The control of gene expression by chromatin remodeling

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? Transcription • 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. Epigenetic Silencing

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

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

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

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 Approximately 147 base pairs of DNA wrapped around a histone octamer 8 histones: 2 each H2A H2B H3 H4 ~ 147 bp DNA +

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

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

12. DNA methylation NH2 NH2 CH3 N N Methyl-cytosine TTCGCCGACTAA DNA can be covalently modified by cytosine methylation. N N O O Methyltransferase ~ ~ cytosine 5-methylcytosine

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

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

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

16. Histone modifications

17. Histone proteins can be modified to affect chromatin structure DNA Histone octamer The amino terminal regions of the histone monomers extend beyond the nucleosome and are accessible for modification. 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 The amino terminus of H3 is often modified at one or more positions, which can contribute to an activation or inhibition of transcription. Me Me P Ac Me Ac Ac Me Me P H3A R T K Q T A R KS 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

20. Example – H3 modifications The amino terminus of H3 is often modified at one or more positions, which can contribute to an activation or inhibition of transcription. Lysine can be acetylated, or mono-, di-, or tri-methylated Me Me P Ac Me Ac Ac Me Me P H3A R T K Q T A R KS 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 Methylated lysine Mono (Kme1) Di (Kme2) Tri (Kme3) + NH3 N CH3 O Acetylated lysine (KAc) Lysine (K) CH3 CH3 + N + NH + NH2 CH3 CH3 CH3 CH3

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

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

23. H3K27me3 is associated with genes H3K27me3 in Arabidopsis is present within the gene-rich region, not the repeat-rich region. BLUE = Gene density RED = Repetitive element density GREEN = H3K27me3 PURPLE = methylcytosine

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

26. Chromatine remodeling factors 1. Chromatinassembly 2. ATPdependentchromainremodeling 3. Histone modification

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