Lecture 18

Question 1

ability to change sex is called

Answer 1

sequential hermaphroditism

Question 2

In eukaryotes DNA is packaged in nucleosomes into

Answer 2

chromatin

inaccessible to proteins; ground state is “off”

Prokaryotes → circular genome not bound to histone proteins

Question 3

In eukaryotes there are ____ chromosomes, cells, cell types

Answer 3

Multiple

→ timing and pattern of expression varies among them

Question 4

In eukaryotes there are ___ RNA polymerases

Answer 4

3 different

Question 5

In eukaryotes Genes are split (____ interrupted by _____)

Answer 5

exons interrupted by introns

no introns in prokaryotes

Question 6

In eukaryotes pre-mRNA is __, __, and ___ from nucleus

Answer 6

(alternatively) spliced, processed (cap and tail), and transported from nucleus

No coupled transcription/translation line in pro (Pro → no nucleus)

Question 7

In eukaryotes there are many genes, ____ gene density, ___ distances between genes

Answer 7

low gene density (actuall coding seq low % of DNA)
long distances between

Operons are absent or very rare (Pro → operons)

Question 8

ways to regulate gene expression in eukaryotes

Answer 8

1) transcriptional regulation
2) mRNA processing
3) regulation of mature mRNA
4) translation
5) post- translation

Question 9

How is the complexity of cell type specific expression achieved?

Answer 9

1. DNA regulatory elements, and protein regulatory factors in eukaryotesa. Alternative promoters
   b. Enhancers
   c. Insulators

Question 10

DNA regulatory elements are ___ acting

these include

Answer 10

cis

core promoters
Enhancers, silencers (proximal and distal)
insulators

Question 11

core promoters are

Answer 11

binding sites for RNA pol and general transcription factors (GTFs) → creates basal transcription apparatus

Question 12

Enhancers, silencers (proximal and distal) are

Answer 12

binding sites for transcription factors
that through bending of DNA interact with basal transcription apparatus

Question 13

insulators are

Answer 13

binding sites that impose barriers or topological domains for enhancer activity

Question 14

Protein regulatory factors are ___ -acting

these include

Answer 14

trans

transcription factors
coactivators / corepressors

Question 15

transcription factors

Answer 15

(both activators and repressors) directly bind enhancers

Question 16

coactivators / corepressors interact with

Answer 16

transcription factors but do not bind DNA directly

Question 17

In eukaryotes is there one promoter-one gene

Answer 17

NO
single gene can have many promotes (>1)

Question 18

___ of human genes have 2 or more alternative promoters

Answer 18

> 50%

Question 19

Alternative promoters produce different ____ and ____

Answer 19

pre-mRNAs
different protein isoforms

Question 20

protein isoforms

Answer 20

functionally similar proteins with similar but not identical amino acid sequence

transcription starts at different points

Question 21

Duchenne muscular dystrophy (DMD)

genetic muscle disorders caused by

Answer 21

loss of function of dystrophin protein in skeletal muscle

Question 22

(DMD) gene spans ___ , up to ___ exons, and encodes up to ___ amino acids

Answer 22

2.2 Mb
79 exons
3,678 amino acids

Question 23

DMD isoforms from promoters

Answer 23

7 isoforms from 7 promoters

7 different promoters are active in different cell types and tissues

7 resulting protein “isoforms” vary from full-length (427 kDa) to only 71 kDa

Question 24

RNA pol II must bind a core promoter and GTF…but promoter choice influenced by ___

Answer 24

specific transcription factors that bind promoter-proximal (brown boxes in figure) and distal enhancers (green boxes in figure)

[Promoter use depends on ‘enhancers’ and cell type-specific regulatory proteins]

Question 25

Loss of Pax6 causes ____ Because ___

Answer 25

eye defects (conserved across species) Pax6 encodes a transcription factor “master controller” of eye (and CNS) development BUT not all Pax6 mutations are in the coding sequence

Question 26

Some patients with eye defects imacted by PAX6, have no mutation in PAX6 gene, but lack ____ thus, defect is due to ____

Answer 26

enhancer due to chromosomal breakage far downstream (~125kb) due to mis-expression of gene, because of enhancer loss

Question 27

Enhancer of Shh is ___ ____ in Shh causes defects

Answer 27

ZRS Single base substitutions in Shh enhancer cause defects

Question 28

Shh: sonic hedgehog gene, regulates

Answer 28

vertebrate digit identity and number

Question 29

ZRS: Zone of polarizing activity Regulatory Sequence, 800 kb upstream! highly ____

Answer 29

conserved enhancer controlling Shh activity during development

Question 30

Representative human phenotypes caused by base substitutions in ZRS

Answer 30

hand changes limb defects

Question 31

If enhancers can stimulate any gene, even in distant areas, what keeps activity in check?

Answer 31

Insulators

Question 32

Insulator is a DNA sequence that

Answer 32

blocks enhancer if bound by insulator-binding protein (CTCF in vertebrates)

Question 33

CTCF-bound insulators form

Answer 33

chromatin loops called → Called Topologically Associated Domains (TADs) “neighborhoods” of regulatory elements & genes

Question 34

If insulator is not in between inhansor and promoter

Answer 34

insulator binds to proteins CTCF TAD can form - allows enhancer and promoter to interact

Question 35

If insulator is between enhancer and promoter

Answer 35

"insulate effects"

Question 36

long-range transcriptional activation in eukaryotes (with activators, enhancers, transcriptional machinery, repressors, insulators)

Answer 36

Transcriptional activators bind enhancers Activators recruit transcriptional machinery & bend DNA long distances Binding by repressors silence enhancers Binding of insulators blocks enhancers between neighborhoods

Question 37

The yeast GAL system is a ____ that _____

Answer 37

model of how eukaryotes coordinate gene expression (no operons!) includes, but goes beyond, mere cis-acting sites and trans-acting factors (chromatin structure!)

Question 38

GAL4 system contains many ____ motifs

Answer 38

zinc fingers - DNA binding motifs

Question 39

In the yeast GAL system genes include

Answer 39

4 genes encoding enzymes that metabolize galactose for energy 3 regulatory genes located at a distance GAL4, GAL3, GAL80 All genes have individual promoters, coordinately controlled by → UAS enhancers (Upstream Activator Sequence (UAS))

Question 40

similarities and differences between Yeast GAL system vs. E. coli lac operon

Answer 40

similarities: - protein-DNA interactions (think: what’s true of E.coli and elephants, sensu Jacob/Monod) - Inducible metabolic pathway regulated by substrate differences: - coordination arises from enhancers, not operon organization - epigenetic modification

Question 41

How GAL4 system works

Answer 41

GAL4 has two domains (activation (dimer) and binding) GAL4 activator binds UAS gal80 (continuously expressed) binds to and blocks activation domain in presence of galactose, GAL3 releases GAL80

Question 42

GAL4 activation domain controls

Answer 42

expression of structural genes

Question 43

GAL80 mutants that cannot bind GAL4

Answer 43

constitutively express structural genes

Question 44

GAL3 mutants that cannot bind GAL80 are

Answer 44

uninducible

Question 45

GAL4 exemplifies an activator protein binding an enhancer to recruit transcriptional machineryover long distances by

Answer 45

bending DNA

Question 46

Glucose overrides induction by

Answer 46

galactose

Question 47

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

Answer 47

an epigenetic modification of histones (deacetylation by Tup1-Mig1 complex - binds to site present) (disassembling histones) this works (in general) is through alternative splicing

Question 48

Estimated that ____ are alternatively spliced

Answer 48

95% of human genes with multiple exons

Question 49

DNase I hypersensitive sites

Answer 49

regions around the genes become highly sensitive to the action of DNase I durring transcrption

Question 50

chromatin-remodeling complexes (ex. SWI-SNF)

Answer 50

alter chromatin structure without altering the chemical structure of the histones directly bind directly to particular sites on DNA and reposition the nucleosomes, allowing other transcription factors and RNA polymerase to bind to promoters and initiate transcription

Question 51

histone code

Answer 51

modifications have sometimes been collectively called this The tails of histone proteins are often modified by the addition or removal of - phosphate groups - methyl groups - acetyl groups. - or ubiquitination

Question 52

mediator

Answer 52

interacts with RNA pol

Question 53

Many enhancers are themselves transcribed into short RNA molecules called

Answer 53

enhancer RNAs (eRNAs)

Question 54

Sometimes a number of enhancers are clustered together to form a

Answer 54

super-enhancer

Question 55

response elements

Answer 55

are regulatory sequences short stretches of DNA that typically contain the same consensus sequences at varying distances from the genes being regulated If the same response element is present at multiple genes, it allows all those genes to be activated by the same stimulus. (ex. heat-shock elements)

Question 56

gene regulation through RNA splicing example

Answer 56

sex determination in fruit flies. Sex differentiation in Drosophila arises from a cascade of gene regulation