Lecture 19

Question 1

Eukaryotyic chromosomes are packed into

Answer 1

chromatin = DNA + histone proteins

Question 2

chromatin compaction varies over cell cycle… _____
and along the length of the chromosome
based on ____

Answer 2

mitosis vs. interphase

transcriptional activity

Question 3

Basic unit of the chromatin is the

Answer 3

nucleosome

complete nucleosome contains histone octamer, H1, and linker DNA

Question 4

____ bp wraped around each octomer

Answer 4

146 bp

Question 5

Histones ____ charged

Answer 5

basic, positively charged
>20% lys, arg

Question 6

types of histones

Answer 6

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)

Question 7

Histone H1 interactions can

Answer 7

condense chromatin further
(interact with each other - circle)

Question 8

Heterochromatin

Answer 8

highly condensed chromatin

considered genetically ‘inert’
(gene poor, transcriptionally silent) - very little activity

Question 9

Euchromatin

Answer 9

is more accessible (then heterochromatin)
- accessible to TFs

though not always transcriptionally active

Question 10

Chromatin architecture(accessibility to enhancers, promoters) correlates with

Answer 10

transcriptional activity

Question 11

Chromatin is maximally accessible at

Answer 11

transcriptional start sites (TSS)

Question 12

epi” from the Greek:

epigenetic ___

Answer 12

upon, on, over
changes arise from chromatin conformation, not DNA sequence

regulation due to changes above level of DNA sequence

Question 13

Chromatin architecture is controlled by several mechanisms including

Answer 13

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

Question 14

Histone marks are

Answer 14

post-translational modifications of histone tails

Question 15

post-translational modifications of histone tails ocour by

Answer 15

addition/removal of acetyl, methyl, other groups (diferent functional groups)
mainly at H3, H4 (core)

Question 16

Nomenclature of “histone code”

ex. H3K9Me1

Answer 16

H3K9Me1
H3 - Histone 3
K9 - amino acid residue - lysine 9
Me1 - modification - add methyl group

Question 17

Histone marks control gene expression in two ways

Answer 17

1) electrostatic DNA-histone and histone-histone interactions destabilize or condense chromatin

2) modified tails serve as binding sites for proteins

Question 18

Acytalation modifications (modified tails) are set or removed by

Answer 18

chromatin modifying enzymes

HDAC: histone deacetylase
HAT: histone acetyltransferase

Question 19

HAT

Answer 19

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”

Question 20

HDAC

Answer 20

histone deacetylase

Deacetylation condenses

Question 21

Acetylated histones are enriched at

Answer 21

transcriptional start sites

ac- actelation - high at start site

Question 22

Glucose overrides induction by galactose in

Answer 22

yeast GAL system

Question 23

In presence of glucose, the Gal system is repressed despite the presence of GAL4, due to

Answer 23

an epigenetic modification of histones

deacetylation by Tup1-Mig1 complex - binds more tightly

Question 24

Histones are methylated by ___

up to ___ _____ groups can be added

Effect is ____

Answer 24

histone methyltransferases (HMTase)

3 methyl

variable; depends on which residues are modified

Question 25

Histone methylation effect in transcription

Answer 25

variable H3K4me3 is enriched near TSS H3K4me1 is less near TSS

Question 26

DNA methylation usually _____ promoters

Answer 26

silences (reminder - NOT histone methylation)

Question 27

DNA methylation often occurs on

Answer 27

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)

Question 28

DNA methyltransferase recognizes

Answer 28

CpG dinucleotides CpG = side-by-side, 5’-CpG-3’(as opposed to base-paired) adds methyl group (CH3) to cytosine base - making 5-methylcytosine

Question 29

another enzyme called ____ convert 5-methylcytosine back to cytosine

Answer 29

demethylases

Question 30

the methylation pattern of DNA is maintained across cell division BY

Answer 30

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.

Question 31

In mammals,_____CpGs methylated genome-wide Exception in CpG of _____

Answer 31

>70% active promoters - Normally protected from methylation

Question 32

In cancer cells, there are aberrant DNA methylation patterns at ____ and ____

Answer 32

at promoters (effect is local) at insulators (and other regulatory elements) with larger scale consequences

Question 33

Aberrant DNA methylation can dysregulate gene expression on

Answer 33

larger scales CTCF binding is methylation sensitive Loss of binding through methylation allows aberrant enhancer-gene interactions

Question 34

3 examples of epigenetic gene silencing as part of normal organismal development

Answer 34

1) Reproductive versus worker casts in honeybees 2) X chromosome inactivation 3) Genomic imprinting

Question 35

____ controls reproductive status in honeybees

Answer 35

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

Question 36

DNA methylation suppress gene expression by

Answer 36

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

Question 37

recise and widely used technique for analyzing DNA methylation is

Answer 37

bisulfite sequencing

Question 38

Female-specific epigenetic silencing of the X chromosome lasts ___ Inactivation established by ____

Answer 38

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)

Question 39

Genomic imprinting is ___ Durring imprinting ____

Answer 39

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

Question 40

Majority of genes in mammals display Mendelian pattern of expression

Answer 40

normal alleles inherited from each parent are expressed equally <1% of genes are imprinted

Question 41

dosage compensation

Answer 41

shits down/inactivates one copy Mechanism involves DNA and histone methylation

Question 42

Differentially imprinted genes tend to be

Answer 42

clustered

Question 43

Differential imprinting is controlled by

Answer 43

DNA methylation of the IC during gametogenesis

Question 44

Prader-Willi Syndrome (PWS) results from

Answer 44

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

Question 45

Angelman Syndrome (AS) results from

Answer 45

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

Question 46

PWS and AS suggests that

Answer 46

we need both copies of this region

Question 47

epigenetic markers

Answer 47

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

Question 48

Crosstalk between epigenetic markers occurs because

Answer 48

histone modifications attract enzymes and proteins that modify other histones.

Question 49

paramutation

Answer 49

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

Question 50

epialleles

Answer 50

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.

Question 51

X-inactivation center

Answer 51

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.

Question 52

Beckwith-Wiedemann syndrome

Answer 52

small deletions on chromosome 11 that interfere with the normal process of imprinting

Question 53

possible explanation for genomic imprinting is the

Answer 53

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.