GIGUERE - LECTURE 5

Question 1

which RNA polymerases are present in eukaryotes

Answer 1

there are 3
Pol I
Pol II
Pol III

Question 2

what is the function of RNA pol I

Answer 2

control of rRNA transcription
most divergent from the other polymerases since it has evolved unique characteristics specialised to its role

Question 3

what is the function of RNA pol II

Answer 3

synthesizes all mRNAs and most ncRNAs

Question 4

what is the function of RNA pol III

Answer 4

primarily tRNAs and 5S rRNA

Question 5

what is the subunit composition of RNA pol I and what does that influence

Answer 5

14 subunits, 7 of which are shared with Pol II and/or Pol III
the subunit composition and structure influences processivity, elongation, complex stability and loading onto the DNA during transcription initiation, making the enzyme more efficient for its role

Question 6

role of RNA pol I in ribosome biogenesis

Answer 6

transcription of rRNA by Pol I is the rate limiting step in ribosome biogenesis
cells can make ~2000 ribosomes per minute
transcription of rRNA by RNA pol I accounts for more than 60% of total nuclear transcription

Question 7

where does transcription of rRNA by RNA pol I happen

Answer 7

in the nucleolus
unique because of its high rate of initiation, polymerase density and organisation

Question 8

what are the two mechanisms that regulate rRNA gene transcription

Answer 8

very dynamic mechanism
epigenetic and TF based

Question 9

how is rRNA present in the chromosomes and what are some important sequences related to this rRNA

Answer 9

Question 10

what are the two states of rRNA chromatin

Answer 10

Question 11

how is the rDNA heterochromatin state established

Answer 11

• established by nucleolar remodelling complex (NoRC)
• NoRC consists in TIP5 (TFF-I interacting protein 5) and remodelling factor SNF2h
• TIP5 interacts with promoter bound TFF-I, recognises acetylated lysine 16 of H4 and associates with promoter RNA (pRNA)
• pRNA is a lncRNA derived from IGS that initiates from a week Pol I promoter 1kb upstream of the TSS
• pRNA is processed into a ~150bp RNA comprising of complementary sequences directly adjacent to TSS
  TIP5 recruits NoRC to rRNA promoter and serves as scaffold for several chromatin modifying enzymes
• DNA methyltransferases, histone deacetylase, histone methyltransferase and poly (ADP-ribose) polymerase
• induce heterochromatin state reinforced by SNF2h placing the promoter bound nucleosome in a downstream position to restrict access for TF binding

Question 12

how is the rDNA euchromatin state established

Answer 12

• NORs are decondensed chromatin regions that remain associated with RNA Pol I even in mitosis
• this feature is dependent on the upstream binding factor (UBF), protein that plays a role in both transcription and chromatin structure
• UBF is a basal RNA pol I TF that binds the rDNA promoter and bends DNA using a domain which has high mobility group boxes
• UBF is also located throughout the pre-rRNA coding region and the IGS
• UBF keeps rDNA in a decondensed state by displacing linker histone H1
• UBF is restricted to euchromatin rDNA and does not bind promoter when methylated
• glutamine methylation of histone H2A demarcates active from silent rRNA genes
• H2AQ104me is present only in nucleolus and correlates with RNA pol I activity
• interacts with histone chaperon FACT which is important for RNA pol I elongation

Question 13

what are the TFs associated to RNA pol I

Answer 13

• during PIC formation, RNA pol I and its basal TF bind upstream control element (UCE) and core promoter (CP)
• UBF is a PIC component essential for its formation and binds to both UCE and CP
• UBF contacts RNA pol I via polymerase associated factors PAF53 and PAF49
• UBF also contacts SL1, a PIC components, which leads to cooperative binding by the two TFs
  -SLI is a major subunit factor comprising the TATA BP, and 5 additional TBP associated factors (TAFs) which recognise the CP in a highly specific manner
• UBF/SLI complex assembled on rDNA promoter, RNA pol I is recruited via accessory transcription initiation factor IA (TIF-IA)

Question 14

which external stimuli tightly regulate pre-rRNA synthesis

Answer 14

Question 15

what do the different pathways that control RNA pol I converge to

Answer 15

Question 16

how is RNA pol I controlled by growth factors

Answer 16

Question 17

which cells have elevated RNA pol I transcription

Answer 17

Question 18

what is an example of a disease caused by impaired RNA pol I transcription

Answer 18

Question 19

which RNAs that RNA pol III transcribe

Answer 19

Question 20

what is the subunit organisation of RNA pol III

Answer 20

17 subunits
7 shared with RNA pol I

Question 21

which are the factors that RNA pol III is associated with

Answer 21

TFIIIA
TFIIIB
TFIIIC

Question 22

where are the promoter elements of most RNA pol III transcribed genes located

Answer 22

Question 23

characteristics of TFIIIA

Answer 23

Question 24

characteristics of TFIIIB

Answer 24

Question 25

characteristics of TFIIIC

Answer 25

Question 26

what key role does TFIIIC play

Answer 26

• key role in transcription complex assembly process
• TFIIIC binds the A and B box
• once bound, promoted binding of TFIIIB upstream of the TSS
• TFIIIC also binds to and stabilises preformed TFIIIA-5S rDNA complexes before recruiting TFIIIB

Question 27

how does RNA pol III transcription initiation happen

Answer 27

Question 28

how does RNA pol III transcription happen

Answer 28

Question 29

how does RNA pol III final tRNA transcript happen

Answer 29

Question 30

what is the full RNA polymerase III transcription cycle

Answer 30

Question 31

how is RNA pol III transcription controlled by MafI

Answer 31

Question 32

how is RNA pol III transcription controlled by mTOR

Answer 32