Nucleosomes, Chromatin, and Chromosome Structure

Flashcards about Nucleosomes, Chromatin, and Chromosome Structure

What is chromatin?

The material of chromosomes, both protein and DNA.

What are histones?

Highly conserved, basic proteins that assemble into octameric complexes around which DNA wraps to form condensed nucleosomes.

What is a nucleosome?

A DNA-condensation particle of eukaryotes around which DNA is wrapped.

What is epigenetic information?

Genetic information that is not coded by the DNA itself.

What is the first evidence that DNA is packaged into regularly organized units?

Studies in which chromosomal DNA was treated with a nonspecific DNA nuclease, such as micrococcal nuclease.

What is the approximate distance between regularly spaced DNA bands, as revealed by nuclease digestion experiments?

About 200 bp apart.

What four histone proteins were found in approximately equimolar ratios upon examination by SDS-PAGE?

H2A, H2B, H3, and H4.

Which histone is present in about half the amount relative to H2A, H2B, H3, and H4?

H1.

What is the range of molecular weights for histones?

Between 11,000 and 21,000.

Which amino acids are histones rich in?

Arginine and lysine.

Which histones are nearly identical in all eukaryotes?

H3 and H4.

What is a key technique used in early studies to investigate the composition and organization of nucleosome units?

Protein cross-linking.

What is histone octamer composed of?

Two copies each of histones H2A, H2B, H3, and H4.

What are core histones?

H2A, H2B, H3, and H4.

What binds to linker DNA between nucleosomes?

Histone H1.

What did visualization of nucleosomes in the electron microscope reveal?

A structure in which the DNA is bound tightly to beads of protein, often regularly spaced like beads on a string.

What is required for the formation of the histone octamer from individual histone proteins under physiological conditions?

The presence of DNA.

What do H3 and H4 subunits form in the absence of DNA?

A tightly associated heterotetramer.

What do H2A and H2B subunits form in the absence of DNA?

A heterodimer.

How many base pairs of DNA are wrapped around a histone octamer?

146 bp.

What is the shape of DNA wrapped around the octamer?

A left-handed solenoidal supercoil.

How much does the supercoil arrangement of DNA on the nucleosome compact the DNA?

Six- to sevenfold.

What is the pattern of DNA segments within supercoil?

Relatively straight 10 bp segments joined by bends.

What is the histone-fold motif?

Three alpha helices linked by two short loops.

What is the elemental structural unit of the nucleosome?

A head-to-tail dimer of histone-fold motifs of either the H3-H4 pair or the H2A-H2B pair.

How many DNA-binding sites does each histone-fold dimer form?

Three.

Where do the contacts between histones and DNA mainly occur?

Between the conserved histone fold and the phosphodiester backbone or minor groove of the DNA.

Why is charge neutralization important in DNA condensation?

Especially in the further stages of compaction.

What is the average DNA twist when wrapped around the histone octamer?

10.2 bp per turn.

What abundance of base pairs facilitates the formation of histones?

Local abundance of A/T base pairs.

How does the winding of DNA affect if DNA is underwound?

Eukaryotic DNA is underwound, even though eukaryotic cells lack topoisomerases that underwind DNA.

What is the effect of the tight wrapping of DNA around the histone core?

Requires the removal of about one helical turn in the DNA.

What are N-terminal histone tails?

Protrude from the core particle and are less ordered.

What is the function of histone tails in nucleosomes?

Form intermolecular contacts with adjacent nucleosome particles and organize nucleosomes into a higher-order chromatin structure.

What is at heart of dynamic regulation of chromatin structure?

The histone tails.

How is net electrical charge, shape, and other properties of histones affected?

Through modification to the tails.

What is the result of tighter internucleosome connections mediated by the histone tails?

The less accessible is the DNA to transcription factors and other proteins.

What is the linker histones affect on histones?

Facilitates the general repressive effect of histones on transcription.

Can transcription factors that bind specific sites on DNA modulate the repressive effect of histones on transcription?

Yes.

What is a chromatosome?

A segment of about 168 bp to which all five histones are bound.

What is a linker histone?

Histone H1; protects an additional 20 to 22 bp of linker DNA adjacent to the nucleosome.

How many H1 subunits are present per chromatosome?

Only one.

What are the three regions of H1?

Short N-terminal region, a central globular domain, and a long C-terminal region.

What are function of DNA binding sites in H1?

To bind each of the two linker DNA strands at the sites where DNA enters and exits the nucleosome.

By binding an additional 20 bp of DNA, what does histone H1 alter?

The DNA entry and exit angles, facilitating the packing of DNA into higher-order chromatin structures.

What do most regions of actively transcribed DNA not include?

Histone H1.

What is avian counterpart of H1 referred to as?

H5

What are 30 nm filaments?

Filaments consisting of nucleosomes condensed with a width of about 30 nm.

Is histone H1 essential for forming the 30 nm filament?

No.

What is crucial for 30 nm Filament formation?

N-terminal tails of the core histones.

With neutron diffraction studies, where can histone H1 be placed?

Center of the filament.

Linker DNA should placed where in the filament?

Center of the filament.

What is the solenoid model?

The nucleosome array adopts a spiral shape, in which the flat sides of adjacent nucleosome disks are next to each other.

What is zigzag model?

Histone pairs stack on each other and twist about a central axis.

How are 30 nm filaments organized in swollen chromosomes?

In loops estimated at 40 to 100 kbp long.

What is chromatin scafoold.

A proteinaceous residue after histone extraction that retains the size and shape of the original chromosome.

What are SMC's function?

Keeping chromosomes togologically constrained.

What are the shapes of higher-order structures?

Coils upon coils upon coils.

What is the nucleoid?

Structure compacting bacterial DNA can occupy a significant portion of the cell volume.

Bacteria contain SMC proteins, and studies in E. coli reveal what structure?

A scaffoldlike structure that seems to organize the circular chromosome into a series of about 500 looped domains, each encompassing 10 kbp, on average

Do bacterial have similiar structure to local organization provide by nucleosomes in eukaryotes?

No.

What the two-subunit protein HU function?

Histone like protein.

One class of proteins that alter nucleosome arrangement comprise of which complex?

Chromatin remodeling complexes

Two types of hisone subunits?

Variant and standard

What do histone subunits do?

Impart Special proeprties to chromatin

What is a histone modifying enzyme?

A enzyme that covently modifies N-terminal tails.

What is a cis acting hisone?

The act of modifying a histone that directly results in a change to the structure.

What is a trans acting histone?

The act of modifying a histone that attracts other proteins, such as transcription factors or chromatin remodelingfactors, that produce the chromatin change.

What is epigenetic inheritance.

The inheritance of genetic properties that are not encoded in the DNA sequence.

What are the purposes of epigenetic marks.

Facilitating or suppressing specific functions such as transcription, replication, DNA repair, and chromosome segregation.

What aresome examples for force measurements on cchromatin?

Clever experimental designs.

What areChromatin remodeling complexes consist of?

2 to 17 subunits and can be divided into three main classes: SWI/SNF (switchsniff, the first remodeling complex discovered), ISWI (imitation switch), and Mi2/NURD

What is the relationship between SWI/SNF and genes?

Gene activaton, ISWI and Mi2/Nurt with gene represion.

What is ChIP-Seq.

Chromatin Immunoprecipitation followed by sequencing technique.

What is ChIP-Chip.

Chromatin Immunoprecipitation with microarray analysis.

How is DNA positioned inside of yeast cell?

Transcriptionally active promoters are usually free of bound nucleosomes and are flanked on either side by a nucleosome with a well-defined position

What are the primary differences in histones that replace wild type?

The primary difference in the histone variants that replace H3 is the availability of residues in the N-terminal tail to modifications such as methylation and phosphorylation to modify their function.

How does H2A variants function?

Variants of H2A differ primarily in the C-terminal tail region, which can recruit various proteins to the nucleosome.

What is H3.3 variant?

Variant in regions where a active gene expression is occuring.

How do H2AZ and H3.3 stabilize DNA?

Stabilize open stated of chromatin facilitating machinerey access.

Why would you use CAF?

Histone chaperone that deposited H3-H4 tetramer.

Why would you use NAP?

Assembles two H2A-H2B heterodimers with the H3-H4 heterotetramer to form the complete nucleosome.

What are the most studied modifications?

The most intensively studied are the acetylation of lysines, methylation of lysines and arginines, phosphorylation of serines, and ubiquitination of lysines (Figure 10-25).

What do HAT's modify?

Histone acetyltransferases is generally associated with enhanced accessibility to DNA and consequent transcriptional activation.

What do HDAC's modify?

Histone deacetylases, the deacetylation of Lys residues generally results in transcriptional repression.

What motif do bromodomain proteins recognize?

Acetylated Lys.

How does histone methylations regulate the genetics?

Histone methylation can result in either gene activation or gene repression.

What do chromodomains bind to?

Methylated Lys residues.

Phosphorylation.

A type of modification commonly found on histone tails of H3 and H4,

How does Histone Modifications May Read a Histone Code for

Histone Modifcation leads to another modication.

Which modifcation does the IFN-B genes start with.

Acetlation.

What does inheriting control do?

Is essentially like inheriting and other trait.

How does epigenetic inheritance different from classical?

Is very different from classical Mendelain Genectics.

What is imprinting?

In which one copy (allele) of a gene is silenced in the fertilized egg and remains turned off in every cell of the developing organism.

What is a hertiability role in DNA.

Requies a perservation of histone modificaiton.

What is lost during replication

how is the epigenetic state preserved in daughter cells

What does hetrochromatine.

tightly condensed DNA silencing its genes

What is barrbody?

The condensed and inactivated X chromo- some

What is lyonization?

inactivation of the X chromosome

What is imprinting?

gene silencing of this type, specifi c to either paternal or maternal genes