Nucleosomes, Chromatin, and Chromosome Structure - Vocabulary

Vocabulary flashcards based on lecture notes about Nucleosomes, Chromatin, and Chromosome Structure.

Nucleosome:

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

Chromatin:

The material of chromosomes, both protein and DNA.

Histones:

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

Micrococcal Nuclease:

A nonspecific DNA nuclease that cuts DNA wherever it is not associated with proteins; used to study DNA packaging.

Core Histones:

Histones H2A, H2B, H3, and H4, which form the histone octamer around which DNA is wrapped in a nucleosome.

Linker DNA:

The DNA between nucleosomes to which histone H1 binds.

Histone Octamer:

A protein complex composed of two copies each of histones H2A, H2B, H3, and H4 around which DNA is wrapped to form a nucleosome.

Histone-Fold Motif:

An internal structure in each of the core histones formed from three alpha helices connected by two loops.

Histone Tails:

The flexible N-termini of histones that protrude from the core particle and are the target of numerous chemical modifications.

Epigenetic Information:

Genetic information that is not coded by the DNA itself, such as histone modifications.

Chromatosome:

A structure consisting of about 168 bp of DNA to which all five histones (H1, H2A, H2B, H3, and H4) are bound.

Linker Histone:

Histone H1, which binds to linker DNA between nucleosomes.

30 nm Filament:

A compact filament with a width of about 30 nm formed by the condensation of nucleosomes under certain experimental conditions.

Solenoid Model:

A model for the 30 nm filament in which the nucleosome array adopts a spiral shape, with the flat sides of adjacent nucleosome disks next to each other.

Zigzag Model:

A model for the 30 nm filament in which zigzag histone pairs stack on each other and twist about a central axis.

Chromosomal Scaffold:

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

Nucleoid:

The structure in which bacterial DNA is compacted.

Chromatin Remodeling Complexes:

Proteins that alter nucleosome arrangement by sliding the nucleosome to a different location, ejecting it from the DNA, or replacing it with a new nucleosome.

Histone Modifying Enzymes:

Enzymes that covalently modify the N-terminal tails of histones.

Epigenetic Inheritance:

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

ChIP-Seq:

A technique of chromatin immunoprecipitation followed by DNA sequencing used to determine the position of nucleosomes within a genome.

ChIP-Chip:

A technique of chromatin immunoprecipitation in which the released DNA is labeled and used to probe a microarray representing the genomic sequences.

Histone Chaperones:

Acidic proteins that bind either the H3-H4 tetramer or the H2A-H2B dimer and assist the assembly of histone octamers onto DNA.

Histone Acetyltransferases (HATs):

Enzymes that perform acetylation of lysine residues on histone tails.

Bromodomain:

A protein domain that recognizes acetylated Lys residues.

Chromodomain:

A protein domain that binds to methylated Lys residues.

Histone Code:

The concept that chemical modifications of histone tails recruit proteins in a stepwise fashion, establishing a pathway that can activate the expression of a particular gene.

SMC Proteins

Proteins that hold DNA strands together, keeping eukaryotic chromosomes topologically constrained

Topoiosomerases

Enzymes that can untwist DNA and keep the long DNA molecules within cellular chromosomes from becoming intertwined.

Condensins and Cohesins

Ring-shaped proteins that encircle DNA segments to hold them tightly together in loops, thus increasing compaction.

Nucleosome Positioning Code

Specific DNA sequences that nucleosomes prefer to bind with intrinsic properties dictating preference.

Heterotetramer (H3-H4)

A tightly associated structure containing two of each subunit, critical for histone octamer formation.

Heterodimer (H2A-H2B)

A less conserved structure, which along with H3-H4, forms the nucleosome in the presence of DNA.

Solenoidal Supercoil

The tight wrapping of DNA around the histone octamer that compacts the DNA six- to sevenfold.

DNA Twist

The average DNA twist when wrapped around the histone octamer is 10.2 bp per turn, compared with the 10.5 bp per turn of unrestricted DNA.

DNA Supercoiling

The solenoidal wrapping of DNA is but one form of supercoiling that can be taken up by underwound (negatively supercoiled) DNA.

Internucleosome Connections

Connections mediated by histone tails that regulate the accessibility of DNA.

Transcription Factor Sp1

A site-specific DNA-binding protein that enhances transcription and protects against histone-mediated transcription repression

Extended Form of Chromosome

Loops of the 30 nm filament are connected to the scaffold in a radial fashion

Mitotic Chromosome

DNA packaging in eukaryotic chromosomes probably involves coils upon coils upon coils.

Scaffold-like Structure (Bacteria)

In E. coli it seems to organize the circular chromosome into a series of looped domains

HU Protein

A well-studied example of a two-subunit histonelike protein in bacteria

ATP-Driven Chromatin Remodeling Complexes

Use the energy of ATP to move nucleosomes around on the DNA.

SWI/SNF

The first remodeling complex discovered, that facilitates gene activation

ISWI

A chromatin remodeling complex often associated with gene repression

Mi2/NURD

A chromatin remodeling complex associated with gene repression

Microarray

Reveals the DNA sequences that associate with the nucleosomes.

Loop propagation

Process causing a nucleosome to slide to a new segment of the DNA in a chromatin remodeling complex

H3.3 Variant

Replaces the wild-type H3 subunit in regions where active gene expression is occurring

H2AZ Variant

An H2A variant that is also associated with nucleosomes located at actively transcribed genes

CENPA

An H3 histone variant associated with the repeated DNA sequences in centromeres

H2AX

An H2A variant associated with DNA repair and genetic recombination

MacroH2A

An H2A variant involved in X chromosome inactivation

CAF-1 chaperone

Deposits an H3-H4 tetramer onto the DNA

NAP-1 chaperone

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

HIRA Protein

A chromatin remodeling complex that helps to ensure the proper assembly and placement of nucleosomes

Histone Deactylases

Enzymes whose deacetylation of Lys residues generally results in transcriptional repression

X Chromosome Inactivation

Process in which one of the two X chromosomes in every cell of the female is converted into highly condensed heterochromatin, silencing its genes.

Lyonization

Another term for inactivation of the X chromosome after its discoverer, Mary Lyon.

Imprinting

Gene silencing of this type, specific to either paternal or maternal genes

XIST RNA

A non-coding RNA that that acts in cis to coat the entire chromosome, encapsulating it

Barr Body

The condensed and inactivated X chromosome

Gcn5 coactivator

Binds to a specific DNA sequence upstream of the gene and is an acetyltransferase (HAT) that acetylates Lys8 of H4 and Lys9 of H3

TATA box

A DNA sequence which transcription activator TFIID binds and recognizes the acetylated Lys9 and Lys14

TFIID

A transcription activator that binds the TATA box

Heterochromatin

A form of very tightly condensed DNA

HAT activity

Enzymatic activity that may account for the activator’s regulatory function

Histone Demethylases

Enzymes that remove methyl groups from histone tails.

Histone Kinase

Phosphorylates Ser10 of H3.

P55 Protein

Contains HAT activity, and can be visualized in the activity gel both in the initial extract and in the column fraction in lane 6 (arrows).

SET1 complex

Acts early and monomethylates H3K4 after FACT recruitment

Histone binding motifs

Bromodomain, chromodomain, PHD finger, WD40 repeat, SANT domain

HP1

Associates with condensed chromosomes and silenced genes

Histone methyltransferase

Spreads the modification to adkacent, unmodified nucleosomes

Acetylation

Usually associated with enhanced accessibility to DNA and consequent transcriptional activation

Methylation

Can result in either gene activation or gene repression.

Phosphorylation

Incorporates a negative charge into a histone tail, yet somehow results in a greater condensation of chromatin structure and repression of transcription

Unmodified H3-H4

Replicated DNA strands are assembled onto the strands by CAF-1 chaperone

H3-H4 heterotetramers

Are distributed randomly on the two daughter DNA strands that lack histones H2A-H2B

Rheboid Predisposition Syndrome

Condition caused by mutations that inactivate the SNF5 subunit, common to all SWI/SNF complexes

H2A-H2B Pairs

Modifed pairs stay together, and segregate from unmodifed pairs

DNA binding sites (Histone H1)

H1 has two DNA-binding sites, through which it makes contact with one arm of linker DNA and the central region of the DNA wrapped around the histone octamer

10.8 13.7

Content of Basic Amino
Acids (% of total) of Lys and Arg respectively on Histone H4

Histone H5

Avian counterpart of H1

High salt concentrations and nonphysiological conditions

Without DNA the histone can not assemble into an octamer

HIRA

Histone Repressor, a class of protein

Lowary and Widom

Defined rules for nucleosome positioning on DNA based on DNA molecule libraries

Roger Kornberg

Performed seminal studies showing that the nucleosome consists of a histone octamer with DNA wrapped around it.

David Allis Laboratory

Discovered a nuclear histone acetyltransferase (HAT) in 1995

Tetrahymena HAT

Protein from Tetrahymena referred to as p55 by the Allis lab because it migrates as a 55 kDa protein.

Gcn5 Protein

the yeast Protein, is homologous to the p55 from the Allis Lab

Histone Tails

Exit the DNA superhelix through channels formed by the alignment of minor grooves of adjacent DNA helices every 20 bp.

Histone Fold Dimer

V-Shaped structure that contians three DNA binding sites that binds to the DNA

Eukaryotic DNA Is Underwound

Reveals why eukaryotic DNA is underwound, even though eukaryotic cells lack topoisomerases that underwind DNA. Recall that the solenoidal wrapping of DNA is but one form of supercoiling that can be takenup by underwound (negatively supercoiled) DNA (see Chap- ter 9

Histone fold

makes most of the contacts with theDNA, mainly with the phosphodiester backbone and minor groove.

SIRT6

Repression by DNA repair

HDAC1, Mammal

Repression by mSin3, Nurd, N-CoR-2

SAS2, Yeast

Coactivation through SAS-1 domain

MYST, ESAI Yeast

Coactivation through NuA4 domain

PCAF Mammal

Coactivation through PCAF domain