Chromatin structure and function

Epigenetic regulation Changes the histone modifications based on the cell's needs

A dynamic process: writers, readers, and erasers of histone code

Barrier DNA Sequences Have special DNA sequence CTCF proteins recognize and bind to insulator sequence and recruit some other proteins to form the barrier function. Now these 2 regions can be regulated separately. So the transcription status in one region won't affect the neighbor DNA

Also called insulators. They separate the chromatin into different domains and prevent the spread of heterochromatin.

Histone tails of the core nucleosome

Aside from H1, what else may aid in the formation of the 30 nm fiber?

Chromatin

Defined as DNA with associated proteins that has highly complex structure with several levels of organization

Interphase chromosomes exhibit a mixture of highly condensed and less condensed chromatin 1.Heterochromatin (dark) Highly condensed ~10% genome Two types A. Constitutive: always condensed-concentrated at telomeres and centromeres, doesn't have functional genes B. Facultative: in some cells some of the time, transcription-inactive genes (conditionally silence) 2.Euchromatin (light) Less condensed Transcriptionally active

Describe the structure of the chromosomes during interphase

Core: Eight histone molecules, 2 each of H2A, H2B, H3, and H4 Basic proteins (rich in arginine and lysine), positively charged in cellular environment Globular, but with unstructured tails Human cell has about 30 million nucleosomes

Describe the structure of the nucleosome.

Mitosis: chromatins condense to form chromosomes, aids in sister chromatid separation and protects fragile DNA Interphase: some regions of chromatin decondense so that the DNA is accessible to proteins for transcription

Dynamic chromatin is required for DNA-based processes. Describe the role of chromatin in mitosis and interphase.

Variant histones produced in small amounts make possible different chromatin structures structurally similar to histones, but they are not conventional histones. e.g. H3, and CENP-A or H2A and macroH2A Replacing histones with Histone variants is another way to remodel chromatin structure. These histone variants are not the splicing variant of the histones, these are encoded by different genes, but they have high homology with the histone proteins.

How do variant histones affect chromatin?

Nucleosome beads repeats about 230 base pairs 147 base pairs bound tightly around the core (1.7 turns in a left-handed coil), remainder is linker DNA 230 - 147 = 83 bp

How many base pairs wraps around histone in a nucleosome?

1. Chromatin is a double stranded helical structure of DNA 2. DNA is complexed with histones to form nucleosomes 3.Each nucleosome consists of eight histone proteins around which the DNA wraps 1.65 times 4. A chromosome consists of the nucleosome plus the H1 histone 5. The nucleosomes fold to produce a 30 nm fiber 6. The 30 nm fibers form loops/scaffolds that are 300 nm in length 7. The 300 nm fibers are compressed and folded to produce a 250-nm wide fiber 8. Tight coiling of the 250-nm fiber produces the chromatid of a chromosome

List the levels of organization of chromatin

Trimethylation of K9 is associated with transcription inhibition K4 trimethylation is associated with transcription activation These meanings create the "histone code"

Some histone tail modifications have meaning. What is the meaning of trimethylation of H3K9 and H3k4?

1. Establish global chromatin environments -partition the genome into euchromatin and heterochromatin (Heterochromatin is often associated with tri-methylation of H3K9) 2. Changes in gene expression/recruitment of proteins involved in gene expression (activators/repressors) 3. Recruitment of proteins involved in DNA repair 4. Recruitment of proteins required for DNA replication

What are some of the functional consequences of histone modifications?

Regulates transcription, DNA replication and repair Controls gene activity and inheritance of traits

What are the functions of chromatin?

1. ATP-driven chromatin remodeling machines act locally to influence chromatin structure importance of these enzymes for normal growth and development is illustrated by disorders and neoplasias linked to mutations 2. Covalent modifications of histone tails affects the stability of the 30nm fiber and higher order structure attracts specific proteins to a portion of the chromatin further compact DNA or facilitate access to DNA Involved in transcriptional activation/inactivation, chromosome packaging, and DNA damage/repair 3. Histone variants - replacing traditional histones w/variants

What are the three primary mechanisms by which chromatin is remodeled?

Histone proteins: H1, H2A, H2B, H3, H4 Non-histone proteins: proteins that regulate transcription, telomere stability, mitotic condensation, etc.

What are the two classes of proteins associated with DNA?

Cell's chromatin must "open" in order for gene expression to take place. This process of "opening" is called chromatin remodeling

What is chromatin remodeling?

11 nm "beads on a string" length

What is the average length of a nucleosome?

Disruption of Barrier Sequences Can Cause dysregulation of genes -globin locus -chicken HS4 separates the -globin locus from an adjacent region of highly condensed chromatin in erythrocytes -mutation of HS4 results in the silencing of the -globin genes In chicken, the 5'HS4 and 3'HS insulator elements define the limits of beta-globin gene locus. HS5/HS4 in human beta-globin locus has similar insulator function

What is the effect of disruption of barrier DNA sequences?

Combinations of modifications and variants have specific meaning for the cell "Code-reader" proteins bind to specific marks Attract other proteins that execute an appropriate biological function Specific chromatin modifications can spread for long distances along a chromosome, H3K9 me3 (it recruits additional proteins that can potentially modify additional tails throughout chromatin)

What is the histone code?

Each tail is subject to several types of modifications Charged lysines that undergo reversible post-translational addition of acetyl, phosphate or methyl groups Perform crucial functions in regulating chromatin structure

What is the mechanism behind covalent modifications of histone tails?

Epigenetic inheritance After DNA replication, some of the specialized chromatin components are passed on to daughter DNA. These components will recruit histone modification enzymes to make the same marks on the new nucleosomes. Histone modification enzymes might stay with the DNA or be recruited to the DNA and modify the histones.

What is the mechanism explaining how chromatin structure can be inherited?

ATP-dependent chromatin remodeling complex bind to the histone cores and the DNA and cause the nucleosome to slide, which makes the DNA more or less accessible to transcription factors. Some ATP-dependent chromatin remodeling complexes can... Remove the H2A-H2B dimers from a nucleosome Replace the H2A-H2B dimer with a variant Risk making some parts less condense

What is the mechanism of some chromatin remodeling complexes?

Histone H1 links nucleosomes into higher order structures it is outside of the nucleosome core and help to stabilize the nucleosome structure. In 30 nm fiber: -H1 binds to linker DNA and contacts core histones -the 30 nm fiber contains one molecule of histone H1 per nucleosome core seals two superhelical turns of DNA on -the nucleosome surface -H1 changes the path of the DNA as it exits from the nucleosome -H1 likely helps direct the relative positioning of successive nucleosomes and the pattern of nucleosome-nucleosome contacts

What is the purpose of H1?