Chromatin structure and remodeling in eukaryotic cells

Lecture 3

Felsenfeld & Groudine, Nature 2003

H2A , H2B , H3 and H4

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

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

Nucleosome composition

H2A , H2B , H3 and H4

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

The presence of NFRs demonstrated that open promoter states are stable and common, even at genes that are transcribed so infrequently

Genomic distribution of nucleosomes

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

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

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

Phasing and rotational position of nucleosomes

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

A method to map nucleosome position at base resolution

Brogaard,…, Widom, Nature 2012, 486 (7404) pp. 496-501

Global features of nucleosome positioning

Distribution of linker DNA lengths

Length ~ 10n + 5bp What could this mean for the higher order chromatin structure?

Chromatin modifications

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)

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

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

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.

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.

Hawkins et al., Cell Stem Cell 2010

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

Chromatin modifications demarcate functional elements in the genome

Zhou, Goren and Bernstein, Nature Rev Genetics, 2011

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

Histone acetylation reaction

HAT Characteristics

HDAC Complexes

De Ruijter, et al. Biochem J. (2002)

Histone Methylation (lysine) Both activation

and repression More stable HKMT HKDM

Histone Demethylases

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.

Bromodomain recognizes K-ac

Bromodomain and lysine acetylation

Chromodomain and lysine methylation

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

Two different views on the propagation of cellular memory

Bonasio et al. Science 2010, 330 pp. 612-6

Transmission of epigenetic states