DNA, Chromosomes, and Genomes 2 (lecture 2) Flashcards
certain types of chromatin structure can be
inherited
A form of inheritance that is superimposed on the genetic inheritance based on DNA
Epigenetics
Epigenetics
A form of inheritance that is superimposed on the genetic inheritance based on DNA
Genomic ______ is the epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner. if the allele inherited form the father is _____, it is thereby silenced, and only the allele from the mother is expressed
Imprinting, Imprinted
Examples of regulation of chromatin structure
-DNA methylation - Chromatin structure - Histone modification
examples of genomic imprinting
Prater Willie (on paternal portion of chromosome 15) Angelman syndrome (on maternal portion of chromosome 15)
Historically, _____ were thought to be just involved in packaging of DNA
Histones (note this is not the case now)
Mammalian chromatin contains equal mass of ___ and _____ proteins
histone and non-histone
histones are ____ conserved
highly
only 2 amino acid differences between mammalian and pea H4; therefore, any change must be
Deleterious
one form of chromatin (______) silences the genes it packages without regard to sequence and is directly inherited by daughter cells
heterochromatin
What challenges 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 (heterochromatin) silences the genes it packages without regard to sequence and is directly inherited by daughter cells
Chromatin that is very condensed
Heterochromatin
other proteins binding to histones is suggestive of
function other than purely structural
Heterochromatin is hout to be
late replicating and genetically inactive
Heterochromatin is highly concentrated at ____ and ___
Centromeres and Telomeres
Heterochromatin contains very few _____; those that are present are
contains very few genes, those that are present are resistant to gene expression
Activity of a gene depends on position on chromosome
Position effect
Position effect
activity of a gene depends on position on chromosome
according to the position effect if a gene is relocated near heterochromatin then it will be
silenced
Less condensed chromatin is known as
Euchromatin
Heterochromatin is replicated
late in S phase
In a typical mammalian cell, more than ____% of the genome is packaged as heterochromatin
10%
When euchromatic regions are converted to heterochromatic state, their genes are
generally switched off
what is silencing of genes
inactivation.
Breakage events that bring heterochromatin near active genes tends to silence them
Position effect variegation
Position effect variegation
breakage events that bring heterochromatin near active genes tends to silence them
The zone of inactivation spreads a ______ distance in different cells
different
early in the developing embryo, ______ forms and spreads into neighboring _____ to different extents in different cells
Heterochromatin, Euchromatin
Amino acid side chains of Histones are subject to a variety of
covalent modifications
Amino acids side chains of histones are subject to a variety of covalent modifications occurring on the ____ of the histone as well as the ____
core, tail
What effect does the Acetylation of lysines on amino acid side chains of histones have
loosens chromatin structure
examples of covalent modifications of amino acid side chains of the four histones in the nucleosome core
- Acetylation of lysines - mono-, di-, and trimethylation of lysines - phosphorylation of serines
Are the covalent modification of the amino acid side chains on histones reversible
yes. (one enzyme adds them and another removes them)
Function of Histone acetyl Transferases (HATs)
acetylation - add acetyl groups to specific lysines
Function of Histone deacetylase complexes (HDACs)
-Remove the acetyl groups for specific lysines
Function of histone methyl transferases
Methylation of lysines - add methyl groups to lysine side chains
Function of histone demethylases
remove methyl groups form the lysine side chains of histones
What recruits the enzymes to the specific sites on the chromatin for the covalent modification of histones
Transcription regulator proteins
function of methylation of the amino acid side chains of histones
leads to tightly packing chromatin and silencing genes
Amino acid side chains of histones are subject to a variety of covalent modifications one of them being the phosphorylation of ____
serines
All the covalent modifications of amino acid side chains of histones are reversible but can _______ after _____ have disappeared. Thereby providing the cell with a memory of
persist long after regualtory proteins have disappeared, thereby providing the cell with a memory of its developmental history
At some positions lysine can be modified either by ___ or by ____, but not both
methylation, acetylation
Why does acetylation of lysines on the N-terminal tails loosen chromatin strucuture
because adding an acetyl group to lysine removes its positive charge, thereby reducing the affinity of the tails for adjacent nucleosomes.
important consequences for the types of proteins the modified DNA attracts: this determines
this determines how/when/if gene expression takes place
Variants exist for each of the core histones except for
H4
Variant histone proteins are present in much _____ amounts than core histones and are ______ _____ conserved
much smaller amounts than core histones and are less well-conserved
Major histones are synthesized during ____ and are assembled into ____ on daughter DNA helices just behind _____
Are synthesized during S-phase and assembled into nucleosomes on daughter DNA helices just behind the replication fork
Variant histones (most anyway) are synthesized during ______ and inserted into _________. This requires _____ catalyzed by ______
are synthesized during interphase and inserted into already-formed chromatin. This requires histone exchange process catalyzed by ATP-dependent chromatin remodeling complex
ATP-dependent chromatin remodeling complexes contain subunits that cause them to bind both to specific sits on _____ and to _____ that carry a particular variant
chromatin and to histone chaperones
due to the ATP-dependent chromatin remodeling complex each histone variant is inserted into chromatin in a
highly selective manner
CENP-A is a variant of histone
H3
What is the special function(s) of H3.3
Transcriptional activation
What is the special function(s) of CENP-A (a variant of H3)
Centromere function and kinetochore assembly
What is the special function(s) of H2AX (variant of H2A)
DNA repair and recombination
What is the special function(s) of H2AZ (variant of H2A)
Gene expression and chromsome segregation
What is the special function(s) of macroH2A (variant of H2A)
Transcriptional repression and X-chromosome inactivation
H2AX is a variant of histone
H2A
H2AZ is a variant of histone
H2A
MacroH2A is a variant of histone
H2A
Thousands of combinations of modifications (methylation, acetylation,phosphorylation) may exist; further diversity is created by
variant histones
Histone code
-One type of marking signals that a stretch of chromatin has been newly replicated, another signals that the DNA in that chromatin has been damaged and needs repair, while others signal when and how gene expression should take place
a _____ allows particular combinations of markings on chromatin to attract additional proteins, so as to execute an appropriate biological function at the right time
reader complex
the histone code has a specific meaning for the cell, determining
how/when DNA is packaged in nucleosome
The histone code is read by the _______, which involves joint recognition of histone tail and covalent modifications
code reader complex
______ involves joint recognition of histone tail and covalent modifications
code reader complex
Histone code can change as
the cell needs change
The code-reader complex binds and attracts other components thus making a protein complex with catalytic activities and additional binding sites which attachment to other components in nucleus leads to
gene expression gene silencing or other biological function
Reading histone code involves joint recognition of marks at other sites on _____ along with ____ recognition
nucleosome along with tail recognition
A large protein complex that contains a series of protein modules each of which recognizes a specific histone mark
Reader complex
The reader complex will bind tightly only to a region of chromatin that contains
several of the different histone marks that it recognizes, therefore only a specific combination of marks will cause the complex to bind to chromatin and attract the additional protein complexes needed to catalyze biological function
The trimethylation of lysine 9 on the histone H3 N-terminal tail attracts the
heterochromatin-specific protein HP1, which induces a spreading wave of further lysine 9 trimethylation followed by further HP1 binding
Trimethylation of lysine 9 one the histone H-3 N-terminal tail has what meaning
heterochromatin formation gene silencing
The trimethylation of lysine 4 with acetylation of lysine-9 on the histone H3 N-terminal tail has what meaning
Gene expression
The trimethylation of lysine-27 on the histone H3 N-terminal tail has what meaning
Silencing of Hox genes X chromosome inactivation
The phosphorylation of serine-10 with the acetylation of lysine-14 on the histone H3 N-terminal tail has what meaning
gene expression
After modifying enzyme marks one or few neighboring nucleosomes, _____ reactions can ensue
chain reactions
______ enzymes spread the mark over the chromosome
Code reader-writer
_____ is an enzyme that creates a specific modification on one or more of the four nucleosomal histones
Writer protein
in order for the reader-writer complex to spread chromatin changes along a chromosome the reader must
recognize the same histone modification mark that the writer produces; its binding to that mark can be shown to activate the writer (note that an ATP-dependent chromatin remodeling complex is required to reposition the modified nucleosomes)
explain the reader-writer complex
- writer enzymes that add or remove modifications to histones in nucleosomes are initially brought to a particular region of chromatin by one of the sequence-specific DNA-binding proteins - after a writer enzyme makes its mark on one or a few neighboring nucleosomes, events that resemble a chain reaction can ensue. - a writer enzyme now works in concert with a reader protein located in the same protein complex. The reader protein contains a module that recognizes the mark and binds tightly to the newly modified nucleosome activating an attached enzyme and positioning it near an adjacent nucleosome - an ATP-dependent chromatin remodeling protein work in concert to either decidedness or condense long stretches of chromatin as the reader moves progressively along the nucleosome-packaged DNA - through many such reader-writer cycles, the reader protein can carry the writer enzyme along the DNA thus spreading the mark in a hand-over hand manner along the chromosome
what are some barrier sequences that halt the spread of chromatin modifications
-Several mechanisms - Physical barriers -Enzymatic barriers
Give an example(s) of an enzymatic barrier that halts the spread of chromatin modification
- -HS4 region -
- The clustering of histones acetylene leads to loose chromatin
- Protects the Beta global locus from silencing
- Contains a cluster of histone acetylene binding sites
- By recruiting a group of highly active histone-modifying enzymes, barriers can erase the histone marks that are required for heterochromatin to spread
- for example, a potent acetylation of lysine 9 on histone H3 will compete with lysine 9 methylation, thereby preventing the binding of the HP1 protein needed to form a major form of heterochromatin
what happens if the HS4 sequence in cells destined to be re blood cells is deleted
-HS4 normally separates the active chromatin domain that contains the human beta-globin locus from an adjacent region of silenced, condensed chromatin. - if the sequence is deleted, the beta-globin locus is invaded by condensed chromatin - this chromatin silences the genes it covers, and spreads to a different extend in different cells, thus causing position effect variegation - the global genes are poorly expressed, and the individuals who carry such a deletion have a severe form of anemia
HS4 acts as an enzymatic barrier because it contains a cluster of binding sites for histone acetylase enzymes. How does this act as a barrier
- Since the acetylation of a lysine side chain is incompatible with the methylation of the same side chain, and specific lysine methylations are required to spread heterochromatin, histone acetylates are logical candidates for the formation of DNA barriers to spreading of heterochromatin
give two examples of physical barriers to block the spread of reader-writer complexes and thereby separate neighboring chromatin domains
- Tethering of a region of chromatin to a large fixed site, such as the nuclear pore complex, can form a barrier that stops the spread of heterochromatin - The tight binding of barrier proteins to a group of nucleosomes can make this chromatin resistant to heterochromatin spreading
Centromeric heterochromatin contains centromere-specific H3 histone, _____, an other proteins that pack the nucleosomes into dense arrangements to form the ______, a structure required for attachment of the mitotic spindle
CENP-A, Kinetochore
The centromere sequences in humans consist of short repetitive DNA sequences called
alpha satellite DNA
new centromeres (neocentromeres) can form spontaneously on
fragmented chromosomes, some of which lack alpha satellite DNA
alpha satellite DNA are also found at non-centromeric positions on chromosomes, indicating
that they are not sufficient to direct centromere formation
Centromeres in complex organisms are defend by _____ , rather than by _____
defined by an assembly of proteins, rather than by a specific DNA sequence
De novo centromere formation requires a _____ event on _______
requires a seeding event on alpha satellite DNA
_____ are directly inherited by the daughter strands at the replication fork
H3-H4 tetramers
Once the initial seeding event on the alpha satellite DNA has occurred
it will be directly inherited in each round of replication
____ chromosomes form amphibian oocytes are the largest chromosomes known
Lampbrush
Lampbrush chromosomes from amphibian oocytes can be
visualized by light microscopy
How the packaging of DNA in chromatin can be inherited following chromosome replication
some of the specialized chromatin components are distributed to each sister chromosome after DNA duplication, along with the specially marked nucleosomes that they bind. After DNA replication, the inherited nucleosomes that are specially modified, acting in concert with the inherited chromatin components, change the pattern of histone modification on the newly formed nucleosomes nearby. This creates new binding sites for the same chromatin components, which then assemble to complete the structure. - A cooperative recruitment of proteins, along with the action of reader-writer complexes, can thus not only account for the spreading of specific forms of chromatin in space along the chromosome, but also for its propagation across cell generations- form parent cell to daughter cells
The lamp brush chromosomes form amphibian oocytes are visualized in a series of
large chromatin loops emanating form the linear chromosome axis
in the lampbrush chromosomes the large loops contain ____ that remains extending in the same manner as the oocyte grows
DNA Sequence
Each chromosome occupies ________ in the nucleus
its own area
Heterochromatin preferentially associates with the
nuclear lamina
Gene-rich regions of chromatin are
dispersed throughout the nucleus
Each of the ___ interphase chromosomes in a human cell tends to occupy its own discrete territory within the nucleus
46
position of a gene in the interior of the nucleus _____ when it becomes highly expressed
changes
most chromsome puffs arise from
the decondensation of a single chromosome band during gene transcription
Chromosome puffs
Decondensation of chromatin during gene transcription
Actively transcribed genes extend
out of its area on an extended chromosome loop
The interior of the nucleus is very
heterogeneous
Distinct biochemical environment of the nucleus have high local concentrations of ___ and _____
enzymes and molecules for specific processes such as DNA repair “foci” and RNA synthesis
Different _____ of the nucleus have effects on gene expression
neighborhoods
Mitotic chromosomes are ____ condensed
highly
final level in chromosome packaging
Mitotic Chromosomes
two daughter DNA molecules replicated in interphase are separately folded to produce _________
two sister chromatids
Chromatids are held together at their
centromeres
how many nanometers wide is a short region of the DNA double helix
about 2 nanometers
how many nanometers wide is a beads on a string form of chromatin
about 11 nanometers wide
How many nanometers is chromatin fiber of packed nucleosomes
about 30 nanometers
who many nanometers is a section of chromosome in extended form
about 300 nanometers wide
How many nanometers wide is a condensed section of chromosome
about 700 nanometers wide
how many nanometers is the entire mitotic chromosome
about 1400 nanometers wide
the net result of mitotic chromosomes packaging is that each DNA molecule has been packaged into a mitotic chromosome that is _______ fold shorter than its extended length
10,000-fold
what is the purpose of condensation of mitotic chromosomes
-Disentanglement of sister chromatids to allow separation for cell division - Protection of fragile DNA molecule as separation occurs
Compaction of DNA is aided by proteins called
condensins
Condensins use _____ to coil the DNA molecules into chromatids
ATP hydrolysis
condensins are a major structural component of the core of every
metaphase chromosome
Cells depleted of condensins have
abnormal condensation
is the exact mechanism of condensation by condensins known
No
Genes that are similar in both sequence and function due to common ancestry
Homologues
Human homologues exist in ____,____,_____ and ____
yeast, worms, fruit flies and bacteria
Recognition of ______ is a major clue to gene and protein function
sequence similarity
_____ are more tightly conserved than genome structure
gene sequences
Size of genome, number of genes, size of introns, abundance of repetitive sequences can be
quite different
number of genes only roughly correlated with ____ complexity of organism
phenotypic
Phenotypic complexity of an organism arises form
duplication and expansion of related gene families
how do genomic changes occur
-as mistakes in DNA replication and repair - movement of transposable elements also play a role
Mistakes in DNA replication and repair are rare and only _______ nucleotide pairs is randomly changed in the germ line every million years
1/1000
what are the range of genomic changes that can occur
-Base pair substitutions - Large Scale rearrangements - Duplications - Deletions - Inversions - Translocations
_____ shows differences between humans and apes
phylogenetic tree
What are some reasons for genome sequence conservations
-not having much time for mutations to occur since lineages separated - purifying selection
what is purifying selection
-Elimination of mutations that interferes with important genetic functions
In comparative genomics we can reconstruct genome evolution by comparing genomes of
contemporary organisms
how many million of years ago did humans diverge from chimpanzees
5 million years
what percent of nucleotide substitution is different between humans and chimpanzees
0.5 percent
the puffer fish genome is ___ billion base pairs compared to ____ billion in other fish
0.4 billion base pairs compared to 1.0 billion in other fish
Can genome size vary considerably
yes
why is the puffer fish genome so small
due to small introns - thus lacks repetitive DNA
in the genome of the puffer fish and humans the intron position of the ____ gene is conserved
huntingtin gene
Sequence comparisons can provide insight into ___ or ____
purpose or function
___% of human genome is conserved, but only ____% codes for proteins
5% of human genome is conserved, but only 1.5% codes for proteins
the 3.5% of the human genome that is conserved and does not code for proteins must have an important function such as
-RNA molecules - Regulatory regions
What are Pseudogenes
a duplicated gene that has become irreversibly inactivated by multiple mutations
explain duplication and divergence in gene duplication? give an example
both copies remain functional while diverging in sequence and pattern of expression - ex. Globin gene family derives form common ancestral gene
in gene duplication with little selective pressure to maintain mutation-free what occurs
many duplication events are likely to be followed by loss-of-function mutations in one or the other gene. This cycle would functionally restore the one gene state that preceded the duplication. Indeed, there are many examples in contemporary genomes where one copy of a duplicated gene can be seen to have become irreversibly inactivated by multiple mutations. Over time, the sequence similarity between such a pseudogene and the functional gene whose duplication produced it would be expected to be eroded by the accumulation of many mutations in the pseudogene - the homologous relationship eventually becoming undetectable
Explain the evolution of the globin gene family
duplication and mutation gave rise to Beta and alpha genes - translocation moved alpha to separate chromosome (chromosome 16) - further duplication and mutation resulted in more specialized beta molecules (both on chromosome 11)
Human DNA sequences vary ____% from one another
0.1%
human and chimp DNA sequences differ ___% from one another
1%
the majority of DNA mutations are neither
harmful or beneficial
______ mutations can become fixed in a population
neutral
What are the intraspecies variations that have been most extensively characterized
single-nucleotide polymorphisms (SNPs)
simply points in the genome sequence where one large fraction of the human population has one nucleotide, while another substantial fraction has another
Single-nucleotide polymorphisms (SNPs)
presence of many duplications and deletions of large blocks of DNA
Copy Number variations (CNVs)
CNVS at some blocks are common and other rare; but the _____ of most is unknown
significance
SNPs (Singl-nucleotide polymorphisms) occur at a high rate of about
1% or more
