Chromosome Structure

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chromatin

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the nucleoprotein complex that DNA is condensed into

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nucleosome

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fundamental unit of chromatin structure

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nucleosome consists of...

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segment of 146 base pairs of DNA wrapped 1.6 times around a nucleosome core particle make up of 8 histone molecules

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the 8 core histones

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H2A, H2B, H3, H4

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properties of core histones

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positively charged

spontaneously dimerize

spontaneously self-assemble into ncp/s

highly conserved

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core histones contain:

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a helix-loop-helix-loop-helix domain

long N-terminal tails

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the conservation of histone amino acid sequences is most likely due to what type of selection?

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purifying selection

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linker DNA

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segments connect adjacent nucleosomes

length varies between taxa

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histone H1

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stabilizes the junction of the linker DNA with the nucleosome core particle

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Nucleosome synthesis

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nucleosomes are displaced and denatured into histone dimers ad tetramers by the replication fork

H3-H4 tetramers quickly reaffiliate with the daughter duplexes ~600 bp behind the fork

H2A-H2B dimers are the added

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histone chaperones

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ASF-1 and CAF-1

facilitate the nucleosome synthesis

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intrinsic mechanisms

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the positions are determined in part by the DNA sequence itself, which can favor or disfavor DNA-histone associations

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Extrinsic mechanisms

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the position of the first nucleosome is a region is controlled by other proteins and this affects the positions of the neighboring nucleosomes

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intrinsic positioning

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not accomplished by fixed DNA motifs, but rather by the general physical properities of the nucleotide sequence

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nucleosome assembly is favored by...

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favored by alternating AT and GC dinucleotides (every 5 base pairs)

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Nucleosomes are excluded by...

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excluded by Poly dAdT tracts

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chromatin lowest level of organization

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10-nm fiber, which has a "beads on a string" appearance

this achieves ~6-fold compaction of the DNA

the 10-nm fiber only exists transiently under normal cellular conditions

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chromatin second level of organization

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under normal conditions, the 10-nm fiber folds into a solenoidal structure that gives rise to the 30-nm fiber

each turn containes 8-10 nucleosomes

this provides a further 6-fold compaction of the DNA

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Higher order chromosomes structures are based on...

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chromatin loops anchored to a nonhistone protein scaffold

each chromatin loop contains 20,00-100,00 bp

loops attach to the chromosome scaffold at matrix attachment regions

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matrix attachment regions

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often associated with DNA repeats called ATC sequences

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Chromatin loops

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cell-dependent and affects gene expression

formed by scaffold proteins

are organized into rosettes and bundles, resulting in a further 250-fold compaction of the DNA

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how many histone molecules make up the nucleosome core particle?

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8

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Approximately how many nucleosomes can fit into a 1 Mb segment of the human genome?

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5000

each nucleosome has 146 bp of DNA wrapped around the nucleosome core particle as well as ~50 bp of linker DNA, for a total of ~200 bp. Dividing 1,000,000 by 200 shows that approximately 5,000 nucleosomes will fit into this segment

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Protamines

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basic proteins that Spermatid DNA is mainly packaged with

bind in the major groove of DNA and neutralize the phosphodiester backbone

__-DNA complexes coil into toroidal structures "donut-loop" of ~50 kb DNA

Sperm DNA is highly condensed and largely transcriptionally silent

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Dinoflagellates

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unique among eukaryotes in lacking nucleosomes

flagellated planktonic protists

their nuclei contain up to 30x as much DNA as human cells

DNA is packaged using a unique class of ___/Viral NucleoProteins also found in Phycodnaviridae viruses

the use of DVNP's appears to be derived, possibly resulting from horizontal transfer of a DVNP gene from a virus

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Heterochromatin

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highly condensed and is transcriptionally repressed (no expressed genes)

shows up as dark chromosome bands (G-bands)

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Euchromatin

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relatively open and contains most expressed genes

shows up as light chromosome bands

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Constitutive heterochromatin

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permanently condensed

transcriptionally repressed

mainly composed of satellite DNA (tandem repeats)

locations: centromeres, telomeres, transposons

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Facultative heterochromatin

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reversibly condensed

contains silent genes that can be activated

differs between cell types

Ex: Barr body formation results in the formation of ___

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During which stage of the cell cycle are chromosomes least condensed?

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interphase

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chromosome condensation

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maximal during metaphase

minimal during interphase

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p arm

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short arm

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q arm

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long arm

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Metacentric chromosomes

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arms are similar lengths

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Submetacentric chromosomes

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distinctly shorter p arms

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acrocentric chromosomes

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very short p arms composed of mainly repetitive satellite DNA

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Telocentric chromosomes

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have a terminal centromere (no p arm)

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karyotype

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shows the number and shape of an organisms chromosomes

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human karyotype:

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5 metacentric chromosomes

13 submetacentric chromosomes

6 acrocentric chromosomes

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Chromosomes territories

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the area that chromosomes occupy during interphase

vary from cell to cell (no fixed locations0

certain chromosomes have a tendency to occupy neighboring ___

chromosomes appear to be anchored in place by their centromeres

within each ___, chromosomes are dynamic and chromosome loops can be seen to change position

location of a specific chromosome region within a __ depends on when it is replicated and whether it is transcribed

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late replicating regions

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tend to occur near the nuclear envelope

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early replicating regions

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tend to occur near the nucleus center

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interchromosome domains

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provides space for proteins and mRNA

transcriptionally active regions tend to occur at territory interfaces

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Chromatin Conformation Capture (3C)

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can be used to identify inter- and intra- chromosomal interactions

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The diameter of a chromosome territory is approximately equal to which of the following?

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1 micro meter

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point centromeres

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are defined by specific DNA sequences (CEN) which bind directly to the kinetochore

CEN sequences are ~120 bp long

contain conserved sequences that attach to single microtubules

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Regional centromeres

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more diffused and are defined by epigenetic modifications

most common forms

made up of heterochromatin

are more variable and can attach to multiple microtubules

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holocentric

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when entire chromosomes function as centromeres

in a few organisms

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CENP-A

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variant histone H3

human centromeres are defined by the presence of ___

mediated the attachment of the kinetochore to the centromere and allows the centromere to be self-replicating

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Meiotic drive

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a form of intragenomic conflict which occurs when certain DNA sequences obtain a transmission advantage during meiosis

leads to violations of Mendel's 1st law

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selfish elements

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driving alleles can spread even when they reduce individual fitness

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one mechanism that can lead to meiotic drive

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competition between centromeres for kinetochore proteins: stronger centromere sequences are preferentially segregated to the ovum

can negatively impact male fitness

can select for drive suppressors

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monkeyflower Mimulus guttatus: centromere-associated drive

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a driving allele D has a 58:42 advantage over non-driving alleles in female meiosis

homozygous individuals suffer reduced polled viability

D is maintained at an intermediate frequency of ~35% in some pop's

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centromere paradox

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although essential for segregation,centromeres and their associated proteins evolve rapidly

Thiscan be explained by meiotic drive. Driving alleles spread through a populationbecause they have a transmission advantage

However, because they reduce malefitness, this leads to selection for drive suppressors.

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Which of the following processes is least likely to be associated withmeiotic drive?

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cancer

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telomeres purpose

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1.Theyprotect the ends of linear chromosomes from DNA damage and damage repairmechanisms.

2.Theycompensate for incomplete DNA replication at chromosome ends.

Telomeres are composed of shortrepeats, telomericproteins (shelterin)and telomericRNAs (TERRA).

Human telomeres contain thousandsof telomericrepeats (TTAGGG) which decrease in size with age.

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Hayflick limit

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continues shortening of telomeres eventually leads to cell senescence

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DNA damage response mechanisms (that telomeres protect chromosome ends from)

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•double-strand break repair

•ssDNA-induced cell cycle arrest

•non-homologous end joining

•homologous recombination

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Shelterin

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acomplex of 6 proteins that cap the telomere

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subtelomeres

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rapidly evolving regions

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subtelomeres

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rapidly evolving regions that lie betweenthe telomericrepeats and the more stable chromosome-specific sequences in the core.

undergo frequent: •segmental duplication•rearrangement•recombination

Mosaic structure containing:•tandem repeats•pseudogenes•gene families•transposable elements

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Subtelomeric genes

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exhibit elevated levels of sequenceand copy number variation between individuals and species.

Thismay facilitate adaptation to changing environmental conditions, especially inhost-parasite interactions

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subtelomeric location

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can also affect expression throughproximity to telomericheterochromatin.

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telomeric expression sites

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only one of ~15 is active

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Telomeric archieves

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arrays of 100's of VSG genes and pseudogenes are contained in____

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minichromosomes

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are 50-100 kb long and have 1 VSG at each end

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Gene conversion

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copies inactive VSG genes from the subtelomeric arrays into the active expression sites

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Reciprocal telomere

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exchange (recombination) moves VSG genes from the ends of the minichromosomes into the expression sites

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mosaic gene conversion

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can assemble novel VSG genes n the expression sites

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Which of the following would you expect to find in a subtelomere?

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telomeric repeats and immunoglobulin genes (no histone genes)