Lecture 10: Splicing and Termination in mRNA Processing

First step in recognizing intron/exon borders

Start with pre-mRNA; introns are being capped while the transcript is synthesized.

Function of U1 snRNP during splicing

Binds to the 5' splice site using snRNA complementary base pairing.

U2AF

U2 Associated Factor, not a snRNP. Binds to Poly(Y) tract and SR proteins.

How U2AF helps U2 snRNP

Helps U2 bind to the branch point (reactive adenosine that is bubbled out).

snRNPs that enter as a complex in splicing

U5, U4, and U6 snRNPs.

Function of U5 snRNP

Binds near both 5' and 3' splice sites; displaces U1 and U4.

Function of U6 snRNP

Acts as a ribozyme to catalyze RNA cleavage at the splice site.

Role of U4 in splicing

Inhibits U6 activity until displaced.

What happens when U6 becomes active

U6 cleaves the 5' splice site.

Formation after the 5' splice site is cleaved

Lariat intermediate where the 5' end of the intron binds the branch point.

What happens after 3' splice site cleavage

Exons are ligated together and all components are recycled.

ESEs and SR proteins

Exonic Splicing Enhancers and splicing regulator proteins that help recruit snRNPs and identify exons.

Alternative splicing

Mechanism where one RNA transcript is spliced in different ways to create multiple proteins.

Regulation of alternative splicing

Using strong/weak splice sites and regulatory elements like ESEs and ESSs.

Weak splice site

A splice site not recognized without ESEs and SR proteins.

Strong splice site

A site usually recognized unless blocked by ESSs.

ESSs

Exonic Splicing Silencers that block strong splice sites.

Role of SR proteins in splicing regulation

They bind to ESE or ESS elements to activate or repress splicing.

Alternative splicing activation

SR proteins bind ESEs at weak splice sites to include exons - a form of positive regulation.

Alternative splicing repression

Repressors block strong splice sites unless no signal is present - a form of negative regulation.

Torpedo Model of transcription termination

After cleavage, the exonuclease Rat1/Xrn2 degrades the remaining RNA from the 5' end, catches up to RNA polymerase II, and knocks it off the DNA, terminating transcription.