Chromatin and Epigenetic Control

What does epi mean?

above or upon

What is epigenetics?

heritable changes in gene expression or phenotypes that occur without a change in the sequence of DNA

What are some molecular mechanisms that mediate epigenetic phenomena?

DNA methylation, histone modifications

Where does DNA methylation typically occur?

cytosines

What is histone modification?

a combination of different molecules can attach to the tails of proteins called histones

What triggers epigenetic changes in gene expression?

development, diet, environmental chemicals, exercise, stress, aging

Where does eukaryotic transcription function?

in a chromatin environment

Is chromatin generally repressive?

yes

What does the structure of chromatin generally prevent?

the transcriptional machinery from gaining access to DNA promoters

What does transcription involve?

regulated changes in chromatin structure

What are mediated by chromatin?

transcriptionally favorable and unfavorable environments

What is DNA packaged into?

chromatin, progressively higher ordered structures

What are the types of chromatin?

euchromatin and heterochromatin

What is euchromatin?

open, transcriptionally active

What is heterochromatin?

condensed, transcriptionally silent

What are the 2 types of heterochromatin?

constitutive and facultative

What is constitutive heterochromatin?

always heterochromatic, highly condensed, enriched at repetitive sequences, always turned off

What is facultative heterochromatin?

reversible form of heterochromatin, can be induced to become euchromatin

What is the first level of chromatin organization?

DNA double helix, 1 packing ration

What is the second level of chromatin organization?

nucleosomes, 6 packing ratio

What is the thirf level of chromatin organization?

solenoid, 40 packing ratio

What is the fourth level of chromatin organization?

loops, 680 packing ratio

What is the fifth level of chromatin organization?

minibands, 1000 packing ratio

What is the sixth level of chromatin organization?

chromosome

What is a common way to visualize nucleosomes?

beads on a string

What are nucleosome?

200 bp of DNA, 8 copies of four histones

What are histones?

small, very highly conserved, basic proteins containing relatively large amounts of lysine and arginine

How are histones charges?

positively

What is the bipartite histone structure?

flexible N terminal tail, globular C terminal domain

What is the structure of the nucleosome?

1.75 turns of DNA per histone octamer

What are the core histones?

H2A, H2B, H3, and H4

What do H3 and H4 form?

a tetramer

What do H2A and H2B form?

2 dimers

What is the site of many post-translational modifications?

the charged N-terminal tail that contains the bulk of the lysine and arginine residues

What is H1?

the linker histone that has a central globular region and highly charged tails

What is missing from the X-ray structure of the nucleosome?

histone tails

What are N-terminal tails accessible for?

DNA and protein interactions

What are the 2 ways to alter chromatin?

ATP-dependent nucleosome remodeling, histone modification

What is ATP-dependent nucleosome remodeling?

several chromatin remodeling machines, all possess a helicase/ATPase that likely disrupts histone/DNA interactions

What are the ways histones can be modified?

acetylation, phosphorylation, methylation, ubiquitination

What can modifications alter?

the charge and DNA binding properties of individual histones as well as mark them for recognition by other proteins

What happens during acetylation?

acetyl groups are added to lysines

What is acetylation carried out by?

histone-acetyl transferases

What removed acetyl groups?

histone deacetylases

What does acetylation of lysines do to them?

makes them neutral, hydrophobic, and bulkier

What is phosphorylation?

phosphate adds a negative charge to the hydroxyl group of serines

What is methylation?

methyl groups are added to lysines and argininesW

What carries out methylation?

histone methyl transferases

What does methylation do to amino acids?

leaves a bulky, hydrophobic group but does not alter the charge

What is ubiquitination?

C terminal carboxyl group of ubiquitin is joined to the free amino group on a lysin

What does ubiquitination do?

neutralizes the charge of lysine and decreases net charge of H2A

What is the histone code hypothesis?

histone modifications may be a code read by regulatory proteins that alter chromatin structure and gene activity

What is the first part of the histone code hypothesis?

specific patterns of histone modifications influence binding affinity of other regulatory proteins to the histone taislW

What is the second part of the histone code hypothesis?

protein domains that recognize specific modifications identified the bromodomain of acetylated lysine and the chromodomain of methylated lysine

What does me-K4 in H3 do?

blocks NuRD binding

What does me-K9 in H3 do?

the binding site for HP1

What is the third part of the histone code hypothesis?

histone modifications influence each other

What is the fourth part of the histone code hypothesis?

not just the levels of histone modification but the patterns of modification dictate biological outcome

What is DNA in acetylated nucleosomes?

more accessible to transcription factors

What is H3 K9 methylation involved in?

gene silencing