Lect. 2 - DNA, chromosomes and Genomes 2 Flashcards
epigenetics
a form of inheritance that is superimposed on the genetic inheritance based on DNA
What are some examples of epigenetics?
DNA methylation, chromatin structure (inherited from parental to daughter cells after cell division), and histone modification
heterochromatin
chromatin that is very condensed - stains darkly throughout the cell cycle, even in interphase. thought to be late replicating and genetically inactive; contains very few genes and those that are present are resistant to gene expression
where is heterochromatin highly concentrated?
at centromeres and telomeres
position effect
activity of a gene depends on position on chromosome - will be silenced if relocation near heterochromatin
euchromatin
all the rest of the chromatin that is less condensed
example of gene silencying from Drosophila
breakage events that bring heterochromatin near active genes tends to silence them, zone of inactivation spreads a different distance in different cells; evidence that heterochromatin when positioned next to genes can silence them and is not localized to one area
histone modifications
aa side chains of histones are subject to a variety of covalent modifications; occurs on the core of the histone as well as the tail
what is the effect of acetlyation of lysines on histones
the chromatin structure is loosened; added by histone acetyl transferases (HATs) and removed by histone deacetylase complexes (HDACs)
What is the mechanism of the mono,di and tri-methylation of lysines?
added my methyl transferases; removed by histone demethylases
In histone modification, what determines how/when/if gene expression takes place?
the types of proteins the modified DNA attracts
variant histone proteins exist for each core histone except for which?
H4
variant histone proteins
present in much smaller amounts than core histones and are less well-conserved;
major histones
synthesized during S-phase and assembled into nucleosomes on daughter DNA helices just behind replication fork
When are variant histone proteins synthesized?
during interphase and inserted into already-formed chromatin. Requires histone exchange process catalyzed by chromatin remodeling complex
Histone Code
thousands of combinations of modifications (methylation, acetylatoin, etc) may exist; further diversity is created by variant histones; code has specific meaning for cell, determining how/when DAN is packaged in nucleosome
What reads the histone code?
code reader complez; involves joint recognition of histone tail and covalent modificaitons; code can change as the cell needs change
H3 modifications to N-terminal tail
reading histone code involves joint recognition of marks at other sites on nucleosome along w/ tail recognition; few meanings known
modified chromatin can spread
after modifying enzyme marks one or few neighboring nucleosomes, chain reaction can ensue; code reader-writer enzymes spread the mark over chromosome
Chromatin remodeling
complexes also contain an ATP-dependent chromatin remodeling protein - all work together to either condense or decondense long stretches of chromatin as reader moves along
What halts the spread of chromatin modifications?
several mechanisms: physical and enzyme barriers; HS4 region - protects the Beta globin locus from silencing, contains a cluster of histone acetylase binding sites
What do centromeric heterochromatin contain?
centromere specific H3 histone, CENP-A, and other proteins that pack the nucleosomes into defense arrangements to form the kinetochore, a structure required for attachments of the mitotic spindle.
What do centromere sequences in humans consist of?
short repetitive DNA sequences called alpha satellite DNa
Alpha satellite DNA
defined by assembly of proteins, not DNA sequence: alpha satellites are found at non-centromeric positions in the genome
Neocentromeres
new centromeres that can form spontaneously on fragmented chromosomes, some of which lack alpha satellite DNA
Inheritance of chromatin structures
de novo centromere formation requires a “seeding event” on alpha satellite DNA; H3-H4 tetramers are directly inherited by the daughter strands at the replication fork; once formed, it is directly inherited in each round of replication
what are the largest chromosomes known?
lampbrush chromosomes from amphibian oocytes - can be visualized by light microscopy
structure of interphase chromosomes
series of large chromatin loop emanating from a linear chromosome axis
Which would be more likely to be being transcribed; the DNA closer to the axis or the DNa in the chromatin loops?
loops - b/c they are more available
What does heterochromatin preferentially associate with?
nuclear lamina
What property does the interior of the nucleus have?
very heterogeneous
How are different activities localized in the nucleus?
Different “neighborhoods” have effects on gene expression; distinct biochemical environments have high local concentrations of enzymes and molecules for specific processes - DNA repair foci & RNA synthesis
Mitotic Chromosomes
Highly condensed; final level in chromosome packing; 2 daughter DNA molecules replicated in interphase are separately folded to produce two sister chromatids
What is the purpose of condensation?
disentangelment of sister chromatids to allow separation for cell division and protection of fragiles DNA molecules as separation occurs
Condensins
proteins that aid compaction; use ATP hydrolysis to coil the DNA molecules into chromatids; major structural component of the core of every metaphase chromosome
Homologues
genes that are similar in both sequence and function due to common ancestry; human homologues exist in yeast, worms, fruit flies and bacteria
Which is more tightly conserved, gene sequences or genome structure?
Gene sequence; size of genome, number of genes, size of introns, abundance of repetitive sequences can be quite different
How do genomic changes occur?
as mistakes in DNA replication and repair; rare; 1/1000 nucleotide pairs is randomly changed in the germ line every million years; movement of transposable elements also play a role
Comparative genomics
reconstruct genome evolution by comparing genomes of contemporary organisms
What are reasons for sequence conservation?
not having much time for mutations to occur since lineages separated; purifying selection
purifying selection
elimination of mutations that interfere with important genetic functions
Genome size can vary considerably
puffer fish genome = 0.4 billion base pairs compared to 1 billion in other fish; small size due to small introns - lacks repetitive DNA
pseudogenes
a duplicated gene that has become irreversibly inactivated by multiple mutations
duplication and divergence
both copies remain functional while diverging in sequence and pattern of expression; globin gene gamily derives from common ancestral gene
SNPs
single nucleotide polymorphisms; points in the genome where one group has one nucleotide and a different group has another; variation occurs at a high rate (1% or more)
CNVs
copy number variants; presence of many duplications and deletions of large blocks of DNA; some blocks are common and others rare; significant of most is unknown
