Revelation 18:4 4 And I heard another voice from heaven, saying, Come out of her, my people, that ye be not partakers of her sins, and that ye receive not of her plagues.

RNA Processing And Nuclear Splicing Timothy G. Standish, Ph. D.

Introduction The Central Dogma of Molecular Biology Cell DNA mRNA Transcription Reverse tanscription Polypeptide (protein) Translation Ribosome

Eukaryotic Transcription DNA Cytoplasm Nucleus Nuclear pores RNA Transcription G AAAAAA RNA Processing mRNA Export G AAAAAA

A “Simple” Eukaryotic Gene Transcription Start Site 5’ Untranslated Region 3’ Untranslated Region Introns 3’ 5’ Exon 2 Exon 3 Int. 2 Exon 1 Int. 1 Promoter/ Control Region 3’ 5’ Exon 2 Exon 3 Exon 1 Int. 2 Int. 1 Exons Terminator Sequence RNA Transcript

Processing Eukaryotic mRNA 3’ Untranslated Region 5’ Untranslated Region Protein Coding Region 5’ G 5’ Cap 3’ 5’ Exon 2 Exon 3 Int. 2 Exon 1 Int. 1 3’ AAAAA 3’ Poly A Tail Exon 2 Exon 3 Exon 1 Int. 2 Int. 1 RNA processing achieves three things: Removal of introns Addition of a 5’ cap Addition of a 3’ tail This signals the mRNA is ready to move out of the nucleus and may control its life span in the cytoplasm

Introns Introns are intervening sequences that “interrupt” eukaryotic genes and must be removed before uninterrupted exons coding for proteins leave the nucleus as mRNA Three types of intron are known: Group I introns - Found in organelle and bacterial genes along with some lower eukaryotes nuclear genes Can self splice without the aid of proteins Require free GTP for splicing Group II introns - Found in organelle and bacterial genes Differ from Group I introns in sequence and mechanism Nuclear introns - Found in eukaryotic nuclear genes Require proteins and other RNAs for splicing

Nuclear Intron Splicing Exon/intron junctions have short but well conserved consensus sequences The generic sequence of an intron is: GTNN . . . NNAG in DNA or GUNN . . . NNAG in RNA This sequence does not apply to the introns of organelles or yeast tRNA genes Splice sites operate in pairs which are generic. Thus, if the end of one intron is mutated, that intron plus the following exon and next intron will be spliced out The splicing apparatus is usually not tissue specific

Nuclear Intron Splicing AG GU 3’ 5’ Ex 2 Ex 3 In 2 Ex 1 In 1 3’ 5’ Ex 2 Ex 3 Ex 1 Mutation in AG to AA AA GU 3’ 5’ AG Ex 2 Ex 3 In 2 Ex 1 In 1 3’ 5’ Ex 3 Ex 1 Mutation in GU to UU GU 3’ AG Ex 2 Ex 3 In 2 5’ UU Ex 1 In 1 3’ Ex 2 Ex 3 AG 5’ UU Ex 1 In 1

Splicing Order Some gene transcripts have been shown to loose their introns in a consistent order The current model says that the hnRNA adopts different conformations after specific introns are removed thus making other introns available for removal Thus, the removal of introns does not proceed sequentially along the transcript

Common Splicing Mechanism Intron Exon 2 Exon 1 AG A GU 3’ 5’ U A C U A A C (Yeast) 18-40 BP Branch site Left (donor) 5’ splice site Right (acceptor) 3’ splice site Py80NPy80Py87Pu75APy95 (Animal-Subscripts indicate percent frequency) The branch sequence allows identification of the 3’ splice site

Common Splicing Mechanism Folding A OH O HO P AG A G U 3’ 5’ U OH O P G N Exon 1

Common Splicing Mechanism Lariat Formation A OH O HO P N OH O P - + Exon 1 G OH O P U OH O P Transesterification reaction between 2’hydroxyl group on adenine in the branch site and phosphate connecting intron with exon 1

Common Splicing Mechanism Lariat Formation A O HO P OH G OH O P N OH O HO P U OH O P Exon 1

Common Splicing Mechanism Lariat Formation l Yee ha! Exon 2 A AG G U 3’ 5’ Exon 1 Intron Lariat Lariat

Common Splicing Mechanism Lariat Removal Exon 2 A O HO P G N OH Intron - + Exon 1 N OH O HO P A second nucleophilic transesterification reaction, this time between 3’ hydroxyl group on nucleotide 1 in exon 1 and the phosphate connecting intron 2 with exon 2

Common Splicing Mechanism Lariat Removal Exon 2 O N HO P OH Exon 1 A second nucleophilic transesterification reaction, this time between 3’ hydroxyl group on nucleotide 1 in exon 1 and the phosphate connecting intron 2 with exon 2

Common Splicing Mechanism Exon 1 Exon 2 5’ 3’ A AG G U Intron lariat Following excision, the lariat is rapidly degraded

Common Splicing Mechanism Exon 1 Exon 2 5’ 3’ Following excision, the lariat is rapidly degraded

The Spliceosome Spliceosomes are structures that form within the nucleus to remove introns from eukaryotic hnRNA This structure is large, on the order of a ribosome subunit Like the ribosome, spliceosomes are composed of both protein and RNA

The End