Lecture 2: DNA, Chromosomes, and Genomes 2 Flashcards
What is epigenetics?
A form of inheritance that is superimposed on the genetic inheritance based on DNA.
*certain types of chromatin structure can be inherited*
What are 3 examples of inheritance that is superimposed on the genetic inheritance based on DNA (epigenetics)?
- DNA methylation
- Chromatin structure
- Histone modification
What is the difference between genetic inheritance and epigenetic inheritance?
- Genetic Inheritance –> transmitted through genes that have been passed from parents to their offspring (children).
- Epigenetic Inheritance –> is an unconventional finding. It goes against the idea that inheritance happens only through the DNA code that passes from parent to offspring. It means that a parent’s experiences, in the form of epigenetic tags, can be passed down to future generations.
- e.g., DNA methylation, chromatin structure, and histone modification are examples of different “tags” passed from parent to offspring.
Historically, histones were thought to be just involved in packaging of DNA. What findings have challenged this view in molecular biology?
- Mammalian chromatin contains equal mass of histone and non-histone proteins.
- other proteins binding to histones; suggestive of function other than purely structural
- Histones are highly conserved.
- only 2 amino acid differences between mammalian and pea H4:
- therefore, any change must be deleterious
- only 2 amino acid differences between mammalian and pea H4:
- Heterochromatin silences the genes it packages without regard to sequence and is directly inherited by daughter cells.
In which regions of the chromosome are heterochromatin found highly concentrated?
- Centromeres
- Telomers
Is the heterochromatin thought to be replicated early or late in the S phase?
Late replicating and genetically inactive.
True or False:
Heterochromatin contains many genes, but they are resistant to gene expression.
False - heterochromatin contains very few genes; those that are present are resistant to gene expression.
When discussing chromatin, what is the position effect?
- Activity a gene depends on position on chromosome.
- gene will be silenced if relocated near heterochromatin
- Another Definition -> is the effect on the expression of a gene when its location in a chromosome is changed, often by translocation. This has been well described in Drosophila with respect to eye color and is known as position effect variegation (PEV).[1]
An example of gene silencing through position effect variegation is classically discussed via the Drosophila model. What is position-effect variegation?
Position-effect variegation is a variegation caused by the inactivation of a gene in some cells through its abnormal juxtaposition with heterochromatin.
* See figure 4-36 in Molecular Biology of the Cell 5e *
You know that amino acid side chains of histones are subject to a variety of covalent modification, but what other portion of the histone can undergo covalent modifications, too?
Occurs on the core of the histone as well as the tail.
What are the 3 tyeps of covalent modifications are we covering in our evaluation of histone modifications?
- Acetylation of Lysines
- Mono, Di, and Tri-Methylation of Lysines
- Phosphorylation of Serines
In modification of histones by covalent modifications, what does acetylation of lysines result in?
- Acetylation of lysines loosens chromatin structure.
- added by histone acetyl transferases (HATs)
- removed by histone deacetylase complexes (HDACs)
What does the covalent modification of histones by mono, di, or tri-methylation of lysines result in?
- Mono, di, and tri-methylation of lysines leads to more heterochromatin, thus silencing a gene.
- added by mehtyl transferases
- removed by histone demethylases
What does the recruitment of covalent modification enzymes depend on?
Gene Regulatory Proteins
We know that recruitment of covalent modification enzymes depend on gene regulatory proteins and that all of the modifications are reversible, but can persist long after regulatory proteins have disappeared. But what are the consequences for the types of proteins the modified DNA attracts?
This determines how/when/if gene expression takes place.
Which of the core histones does not have any variants?
Variants exist for each of the core histones except H4.
True or False:
Variant histone proteins are present in much smaller amounts than core histones and are less well-conserved.
True
When are major histones synthesized and how/what are they assembled?
- Synthesized during S-phase
- Assembled into nucleosomes on daughter DNA helices just behind the replication fork
When are most variant histones synthesized and where are they inserted?
- Synthesized during interphase
- Inserted into already-formed chromatin
*requires histone exchange process catalyzed by chromatin remodeling complex*
What does the synthesis and insertion of variant histones require in order to be carried out?
Requires histone exchange process catalyzed by chromatin remodeling complex.
Which histone is found in areas where there is a lot of DNA damage? (hint: its special function is DNA repair and recombination)
H2AX
What variant histone has the special function of centromere function and kinetochore assembly?
CENP-A
Which variant histone has a special function involved in gene expression and chromosome segregation?
H2AZ
What importance does the histone code have for the cell?
Histone code has specific meaning for cell, determining how/when DNA is packaged in nucleosome.
How does the histone code aquire its diversity?
- Thousands of combinations of modifications my exist.
- methylation, acetylation, phosphorylation..etc
- Further diversity is created by variant histones.
How does the histone code (markings) get read so that gene expression, gene silencing, or other biological function that are coded for get carried out by cellular machinery?
- Read by the code reader complex.
- involves joint recognition of histone tail and covalent modifications
- Histone code can change as the cells needs change.
**mechanism discussion:
- the code-reader complex binds to specific histone modification on nucleosome
- the binding of the CRC attracts other components
- the protein complex with catalytic activities and additional binding sites attaches to the CRC
- this leads to attachment to other components in nucleus, leading to gene expression, gene silencing, or other biological function
What does the reading of the histone code involve?
Joint recognition of marks at other sites on nucleosome along with tail recognition.
**few meanings are know of the histone code**
**figure 4-44b has an example of H3 tail modification to N-terminal tail** on slide 10 in Powerpoints**
Can modified chromatin spread?
Yes
What spreads the modified chromatin?
- Code reader-writer enzymes spread the mark over chromosome.
- After modifying enzyme marks one or few neighboring nucleosomes, chain reaction can ensue.
Which two proteins compose the code reader-writer complex?
- Histone modifying enzyme (“writer”)
- Code-reader protein
*the gene regulatory protein brings in the first histone modifying enzyme (“writer”) and then the code reader protein comes in and binds to the histone modificaton (mark) on the histone and interacts with the histone modifying enzyme (“writer”) - a chain reaction can ensue*
The reader-writer complex can also contain an ATP-dependent chromatin remodeling protein. What does the formed complex function to do?
They all work together to either condense or decondense long stretches of chromatin as the reader moves along.
What complexes work together to either condense or decondense long stretches of chromatin as the reader moves along?
- “reader-writer” complex
- consists of:
- histone modifying enzyme
- code-reader protein
- consists of:
- ATP-dependent chromatin remodeling protein
How is chromatin remodeling contained to one area of the chromosome?
Barrier sequences halt the spread of chromatin modifications.
- physical barriers
- enzymatic barriers
- HS4 region
How does the HS4 region halt the spread of chromatin modifications, and what does it specifically protect?
- Contains a cluster of histone acetylase binding sites.
- acetylation causes to be more negatively charged, thus DNA doesn’t bind as tightly
- Protects the beta-gloin locus from silencing
What is the kinetochore?
- Dense arrangements of nucleosomes form the kinetochore.
- Structure required for attachment of the mitotic spindle.
What do centromere sequences in humans consist of?
Centromere sequences in humans consist of short repetitive DNA sequences called alpha-satellite DNA.
What does centromeric heterochromatin contain?
Contains centromere-specific H3 histone, CENP-A (variant histone), and other proteins that pack the nucelosomes into dense arrangements to form the kinetochore, a structure required for attachment of the mitotic spindle.
True or False:
Centromeric heterochromatin is defined by assembly of proteins, not the DNA sequence.
True
- alpha-satellites are found at non-centromeric positions in the genome
- new centromeres (neocentromeres) can form spontaneously on fragmented chromosomes, some of which lack alpha-satellite DNA
What defines what a centromere is?
- Defined by assembly of proteins, not DNA sequence:
- alpha-satellites are found at non-centromeric positions in the genome
- new centromeres (neocentromeres) can form spontaneously on fragmented chromosomes, some of which lack alpha satellite DNA
*can also have de novo cnetromere formation = neocentromeres formed without alpha-satellite DNA*
What kind of event is required for de novo centromere formation?
requires a “seeding” event
True or False:
H3-H4 tetramers are directly inherited by the daughter strands at the replication fork.
True
True or False:
Once the de novo centromere is formed, it is directly inherited in each round of replication.
True
* look at slide 15 in lecture for figure *
What type of cell has the largest (interphase) chromosomes known?
Lampbrush chromosomes from amphibian oocytes.
What does the lampbrush chromosome contain on its linear axis that is unique?
Series of large chromatin loops emanating from a linear chromosome axis – the extended chromatin in loop can be acted on by any proteins in the cell.
Where does heterochromatin preferentially associate in the nucleus?
Nuclear Lamina
*each chromosome occupies its own area in the nucleus*
We know that chromatin structures and location changes are important during gene expression. When does decondensation of chromatin occur?
- Decondensation of chromatin during gene transcription:
- “chromosome puffs”
We know that chromatin structure and location changes are important during gene expression. What happens in genes needing to be actively transcribed?
Actively transcribed genes extends out of its area on an extended chromosome loop.
True or False:
The interior of the nucleus is very heterogeneous.
True
Look at slide 21 in lecture 2 Powerpoints.
Title of Slide: How are different activities localized in the nucleus?
- interior nucleus very heterogeneous
- 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
* the figure shows how genes move to different “neighborhoods” within the cell on an extended chromosome loop.
* they move to a “neighborhood” depending on what activity they are seeking – expression, silencing…etc.
You know that two daughter DNA molecules replicated in interphase are separately folded to produce two sister chromatids. How are these chromatids held together?
Chromatids are held together at their centromeres.
In which cell cycles is DNA the most packed?
- Mitotic Chromosomes are highly condensed.
- Net Result:
- each DNA molecule has been packaged into a mitotic chromosomes that is 10,000-fold shorter than its extended length
What is the purpose of the tight, condensed state of a mitotic chromosome?
- Disentangelment of sister chromatids to allow separation for cell division.
- Protection of fragile DNA molecules as separation occurs.
What proteins aid in the compaction of mitotic chromosomes? Also, what do these proteins require to coil the DNA?
- Compaction aided by proteins called condensins.
- use ATP hydrolysis to coil the DNA molecules into chromatids
- major structural component of the core of every metaphase chromosome
What is the major structural component found in the core of every metaphase chromosome?
Condensins
Is the exact mechanism of how condensins work known?
NO - exact mechanism is unknown.
* cells depleted of condensins have abnormal condensation *
What is the definition of homologues?
Genes that are similar in both sequence and function due to common ancestry.
- human homologues exist in yeast, worms, fruit flies, and bacteria
True or False:
Gene sequences are more tightly conserved than genome structure.
True
*size of genome, number of genes, size of introns, abundance of repetitive sequences can be quite different*
** 50% of our DNA material is of repeated sequences **
What is the major clue to gene and protein function when studying genome evolution?
Recognition of sequence similarity.
You know that the number of genes only roughly correlates with phynotypic complexity of an organism. What else adds to the complexity of an organsims genotype?
complexity arises from duplication and expansion of related gene families
How do genomic changes occur?
- Occur as mistakes in DNA replication and repair.
- rare occurrence: 1/1000 nucleotide pairs is randomly changed in the germ line every million years
- movement of transposable elements also play a role
What are the different types of changes that can occur to change the genome?
- Range of changes can occur:
- base pair substitutions
- large scale rearrangements
- duplications
- deletions
- inversions
- translocations
What are the reasons that there is not many changes between organisms in the phylogenetic tree?
- not enough time has yet passed
- recall: rare occurrence of 1/1000 nucleotide pairs is randomly changed in the germ line every million years
- purifying selection:
- elimination of mutations that interfere with important genetic functions
Genome size can vary considerably. Why is the Puffer fish genome 0.4 billion base-pairs and other fish have a 1 billion base-pair genome?
- small size due to small introns in Puffer fish genome
- lacks repetitive DNA
- Intron position of huntingtin gene conserved compared to human gene
What cna multispecies sequence comparisons provide insight into?
Purpose of function of the sequence.
- 5% of human genome is conserved, but only 1.5% codes for proteins
- must have an important function since it is highly conserved
- RNA molecules
- Regulatory regions
- Much is unknown
- must have an important function since it is highly conserved
What is a pseudogene?
A duplicated gene that has become irreversibly inactivated by multiple mutations.
When gene duplication, what is meant by duplication and divergence? Also, give an example.
- Both copies remain functional while diverging in a sequence and pattern of expression.
- Globin gene family derives from common ancestral gene.
When discussing the evolution of the globin gene family, what has happened over the last 500 million years?
- Duplication and mutation gave rise to beta and alpha genes that were still both on chromosome 11.
- Translocation separated alpha and beta genes and moved alpha to chromosome 16.
- Further duplication and mutation resulted in more specialized beta molecules on the 11th chromosome.
What is a single-nucleotide polymorphism (SNPs)?
- 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 is a copy number variant (CNVs)?
- presence of many duplications and deletions of large blocks of DNA
- some blocks are common and others rare
- significance of most is unknown
** SNPs and CNVs are used in forensics and in the clinic (bone marrow transplants) **
What percentage do human sequences vary from one to another ?
0.1%
- human and chimps differ 1%
- majority of mutation are neither harmful or beneficial
- neutral mutations can become fixed in a population
