allele Female mammals are genetic mosaics

36. The Dosage Compensation Complex in Drosophila from Gilfillan et al., FEBS Lett. 567, 8 (2004) SXL in females prevents MSL2 translation MSL2 in males stabilizes roX, MSL1, and MSL3 DCC binds to high affinity sites on X chromosome DCC spreads to nearby sites on active chromatin H4K16 acetylation impedes formation of condensed chromatin structure

37. from Straub and Becker, Nature Rev.Genet. 8, 47 (2007) DCC is Localized to the X Chromosome DCC localization is determined by staining of polytene chromosomes with anti-MSL1 DCC associates almost exclusively with transcribed regions