Chromatin structure and remodeling in eukaryotic cells

1. Lecture 3 Chromatin structure and remodeling in eukaryotic cells

2. H2A , H2B , H3 and H4 Felsenfeld & Groudine, Nature 2003

3. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

4. Nucleosomes • The formation of chromatin through the binding of histones to DNA allows the DNA to be folded into chromosomes and compacted by as much as a factor of 10,000. • Packaging of DNA into nucleosomes obstructs access to DNA by transcription factors and other nuclear machinery • But it also provides opportunities for these factors to access specific regions of the genes (such as TSS) more quickly

5. Nucleosome composition H2A , H2B , H3 and H4

6. Cizhong Jiang, B Franklin Pugh, Nature Review Genetics, 2009 vol. 10 (3) pp. 161-72

7. Genomic distribution of nucleosomes • The presence of NFRs demonstrated that open promoter states are stable and common, even at genes that are transcribed so infrequently Cizhong Jiang, B Franklin Pugh, Nature Review Genetics, 2009 vol. 10 (3) pp. 161-72

8. Phasing and rotational position of nucleosomes • Nucleosome spacing is regulated by chromatin remodeling factors such as ISWI and linker histone H1 • Nucleosome spacing in different species may differ (185bp in human, 165 in yeast) Cizhong Jiang, B Franklin Pugh, Nature Review Genetics, 2009 vol. 10 (3) pp. 161-72

9. Phasing and rotational position of nucleosomes • Nucleosome spacing is regulated by chromatin remodeling factors such as ISWI and linker histone H1 • Nucleosome spacing in different species may differ (185bp in human, 165 in yeast) • Nucleosome position patterns in vivo is likely driven by a combination of random positioning and statistical positioning Cizhong Jiang, B Franklin Pugh, Nature Review Genetics, 2009 vol. 10 (3) pp. 161-72

10. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

11. A method to map nucleosome position at base resolution Brogaard,…, Widom, Nature 2012, 486 (7404) pp. 496-501

12. Global features of nucleosome positioning

13. Distribution of linker DNA lengths Length ~ 10n + 5bp What could this mean for the higher order chromatin structure?

14. Chromatin modifications

15. Profiling chromatin marks in the genome crosslink sonicate • ChIP-chip or ChIP-seq analysis is a general approach for mapping chromatin modifications in the genome • It is critical to use specific antibodies • Typically a lot of cells are needed (10^6) Chromatin IP input

16. Profiling chromatin marks in the genome • ChIP-chip or ChIP-seq analysis is a general approach for mapping chromatin modifications in the genome • It is critical to use specific antibodies • Typically a lot of cells are needed (10^6) Park PJ. Nature Reviews Genetics 10, 669-680

17. Barski et al., Cell 2007 vol. 129 (4) pp. 823-837

18. Producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. • Mapping DNA methylation, histone modifications, chromatin accessibility and RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. • Rapid release of raw sequence data, profiles of epigenomic features and higher-level integrated maps. The consortium homepage: http://epigenomebrowser.org All protocols in use can be found here, as well as information about quality metrics, news, publications, general program information, and links to other associated websites.

19. Hawkins et al., Cell Stem Cell 2010

20. Characteristic patterns of chromatin modification exist at promoters and enhancers • Enhancers are marked by H3K4me1 but NOT H3K4me3 • Promoters are marked by H3K4me3 and a depletion of H3K4me1

21. Chromatin modifications demarcate functional elements in the genome Zhou, Goren and Bernstein, Nature Rev Genetics, 2011

22. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

23. Histone acetylation reaction

24. HAT Characteristics

25. HDAC Complexes De Ruijter, et al. Biochem J. (2002)

26. Histone Methylation (lysine) • Both activation and repression • More stable • HKMT • HKDM

28. Histone Demethylases

29. Two models of histone modifications’ roles • Histone modifications could directly alter chromatin folding. • Modified histone residues could alter the ability of histones to recruit non-histone preotinrs to chromatin, which in turn alter the abiligy of the transcriptional machinery to recognize the template.

30. Bromodomain recognizes K-ac

31. Bromodomain and lysine acetylation

32. Chromodomain and lysine methylation

33. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

34. Two different views on the propagation of cellular memory Bonasio et al. Science 2010, 330 pp. 612-6

35. Transmission of epigenetic states