Lesson 7 - Cis-acting elements in gene expression

Question 1

Eukaryotic gene expression is usually controlled at the level of initiation of transcription by the

Answer 1

opening of chromatin

Question 2

Whether a gene is expressed depends on

Answer 2

the structure of chromatin locally (at the promoter) and in the surrounding domain

Question 3

Chromatin must be opened before ______ can bind the promoter

Answer 3

RNA polymerase

Question 4

Transcription factor (TF)

Answer 4

Any protein that is needed for transcription initiation, but it is not itself a part of RNA polymerase

Question 5

Basal transcription factors

Answer 5

A group of TFs that are needed for initiation of transcription at all RNA polymerase promoters

Question 6

cis-acting regulatory elements are

Answer 6

sequences or structures found on DNA or RNA molecules

Question 7

Many transcription factors act by recognizing

Answer 7

cis-acting sites on DNA

Question 8

Core promoter

Answer 8

The shortest sequence at which an RNA polymerase can initiate transcription

Question 9

The TATA box consists of

Answer 9

an A-T rich octamer located ~30 bp upstream of the start point

Question 10

Silencer

Answer 10

A short sequence of DNA that can inactivate expression of a gene in its vicinity (binds negative regulators)

Question 11

Housekeeping genes

Answer 11

Genes that are (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types

Question 12

Coactivator

Answer 12

A transcriptional co-regulator that binds an activator (a TF) to increase the rate of transcription

Question 13

Most prominent of the three main RNA polymerases with regard to their activity

Answer 13

RNA pol I

Question 14

RNA polymerase I promoter consists of

Answer 14

a core promoter and an upstream promoter element (UPE)

Question 15

RNA polymerase I has a ______ promoter

Answer 15

bipartite

Question 16

Ribosomal genes are organized in

Answer 16

repeated transcription units (repeats)

Question 17

Non-transcribed intergenic spacer (IGS)

Answer 17

The region between transcription units in a tandem gene cluster

Question 18

SL1 factor binds to the

Answer 18

core promoter

Question 19

UBF1 binds to

Answer 19

UPE

Question 20

RNA polymerase I binds to the ______ complex at the core promoter

Answer 20

UBF1-SL1

Question 21

RNA polymerase III uses ______ and ______ promoters

Answer 21

upstream; downstream

Question 22

Internal promoters in RNA pol III cause initiation to occur at

Answer 22

a fixed distance upstream

Question 23

Upstream promoters in RNA pol III contain three short consensus sequences upstream of the start point that are

Answer 23

bound by transcription factors

Question 24

Assembly factors

Answer 24

Proteins that are required for formation of a macromolecular structure but are not themselves part of that structure

Question 25

Preinitiation complex

Answer 25

The assembly of transcription factors at the promoter before RNA polymerase binds in eukaryotic transcription

Question 26

TAF stands for

Answer 26

TATA-binding protein-associated factors

Question 27

Enhancer

Answer 27

cis-acting DNA sequence that increases the utilization of (most) eukaryotic promoters

Question 28

Enhancers contain _______ elements that assist initiation

Answer 28

bidirectional

Question 29

Enhancers form complexes of _____ that interact directly or indirectly with the promoter

Answer 29

activators

Question 30

Repressor

Answer 30

A protein that inhibits expression of a gene

Question 31

Enhancers can regulate gene expression by forming a

Answer 31

loop with the promoter region of the target gene

Question 32

Chromatin is spatially organized into large domains called

Answer 32

topologically associated domains (TADs)

Question 33

An enhancer typically activates the promoter

Answer 33

nearest to itself

Question 34

An upstream activating sequence (UAS) in yeast behaves like

Answer 34

an enhancer (but only upstream of the promoter)

Question 35

Upstream activating sequence (UAS)

Answer 35

The equivalent in yeast of the enhancer in higher eukaryotes

Question 36

Stem-loop

Answer 36

A secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single-stranded RNA

Question 37

Eukaryotic mRNAs begin with a

Answer 37

cap

Question 38

Eukaryotic mRNAs end with a

Answer 38

poly(A) tail

Question 39

The majority of histone mRNAs in mammals have a _______ in place of a poly(A) tail

Answer 39

3’ terminal stem-loop

Question 40

_____ in an mRNA affect its rate of degradation

Answer 40

Specific cis-elements

Question 41

Destabilizing elements (DEs) can ______ mRNA decay, while stabilizing elements (SEs) can ______ it.

Answer 41

accelerate; reduce

Question 42

AU-rich elements (AREs) are

Answer 42

common destabilizing elements in mammals

Question 43

Iron-response element (IRE)

Answer 43

A cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration

Question 44

Oligo(A) tail

Answer 44

A short poly(A) tail, generally referring to a stretch of less than 15 adenylates

Question 45

Average 5’UTR length (H. sapiens, other mammals, invertebrates, plants)

Answer 45

H. sapiens - 210
Other mammals - 141
Invertebrates - 167
Plants - 133

Question 46

Average 3’UTR length (H. sapiens, other mammals, invertebrates, plants)

Answer 46

H. sapiens - 1030
Other mammals - 440
Invertebrates - 403
Plants - 239

Question 47

Polymerase binding process

Answer 47

1. Opening of the chromatin
2. Binding the basal TFs
3. Binding the polymerase