Lecture 21: RNA Processing

Question 1

premRNA processing

Answer 1

1. Transcription and 5’ Cap
2. Poly(A) site cleavage
3. PolyAdenylation
4. RNA splicing

Question 2

5’ Capping of pre mRNA

Answer 2

Once the RNA has reached 25 nt the 7’ methylguanylate cap is added to 5’ by 5’5’ triphosphate link
Animal and higher plant 2’ methylation of first nt
Vertebrates methylate 2nd nucleotide

Question 3

Benefits to capping

Answer 3

protects pre-mRNA from degradation
facilitates nuclear export
assists recognition by translation factors

Question 4

RNA capping and transcription

Answer 4

RNA Pol II has CTD rich of Ser-rich 7-mer repeats

YSPTSPS(52) humans
‘‘(26) for yeast

CTD phosphorylated at pause stage of transcription

Question 5

Ser2 phosphorylation vs Ser5

Answer 5

Ser 5 phosphorylated at pausing stage then Ser2 phosphorylated after pause to recruit more processing proteins

Question 6

Pol I,II,III and CTDs

Answer 6

Only Poly II has a CTD so their mRNAs are capped

Question 7

Cleavage and polyadenylation

Answer 7

Polym II released at terminator
3’ AAUAAAxxxxxG/U recognized by CPSF,CStF,CFI and CFII.
Cleave at polyA site then PAP make poly A tail

Question 8

Two Phases of PolyAdenylation

Answer 8

slow phase where PAP adds 12 A

Fast fast by PABPN1 200A

Question 9

mRNA with no poly A tail

Answer 9

Histone mRNAs because unique 3’ UTR region secondary structure

Question 10

hnRNPs

Answer 10

hnRNP contribute to further steps of NRA processing
They are modular containing one or more RNA binding domains and IDPD (intrinsically disordered protein domains)

Question 11

Common RNA binding domains

Answer 11

KH
RGG
Pumilio/Puf

Question 12

hnRNPs Funciton

Answer 12

hnRNPs stop secondary sequence specific structures and impose a uniform structure recognizable by processing enzymes

Can regulate pre-mRNA splicing if bound near splice sites

hnRNPs can cycle in and out of the nucleus so useful for export of the RNA

Question 13

RNA Splicing

Answer 13

Removal of Introns

Question 14

Introns

Answer 14

Discovered from discrepancy between gene size and complexity

Question 15

Intron Borders

Answer 15

highly conserved but not sufficient for in silicon prediction of mRNA sequences

Question 16

Intron splicing

Answer 16

Trans-esterification
hydroxyl attacks 5’ P of G to make lariat

free 3’ of preceeding exon attacks the 5’ P of first residue