Mtc: Jan 10 Part 1-Transcription Of Eukaryotic Genes

Front 1

Where do cell type differences arise?

Back 1

-When specific genes are transcribed into RNA

Front 2

The _______ of transcription can occur at multiple points in gene expression.

Back 2

-Regulation

Front 3

In general, each cell expresses only __-___% of the total number of genes.

Back 3

20-50%

Front 4

What aer used to demonstrate the specific mRNA expression profile of a given cell?

Back 4

-Expression microarray

Front 5

What is of critical importance for the genome as deomonstrated by examples of dosage compensation in the human genome?

Back 5

-Control of transcription

Front 6

Genes for protein complexes that are assemebled from multiple subunits are also ___ transcriptional regulated. (What are some examples)

Back 6

-Tightly
-Alpha and Beta-globins

Front 7

Types of RNA

Back 7

-rRNA
-tRNA
-snRNA
-mRNA

Front 8

3 RNA polymerase complexes in eukaryotes

Back 8

-RNA polymerase I
-RNA polymerase II
-RNA polymerase III

Front 9

What transcribes rRNA

Back 9

-RNA polymerase I
-RNA polymerase III

Front 10

What transcribes tRNA

Back 10

-RNA polymerase III

Front 11

Together, RNA polymerase I and III account for ____% of all cellular trancription.

Back 11

95%

Front 12

What transcribes mRNA

Back 12

RNA polymerase II

Front 13

Drugs can be used to distinguish between transcription by different polymerases

Back 13

-Alpha-amanitin (RNA polymerase II=high senstivity; RNA polyermase III=moderately sensitive; RNA polymerase I=insensitive)
-Actinomyocin D: intercalates in DNA and inhibits trancription; RNA polymerase I=sensitive

Front 14

Actinomyocin

Back 14

intercalates in DNA and inhibits trancription; RNA polymerase I=sensitive

Front 15

Alpha-amanitin

Back 15

RNA polymerase II=high senstivity; RNA polyermase III=moderately sensitive; RNA polymerase I=insensitive

Front 16

Initiator (INR)

Back 16

Encompasses the transcritpion start site (usually the A in the consensus sequence YYANWY

Front 17

TATA box

Back 17

26-31 nucleotide upstream of the initiator

Front 18

DPE

Back 18

28-33 nucleotide sequence downstream of the start site

Front 19

Genes with weak TATA boxes often have a strong _____, and vice versa.

Back 19

DPE

Front 20

What do eukaryotic RNA polymerase II also need to bind to promotors?

Back 20

-Basal and general transcription factors

Front 21

Transcription initiation requires the assembly of __ ____ ____ using a number of ___ ___ ____

Back 21

-Pre-initiation complex (PIC)
-Genearl transcription factors

Front 22

A key factor for transcription initiation is the -__ ___ ___ which first recongizes and binds to the TATA box in promotors that contain one.

Back 22

TATA-binding protiein (TBP)

Front 23

Why is TBP a necessary par tof PIC?

Back 23

-Importnat for transcription by RNA polymerase I and III

Front 24

TBP is part of a larger complex termed _______, includes additional factors called _____.

Back 24

-TFIID
-TAF

Front 25

What is the function of some TAFs?

Back 25

Capable of recognizing the other promotor sequence motifs, including INF and DPE

Front 26

TFIID is bound by _______, which can also bind to ____ just upstream and/or downstream of the TATA box.

Back 26

TFIIB

Front 27

What happens after RNA polymerase II recruited to the promotor?

Back 27

-Recruited to promotor
-Binds TFIIB through another factor called TFIIF
-Additional factors bind to the complex, including TFIIE and TFIIH, each of which consists of multiple subunits

Front 28

What do both TFIIF and TFIIH complexes include? What's its function?

Back 28

-DNA helicase that unwinds DNA at the promotor

Front 29

DNA unwinding at the promotor is termed ___ ____. This completes the formation of the ____ and ____ transcription can initiate.

Back 29

-Promotor melting
-PIC
-Transcription

Front 30

C-ternminal domain (CTD)

Back 30

-C-terminal end of RNA polymerase II consists of 52 repeats of heptapeptide YSPTSPS

Front 31

What does TFIIH complex include? Whats its function? What does it allow?

Back 31

-Kinase subunit
-Phosphorylates the CTD at Ser5 (the second S in the heptapeptide)
-This phosphorylation event allows the RNA polymerase II to escape the promotor region

Front 32

Promotor Clearance

Back 32

-Phosphorylation that allows the RNA polymerase to escape the promotor region
-Synthesis of the nascent transcript begins

Front 33

Transcriptional Pausing

Back 33

-Phosphorylated CTD is bound by other factors (DSIF, NELF) that prevent the RNA polymerase from elongating
-Necessary to allow RNA processing

Front 34

Why is transcriptional pausing necessary?

Back 34

-To allow DNA processing-- in this case the 5' capping of mRNA---to occur properly

Front 35

Once the 5' cap has been added, the capping enzyme recriutn and additional factor, termed ___ ___ ___ ___ __.

Back 35

Positive transcription elongation factor b (PTEF-b)

Front 36

Function of PTEF-b

Back 36

-Phosphorylates the CTD of RNA polymerase II, but at a different site than TFIIH (SER2, the 2nd S in the heptapeptide)
-Phosphorylates DSIF=results in dossciation of DSIF and NELF, and the release of RNA polymerase II from transcriptional pause

Front 37

During elongation, _____ remains associated with RNA polymerase II.

Back 37

-TFIIF

Front 38

What occurs when transcription is finally terminated?

Back 38

-Transcript of RNA polymerase are both released
-RNA polymerase is dephosphorylated at the CTD, and re-recriuted to form another PIC

Front 39

The processing of RNA occurs with ____ _____.

Back 39

Transcriptional elongation

Front 40

What serves as a platform for RNA processing factors during elongation?

Back 40

-CTD

Front 41

The degree to which the _____ is phosphorylated determines whether pausing, splicing, or polyadenylation should occur

Back 41

-CTD

Front 42

Absence of trans-activaor or transcription (Tat) in HIV

Back 42

HIV transcription initiates, but results in the formation of only short transcripts, as RNA polymerase II pauses and evetually fall off the template

Front 43

What does trans-activator or transcription in HIV?

Back 43

-Recognizes a specific structure in the 5' portion of the HIV transcript and recruits PTEF-b
-Phosphorylation of RNA polymerase II by PTEF-b results in efficient HIV elongation

Front 44

HIV latency

Back 44

-Infection characterized by the absence of production of full-length HIV
-Only short transcripts are produced

Front 45

When is latent HIV activated?

Back 45

-When supplied with Tat (could be activated by stress)

Front 46

___ is a drug that inhibits the PTEF-bkindase.

Back 46

DRB

Front 47

What does treatment of cells with DRB do?

Back 47

-Inhibits elongation by RNA polymerase II

Front 48

Why doesn't pre-initiation complex assembly happen at all promotors at all times?

Back 48

-Preinitiation complex assembly for RNA polymerase II is inefficient and the core promotor region is often not sufficient.
-Eukaryotic DNA is packaged into chromatin, which can render promotors inaccessible to some or all of the basal machinary

Front 49

What subjects all eukaryotic promotrs to regulation?

Back 49

Specific transcription factors

Front 50

Specific transcription factors

Back 50

Proteins that bind immediately upstream of a promotor

Front 51

The outside of the DNA helix can be "read" by ___ ___ ____ ____.

Back 51

DNA-binding transcription factors

Front 52

Types of DNA -binding domains

Back 52

-Helix-turn-helix
-Zinc finger
-Leucine finger

Front 53

Helix-turn-helix domain

Back 53

-type of DNA-binding domain
-2 alpha-helices joined by a short arm
-->Recognition helix (one of the helix)
---> Other helix is required for positioning of the recognition helix with respect to the rest of the molecule

Front 54

Zinc Finger Domain

Back 54

-Characterized by various combinations of protein secondary structures which contain His and Cys residues at critical positions that coordinate an atom of zinc

Front 55

What 2 amino acids do Zinc Finger Domain interact?

Back 55

-His and Cys

Front 56

Leucine Zipper Domain

Back 56

-When every 7th residue of an alpha-helix is hydrophobic (e.g.leucine), they are arranged on one side and can interact with another similarly organized alpha-helix and dimerize with it.

Front 57

Transcriptional activators can interact within gene regulatory sequences:

Back 57

-Binding of one factor can facilitate binding of another
-Two factors that facilitate different steps of transcription can work synergistically to activate gene
-Transcription factors are often components of larger multiprotein complexes, and so binding of one factor to a promoter results in the association of the entire complex

Front 58

Activation domains can work in several ways, but the general rule is _____.

Back 58

-Recruitment (they directly interact with general transcription factors, thus facilitating their association with the promotor)

Front 59

What is the major function of the activation domains of transcription factors?

Back 59

-Recruitment of additional factors that serve to modify chromatin structure

Front 60

What is transcription complex assembly inhibited by?

Back 60

-Packaging of eukaryotic DNA into chromatin

Front 61

What is the regulatory region of a gene characterized by?

Back 61

The presence of specific DNA sequences near the promoter that facilitate the binding of specific transcription factors

Front 62

What can facilitate preinitiation complex formation? How does this occur?

Back 62

-Specific transcription factors
-By recruiting components of the general transcription machinery or chromatin modifying activities through the activation of domains on the transcription factor

Front 63

________ is a helix-loop-helix transcription factor that is expressed in hemtopoietic progenitor cells, but down-regulated during differention.

Back 63

SCL/TAL 1

Front 64

_____ is widely expressed in many tissues, and is not down-regulated during hematopoietic differentiation.

Back 64

SIL

Front 65

The most common chromosomal rearrangement in T-cell acute lymphoblastic leukemia (T-ALL) involve _____. (What does this result in?)

Back 65

-SCL
-Misexpression of SCL/TAL1, which contributes to T-ALL by directing the misexpression of all the genes that SCL/TAL1 regulates

Front 66

Transcription factors can also act as ____ _____. (How?)

Back 66

-Transcription repressors
-The pattern of gene expression often demand more specific mechanisms to shut down the transcription of certain genes
-They can work by a variety of mechanisms: interference with binding of activators to DNA or with their activity, recruitment of different histone- or chromatin-modifying factors, etc

Front 67

Example of multiple promotors

Back 67

the enzyme porphobilinogen (PBG) deaminase=an enzyme in heme biosynthesis that is required in all cells ; has 2 promoters (one active in all cells, one only in erythroid cells)

Front 68

Enhancers

Back 68

-DNA sequences that mediate transcriptional activation
-Represent distance- and position-independent activating sequences

Front 69

How are Enhancers defined...

Back 69

-Ability to mediate transcriptional activation regardless of how far they are
-Can activated gene transcription whether located upstream or downstream of the promoter, or within a gene
-Dominant regulatory elements in transcriptional regulation genome-wide

Front 70

Mechanisms of Enhancers: 2 General Ideas

Back 70

-Looping: enhancer physically interacts with promoter, with intervening DNA looped out
-Linking: multiprotein complex nucleates at the enhancer complex nucleates at the enhancer, and then propagates along DNA to the promoter

Front 71

What mechanisms protect neighboring promoters being activated by an enhancer?

Back 71

-Specificity: Promoter does not interact with all enhancers
-Inactivity: nearby genes are actively silence, so the enhancer has only one possible target
-Insulators: regulatory sequences that block enhancer activity

Front 72

Transcription factors can regulate large subsets of genes....

Back 72

-Singe transcription factor can be primarily responsible for the activation of multiple genes
-Single factor can specify the formation of a given cell type, tissue type, or organ

Front 73

Transcription factors can form ____ ____. Give example

Back 73

-Regulatory circuits
-Transcription factor can activate transcription of its own gene, producing a positive feedback loop