Lecture 19 Flashcards
Eukaryotyic chromosomes are packed into
chromatin = DNA + histone proteins
chromatin compaction varies over cell cycle… _____
and along the length of the chromosome
based on ____
mitosis vs. interphase
transcriptional activity
Basic unit of the chromatin is the
nucleosome
complete nucleosome contains histone octamer, H1, and linker DNA
____ bp wraped around each octomer
146 bp
Histones ____ charged
basic, positively charged
>20% lys, arg
types of histones
5
H2A, H2B, H3, H4 - form octamer around which DNA is wrapped
linker histone: H1 - binds DNA that links adjacent nucleosomes (acts as tape - seals coilid DNA)
Histone H1 interactions can
condense chromatin further
(interact with each other - circle)
Heterochromatin
highly condensed chromatin
considered genetically ‘inert’
(gene poor, transcriptionally silent) - very little activity
Euchromatin
is more accessible (then heterochromatin)
- accessible to TFs
though not always transcriptionally active
Chromatin architecture(accessibility to enhancers, promoters) correlates with
transcriptional activity
Chromatin is maximally accessible at
transcriptional start sites (TSS)
epi” from the Greek:
epigenetic ___
upon, on, over
changes arise from chromatin conformation, not DNA sequence
regulation due to changes above level of DNA sequence
Chromatin architecture is controlled by several mechanisms including
replacement of histones with histone variants
“remodeling” of nucleosomes
→ movement of nucleosomes along DNA
covalent modification of histones (“marks”)
→ post-translational modifications to histone “tails” in nucleosome
DNA methylation
Histone marks are
post-translational modifications of histone tails
post-translational modifications of histone tails ocour by
addition/removal of acetyl, methyl, other groups (diferent functional groups)
mainly at H3, H4 (core)
Nomenclature of “histone code”
ex. H3K9Me1
H3K9Me1
H3 - Histone 3
K9 - amino acid residue - lysine 9
Me1 - modification - add methyl group
Histone marks control gene expression in two ways
1) electrostatic DNA-histone and histone-histone interactions destabilize or condense chromatin
2) modified tails serve as binding sites for proteins
Acytalation modifications (modified tails) are set or removed by
chromatin modifying enzymes
HDAC: histone deacetylase
HAT: histone acetyltransferase
HAT
histone acetyltransferase - neutralizes pos. charge of K; loosens association with negatively charged DNA
lysince has pos charge - interacts with DNA (-) to condence - add acytl group - nutralizes pos charge so + and - interaction occours with less strength
Acetylation “opens”
HDAC
histone deacetylase
Deacetylation condenses
Acetylated histones are enriched at
transcriptional start sites
ac- actelation - high at start site
Glucose overrides induction by galactose in
yeast GAL system
In presence of glucose, the Gal system is repressed despite the presence of GAL4, due to
an epigenetic modification of histones
deacetylation by Tup1-Mig1 complex - binds more tightly
Histones are methylated by ___
up to ___ _____ groups can be added
Effect is ____
histone methyltransferases (HMTase)
3 methyl
variable; depends on which residues are modified
Histone methylation effect in transcription
variable
H3K4me3 is enriched near TSS
H3K4me1 is less near TSS
DNA methylation usually _____ promoters
silences
(reminder - NOT histone methylation)
DNA methylation often occurs on
cytosine nucleotides that are immediately adjacent to guanine nucleotides
referred to as CpG dinucleotides
(where p represents the phosphate group that connects the C and G nucleotides)
DNA methyltransferase recognizes
CpG dinucleotides
CpG = side-by-side, 5’-CpG-3’(as opposed to base-paired)
adds methyl group (CH3) to cytosine base - making 5-methylcytosine
another enzyme called ____ convert 5-methylcytosine back to cytosine
demethylases
the methylation pattern of DNA is maintained across cell division BY
Immediately after semiconservative replication, the cytosine base on the template strand is methylated, but the cytosine base on the newly replicated strand is unmethylated.
Methyltransferase enzymes recognize the hemimethylated state of CpG dinucleotides and add methyl groups to the unmethylated cytosine bases,
resulting in two new DNA molecules that are fully methylated.
In mammals,_____CpGs methylated genome-wide
Exception in CpG of _____
> 70%
active promoters - Normally protected from methylation
In cancer cells, there are aberrant DNA methylation patterns
at ____ and ____
at promoters (effect is local)
at insulators (and other regulatory elements) with larger scale consequences
Aberrant DNA methylation can dysregulate gene expression on
larger scales
CTCF binding is methylation sensitive
Loss of binding through methylation allows aberrant enhancer-gene interactions
3 examples of epigenetic gene silencing as part of normal organismal development
1) Reproductive versus worker casts in honeybees
2) X chromosome inactivation
3) Genomic imprinting
____ controls reproductive status in honeybees
DNA methylation
queen and woker - identical genetic material
Royal jelly - fed only to queen bees - blocks methylation (silencing expresson of Dnmt3 - normally adds methyl groups)
DNA methylation is responsible for worker phenotype
DNA methylation suppress gene expression by
1) presence of the methyl group in the major groove inhibits the binding of transcription factors and other proteins required for transcription to occur.
2) 5-methylcytosine also attracts certain proteins that directly repress transcription
3) DNA methylation attracts histone deacetylase enzymes, which remove acetyl groups from the tails of histone proteins, altering chromatin structure in a way that represses transcription (s
recise and widely used technique for analyzing DNA methylation is
bisulfite sequencing
Female-specific epigenetic silencing of the X chromosome lasts ___
Inactivation established by ____
a lifetime
Mechanism of dosage compensation (shits down/inactivates one copy) involving DNA and histone methylation
Inactivation established by large noncoding RNA - transcript exists - recruits factors - methylate - inactivation
(XIST: X-inactivation-specific transcript
specified by the X-inactivation center (XIC) on the X to be inactivated)
Genomic imprinting is ___
Durring imprinting ____
gender-specific gene silencing
maternal/paternal alleles differentially marked by DNA methylation (of IC, imprinting center) during gametogenesis
results in mono-allelic parent-of-origin-specific expression of subset of genes
Majority of genes in mammals display Mendelian pattern of expression
normal alleles inherited from each parent are expressed equally
<1% of genes are imprinted
dosage compensation
shits down/inactivates one copy
Mechanism involves DNA and histone methylation
Differentially imprinted genes tend to be
clustered
Differential imprinting is controlled by
DNA methylation of the IC during gametogenesis
Prader-Willi Syndrome (PWS) results from
loss of expression from paternal-only expressed genes on chr 15
Loss of expression most commonly caused by interstitial deletions of chr 15
Characterized by infantile feeding problems, hyperphagia, developmental delay, intellectual disability, behavioral problems
Angelman Syndrome (AS) results from
loss of expression from maternal-only expressed genes on chr 15
Loss of expression most commonly caused by interstitial deletions of chr 15
Characterized by infantile feeding problems, hyperphagia, developmental delay, intellectual disability, behavioral problems
PWS and AS suggests that
we need both copies of this region
epigenetic markers
histone modifications, as well as changes to DNA that do not involve the base sequence, have been shown to be associated with the level of transcription
Crosstalk between epigenetic markers occurs because
histone modifications attract enzymes and proteins that modify other histones.
paramutation
an interaction between two alleles that leads to a heritable change in the expression of one of the alleles
Some epialleles may undergo paramutation, a trans-interaction between alleles that induce heritable expression change in one allele.
fetures
- tramited even when the allele that brought about the alteration is no longer present.
- altered allele is now able to convert other alleles to the new phenotype
- no associated DNA sequence changes in the altered alleles
epialleles
Alleles that do not differ in their base sequence but have epigenetic differences that produce heritable variations in phenotypes.
Some epialleles may undergo paramutation, a trans-interaction between alleles that induce heritable expression change in one allele.
X-inactivation center
a particular segment of the X chromosome that controls the particular X chromosome inactivated within a cell
key player in X inactivation is a gene called Xist (for X-inactive specific transcript), which encodes a long noncoding RNA (lncRNA)
however Several genes within the X-inactivation center interact to bring about the inactivation of one X chromosome while keeping the other X chromosome active.
Beckwith-Wiedemann syndrome
small deletions on chromosome 11 that interfere with the normal process of imprinting
possible explanation for genomic imprinting is the
genetic conflict hypothesis
suggests that there are different and conflicting evolutionary pressures acting on maternal and paternal alleles for genes (such as Igf2) that affect fetal growth.
