1. The control of gene expression by chromatin remodeling

2. Epigenetics Any potentially stable and heritable change in gene expression that occurs without a change in DNA sequence

3. What does “epigenetics” mean? Literally, epigenetics means above, or on top of, genetics. Usually this means information coded beyond the DNA sequence, such as in covalent modifications to the DNA or modifications to the chromatin structure. Transcription Epigenetic Silencing

4. What does “epigenetics” mean? Practically, epigenetics describes phenomena in which genetically identical cells or organisms express their genomes differently, causing phenotypic differences. Genetically identical cells or individuals Different epigenetic modifications leading to different expression patterns

5. Epigenetic programming in plants helps control developmental transitions Embryonic development Vegetative development Reproductive development Vegetative to reproductive transition Embryonic to vegetative transition

6. XX X chromosome inactivation involves epigenetic silencing X X X X XX XX XX XX XX XX XX XX XX XX XX XX In female mammals, one copy of the X chromosome in each cell is epigenetically inactivated. Fur color in cats is determined in part by oran ge, an X-linked gene. A female cat that is hete rozygous for the orange gene shows black an d orange patches, corresponding to which X c hromosome is active. XX

7. Epigenetic programming in plants helps silence transposons and maintain centromere function

8. Epigenetic marks and their maintenance DNA methylation Histone modifications Epigenetic genome regulation in plants Transposon silencing Control of flowering time Control of imprinted genes Gene silencing in trans; paramutation Resetting the epigenome

9. Eukaryotic DNA is packaged in nucleosomes ~ 147 bp DNA+ 8 histones: 2 each H2A H2B H3 H4 Approximately 147 base pa irs of DNA wrapped around a histone octamer

10. Chromosomes consist of heterochromatin and euchromatin Densely packaged heterochromatin Less densely packaged euchromatin DNA around the centrome re is usually packaged as heterochromatin. CENTROMERE

11. Heterochromatin and euchromatin form distinct domains in nuclei Euchromatin DAPI DNA stain Merged Centromeric heterochromatin

12. DNA methylation O N NH 2 N ~ O N N ~ CH3 cytosine5-methylcytosine Methyltransferase DNA can be covalently modified by cytosine me thylation. TTCGCCGACTAA Methyl-cy tosine

13. CG methylation can be propagated during DNA replication MET1 5’ A T G C G T A C T A T G C G T A C T T A C G C A T G A REPLICATION “MAINTENANCE” METHYLATION A T G C G T A C T T A C G C A T G A A T G C G T A C T T A C G C A T G A 3’ T A C G C A T G A A T G C G T A C T T A C G C A T G A

14. Some sites are maintained by small interfering RNAs (siRNAs) A T G C A A A C T T A C G T T T G A REPLICATION 3’ T A C G T T T G A A T G C A A A C T T A C G T T T G A DRM1/2 A T G C A A A C T T A C G T T T G A

15. Heterochromatin DNA is highly methylated Although CG methylation is more abundant in pericentro meric regions, a higher prop ortion of CHH methylation is found there. BLUE = Gene density RED = Repetitive element density

16. Histone modifications

17. Histone proteins can be modified to affect chromatin structure DNA Histone octamer The amino terminal regions of the histo ne monomers exte nd beyond the nucl eosome and are ac cessible for modific ation. NUCLEOSOME

18. The Histone Code Histones can be modified by –Acetylation (Ac) –Ubiquitination (Ub) –Methylation (Me) –Phosphorylation (P) –Sumoylation (Su) Depending on their position, these can contribute to transcriptional activation or inactivation.

19. Example – H3 modifications H3 A R T K Q T A R K S T G G K A P R K Q L A T K A A R K S 4 9 10 14 1718 23 262728 MeMe PMe AcMe Me PAc The amino terminus of H3 is often modified at one or more positions, which can contribute to an activation or inhibition of transcription.

20. Example – H3 modifications H3 A R T K Q T A R K S T G G K A P R K Q L A T K A A R K S 4 9 10 14 1718 23 262728 MeMe PMe AcMe Me PAc The amino terminus of H3 is often modified at one or more positions, which can contribute to an activation or inhibition of transcription. + NH 2 CH 3 + NH CH 3 +N+N Lysine can be acetylated, or mono-, di-, or tri-methylated Methylated lysine Mono (Kme1) Di (Kme2) Tri (Kme3) + NH 3 Lysine (K) NCH 3 O Acetylated lysine (KAc)

21. Histone modification affects chromatin structure Open configuration Me P Ac K4 S10 K14 H3 Closed configuration Me Me P K9 K27 S28 H3

22. Different histone modifications are associated with genes and transposons Red = high correlation Green = low correlation H3K9me is associated with methylated DNA (Me-C) and transposons. H3K9me Me-C Transposon mRNA H3K4me Gene H3K4me is associated with actively transcribed genes and mRNA.

23. H3K27me3 is associated with genes GREEN = H3K27me3 PURPLE = methylcytosine BLUE = Gene density RED = Repetitive element density H3K27me3 in Arab idopsis is present within the gene-ric h region, not the re peat-rich region.

24. Summary – epigenetic marks Histone deacetylation Histone acetylation Histone (de) methylation DNA methylation DNA demethylation Histone variants

26. Chromatine remodeling factors 2. ATP dependent chromain remodeling 3. Histone modification 1. Chromatin assembly

27. Fig 7-48. An order of events leading to transcription initiation at a specific promoter

28. Eucaryotic gene activator proteins modify local chromatin structure Fig 7-45 Local alterations in chromatin structure directed by eucaryotic gene activator proteins

29. Fig 7-46 Two specific ways that local histone acetylation stimulate transcription initiation