Lecture 2 Flashcards
What is the difference between genetic inheritance and epigenetic inheritance?
Genetic inheritance is a change in DNA sequence that gets passed on to progeny.
Epigenetic is a change in chromatin, not in DNA.
the chromatin can turn off a gene in DNA but once the gene is in a germ cell the chromatin is removed and the DNA is turned on.
What is epigenetics?
A form of inheritance that is superimposed on the genetic inheritance based on DNA
What are examples of epigenetic inheritance?
DNA methylation
Chromatin structure
Histone modification
What are three facts that challenge the view that histones are only involved in packaging of DNA?
- Mammalian chromatin contains equal mass of histone and non histone proteins
- Histones are highly conserved
- One form of chromatin silences the genes it packages without regard to sequence
What is heterochromatin?
Form of chromatin that silences the genes it packages without regard to sequence and is directly inherited by daughter cells
What are characteristics of heterochromatin?
Chromatin that is very condensed (stains darkly)
Last DNA to be replicated during cell cycle and is genetically inactive
Highly concentrated at centromeres and telomeres
Contains very few genes; those that are present are resistant to gene expression
What is the position effect?
Activity of a gene will be silenced if relocated near heterochromatin
Position effect variegation: breakage events that bring heterochromatin near active genes tends to silence them.
Zones of inactivation spreads a different distance in different cells
What is euchromatin?
Less condensed chromatin that can be transcribed
What separates heterochromatin from euchromatin?
A barrier that protect genes that need to be expressed
What covalent modifications occur to the core and tail of histones during acetylation?
Acetylation of lysines loosens chromatin structure. It is added by histone actyl transferases and is removed by histone deacetylase complexes
What histone modification occurs with methyl transferases and histone demethylases?
Mono, did and tri methylation of lysines. Added by methyl transferases and removed by demethylases
What histone modification occurs with the modification of serines?
Phosphorylation
What does the recruitment of histone modifying enzymes depend on?
Gene regulatory proteins
Are histone modifications permanent?
No, they are all reversible but can persist long after regulatory proteins have disappeared.
What are important consequences for the types of proteins the modified DNA attracts?
Determines how/when/if gene expression takes place
What are variant histone proteins?
Variants that exist for each of the core histones except for H4
How common are variant histone proteins?
Present in much smaller amounts than core histones
Are variant histone proteins conserved or non conserved?
They are less well conserved than core proteins
When are regular core histone proteins synthesized and where are they assembled into nucleosomes?
During S-phase and assembled into nucleosomes on daughter DNA helices just behind replication fork.
So when DNA is replicated more histones are needed so during S-phase, more are made.
When are most variant histones synthesized and inserted? What is required during this process?
Most are synthesized during interphase and inserted into already-formed chromatin. Requires histone exchange process catalyzed by chromatin remodeling complex
Not when DNA replication is not going on.
What is the purpose of variant histone CENP-A?
Centromere function and kinetochore assembly
What is the purpose of variant histone H2AX?
When DNA is damaged, it helps in DNA repair and recombination
What is the purpose of H2AZ?
Gene expression and chromosome segregation
What is the purpose of macroH2A?
Transcriptional repression and X-chromosome inactivation
What do the modifications that can occur on the histone tail result in?
There are thousands of combinations of modification (methylation, acetylation, etc.) may exist that cause further diversity to be created by variant histones
infinite combinations can occur.
What is the histone code?
Code has specific meaning for cell, determining how/when DNA is packaged in nucleosome
What is the code reader complex?
Combination of proteins that read the histone code. Protein modules binding to specific histone modifications on nucleosomes. Involves joint recognition of histone tail and covalent modifications.
If the cells need change what happens to the code?
Code can change as the cells need change
What can the code reader complex bring in?
Bring in other components in nucleus that can lead to gene expression, gene silencing, and other biological function
What can happen after modifying enzyme marks one or few neighboring nucleosomes?
Chain reaction can ensue. Code reader -writer enzymes spread the mark over chromsome
Along with the code reader-writer, what do complexes also contain? What do they do?
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?
Barrier sequences.
-Physical barriers
-Enzymatic barriers
HS4 region
-protects the beta globin locus from silencing
-contains a cluster of histone acetylase binding sites
What does centromeric heterochromatin contain?
Contains centromere-specific H3 histone, CENP-A, and other proteins that pack the nucleosomes into dense arrangements to form the kinetochore
What is important about a kinetochore?
It is a structure that is required for attachment of mitotic spindle
What do centromere sequences in humans consist of?
Short repetitive DNA sequences called alpha satellite DNA
What are centromeric heterochromatin defined by?
Assembly of proteins, not DNA sequence
- alpha satellites are found at non-centromeric position in the genome
- New centromeres can form spontaneously on fragmented chromosomes, some of which lack alpha satellite DNA
How is the centromeric chromatin organized?
2 alternating types of chromatin
- nucleosomes with CENP-A on the outside fold
- –CENP-A binds to kinetochore
- Nucleosomes with normal H3 on the inside
What is the theory of 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 Lampbrush chromosomes?
Chromosomes from amphibian oocytes that are the largest chromosomes known.
They can be visualized by light microscopy
A series of large chromatin loops emanating from a linear chromosome axis can be seen
What are the loops of lampbrush chromosome?
Extended chromatin that can be transcribed. Chromatin along the axis is highly condensed
What is the location of chromatin in the nucleus?
Each chromosome occupies its own area in the nucleus.
Heterochromatin (red) outline the nucleus (preferentially associates with the nuclear lamina)
Gene-rich regions that are transcribed are dispersed throughout
What changes during gene expression in the nucleus?
Chromatin structure and location
What are chromosome puffs?
Decondensation of chromatin during gene transcription
What do actively transcribed genes do in the nucleus?
Extends out of its area on an extended chromosome loop
Are the locations of chromatin random in the nucleus?
No. Now there is a map that can show where each chromosome is in the nucleus
What are “neighborhoods” in a nucleus?
Neighborhoods are a heterogeneous mix of proteins, enzymes, and molecules for specific processes. Different “neighborhoods” have different effect on gene expression
Some can be for gene silencing, gene expression etc
What do distinct biochemical environments have?
High local concentrations of enzymes and molecules for specific processes.
- DNA repair “foci”
- RNA synthesis
What are mitotic chromosomes?
Highly condensed chromosomes that are in the final level in chromosome packaging
What are sister chromatids?
Two daughter DNA molecules replicated in interphase that are separately folded. They are held together at their centromeres
What do two sister chromatids form?
A chromosome
What are the steps of folding to create a mitotic chromosome?
- DNA double helix + histones form “beads on a string” chromatin
- Chromatin fiber is zig zagged (theory) packed - nucleosomes
- Chromosome condense further and the net result:
- Each DNA molecule has been packaged into a mitotic chromosome that is 10,000 fold shorter than its extended length
What is the purpose of condensation?
Disengagement of sister chromatids to allow separation for cell division.
Protection of fragile DNA molecule as separation occurs
What aids in compaction?
Proteins called condensins
Who do condensins compact DNA?
-Use ATP hydrolysis to coil the DNA molecules into chromatids
What is the major structural component of the core of every metaphase chromosome?
Condensins
What is the exact mechanism of condensins?
Unknown
What is known: cells depleted of condensins have abnormal condensation
What are homologues?
Genes that are similar in both sequence and function due to common ancestry
Where do human homologues exist?
Yeast, worms, fruit flies, and bacteria
What is the difference between homologues and syntany
Syntany- large blocks of genes are conserved in the same order on the chromosome between species
Homologues-not only similar in sequence but also function
What is a major clue to gene and protein function?
Recognition of sequence similarity
What is more tightly conserved? Gene sequences or genome structure? Why?
Gene sequences are more tightly conserved
-Size of genome, number of genes, size of introns, abundance of repetitive sequences can be quite different
What do the number of genes roughly correlate with? Why
Number only roughly correlated with phenotypic complexity of organism.
Complexity arises from duplication and expansion of related gene families
How do genomic changes occur?
Occur as mistakes in DNA replication and repair
How often do genomic changes occur?
Rare occurrence: 1/1000 nucleotide pairs is randomly changed in the germ line every million years
What also may play a role in genomic changes?
Movement of transposable elements
What range of change can occur?
Base pair substitiution
Large scale rearrangements
-duplications, deletions, inversion, translocations
How can genome evolution be reconstructed?
By comparing genomes of contemporary organisms
What is the phylogenetic tree?
Shows differences between species and the last common ancestor
What are reasons for sequence conservation?
Not having much time for mutations to occur since lineages separated
Purifying selection
What is purifying selection?
Elimination of mutations that interfere with important genetic functions. Darwin’s effect
What can cause genome size to vary considerably?
Small size due to small introns - lacks repetitive DNA
How much of the human genome is conserved?
5% but only 1.5% code for proteins
What is the reason that 5% of the human genome is conserved but only 1.5% codes for proteins?
Must have an important function since it is highly conserved Possibly: -RNA molecules -Regulatory regions -Much is unknown
What allows gene duplication?
Little selective pressure to maintain mutation-free
What are pseudogenes?
Duplicated gene that has become irreversibly inactivated by multiple mutations
What can cause duplication and divergence?
Both copies remain functional while diverging in sequence and pattern of expression
What is an example of duplication and divergence of genes?
Globin gene family derives from common ancestral gene
Gave rise to beta and alpha genes
Translocation moved alpha to separate chromosome
Further duplication and mutation resulted in more specialized beta molecules
How much do human sequences vary?
0.1% from one to another
What do the variations in human sequences cause?
Majority of mutations are neither harmful or beneficial
Neutral mutations can become fixed in a population
What are SNPs single nucleotide polyporphisms
Points in the genome where one group has one nucleotide and another group has another.
Variation occurs at a high rate (1% or more)
What are CNVs-copy number variants?
Presence of many duplications and deletions of large blocks of DNA
Some blocks are common and others rare-significance of most are unknown
