Chromosomes, Chromatin, and the Nucleosome

Chromosomes: DNA associated with proteins

1. The chromosome is a compact form of the DNA that readily fits inside the cell.

2. Packaging the DNA into chromosomes serves to protect the DNA from damage.

3. Only DNA packaged into a chromosome can be transmitted efficient to daughter cells.

Table I: variation in chromosome makeup in different organisms

The traditional view is that prokaryotic cells have a single, circular chromosome,and eukaryotic cells have multiple, linear chromosomes.

Table 2. Comparison of the gene density in different organisms’

genomes

Comparison of the chromosomal gene density for different organisms

65kb region

The organization and content of the human genome

Pseudogenes arise from the action of an enzyme called reverse transcriptase

(dinucleotide repeats)

( greater 100bp, mostly transposable element)

The majority of human intergenic sequences areComposed of repetitive DNA

Table 7-3

Contribution of introns and repeated sequences to different genomes

introns (p. 135)

Chromosome duplication and segregation

Eukaryotic chromosomes require Centromeres, Telomeres, and Original of Replication to be maintained during cell division

More or less than one centromere leads to chromosome loss or breakage

Centromere size and composition varies dramatically

Telomeres

1. Telomeres are bound by a number of proteins. These proteins distinguish the natural ends of the chromosome form sites of chromosome breakage and other DNA breaks in the cell. DNA ends are the sites of frequent recombination and DNA degradation. The Proteins at telomeres form a structure that is resistant to both events.2. Telomeres act as a specialized origin of replication that allows the cell to replicate the ends of the chromosomes.

The eukaryotic mitotic cell cycle

Each chromosome of the duplicated pair is called a chromatid, the two chromatids of a given pair are called sister chromatids.

The events of mitosis

Changes in chromatin structure-DNA condensation and decondensation

Chromosomes are maximally condensed in M phase

• Sister Chromatid cohension and Chromosome condensation are mediated by SMC ((structural maintenance of

chromosome) proteins

Models for the structure of cohesins and condensins

The structural of cohesin is a large ring composed of two SMC proteins and a third non-SMC protein. SMC (structural maintenance of chromosome) proteins

Mitosis maintains the parental chromosome Number

Meiosis reduces the parental chromosome number

Formation of chiasma

Homologous recombination

cohesion is lost

Formation of chromatin structure

nucleosome- building blocks of chromosomes

H2A: redH2B: yellowH3: purpleH4: green

Histones are small, positively-charged proteins

The assembly of a nucleosome

The N-terminal tails are accessible to protease trypsin (specifically cleaves protein positively-charged amino acids)

The nucleosome has an approximate twofold axis of symmetry

Interactions of the histones with nucleosomal DNA

H3.H4 tertramer H2A.H2B dimer

central 60bp region and two ends

Each associate with about 30 bp of DNA on either side of the central 60 bp

Histones contact the minor groove of the DNA by forming a large number of hydrogen bonds

The large number of the hydrogen bonds provide the driving force to bend the DNA

Higher-order chromatin structure

H binds to linker DNA at one end ofThe nucleosome and the central DNA helix

The addition of H1 leads to more compact nucleosomal DNA

Without H1

Histone H1 induces tighter DNA wrapping around the nucleosome

30-nm fiber

Superhelix, 6 nucleosome per turn, supported by EM and X-ray studies

Based on zigzag pattern upon H1 addition, requires linker DNA to pass through central axis,

The core Histone N-terminal tails are required for the formation of the 30-nm fiber

The tail of H2A, H3 and H4 interact with adjacent nucleosome

Higher compaction of DNA involves large loops ofnucleosomal DNA

Nuclear scaffold (Topo II, SMC)

Histone variants alter nucleosome function1. H2A.z histone inhibits nucleosome from forming repressive chromatin structures, creating regions of easily accessible chromatin that are more compatible with transcription

2. CENP-A replace H3, is associated with nucleosomes that include centromeric DNA

Regulation of chromatin structureThe interaction of DNA with histone octamer is dynamic

Unwrapping of the DNA from nucleosome is responsible for the accessibility of the DNA

Nucleosome movement by nucleosome remodeling complexes

restructure

ATP-dependent chromatin remodeling complex

SWI/SNF 8-11 subunits Bromodomain

ISWI 2-4 subunits No

Mi2/NuRD 8-10 subunits chromodomain

Nucleosome Positioning by DNA-binding proteins

exclusion

Nucleosome Positioning by DNA-binding proteins

Inducing assembly

Modifications of the histone N-terminal tails alters the function of chromatin

Acetylation: transcription activation

Effects of histone tail modification

Nucleosome modifying enzymes

Chromatin remodeling complex and histone modifying enzymes work together to alter chromatin structure

Nucleosome AssemblyThe inheritance of histones after DNA replication The old histones are present on both of the daughter chromosome

H3.H4 tetramers remain bound to one of the two daughter duplexe at random but H2A.H2B dimers are released and enter the local pool for new nucleosome assembly.

Inheritance of parental H3.H4 tetramers facilitate the inheritance of chromatinstate

Nucleosome Assembly

The assembly of nucleosomes is not a spontaneous process, it requires high salt condition in-vitro.

Proteins required to direct the assembly of histones to DNA are histone chaperones.

Name histones bound

CAF-1 H3. H4

RCAF H3. H4

NAP-1 H2A.H2B

(negatively-charged protein)

How histones chaperones facilitate the assembly of nucleosomeduring DNA replication

(sliding clamp)