Lecture 25 - Alternative Splicing Flashcards
What is PABPN1 short for?
Poly A Binding Protein N (found in nucleus) 1
What is a pervasive transcription?
It is a non-coding and unstable generalized transcription.
Why are antisense transcripts rapidly degraded?
In antisense transcripts, there are very few binding sites for U1 snRNPs and there are a number of polyadenylation signal sequences. U1 and its corresponding snRNPs have the ability to block the binding of the core multiprotein complex that will add the poly A tail and cleave the transcript. So in the absence of U1 snRNP binding sites and a high frequency of poly A signals, the anti-sense transcripts end up being cleaved and chewed up by 5’-3’ exonuclease activity.
What protein recognizes where the exon is at the 3’ end of an intron?
U2AF
What happens when U2AF settles down on the A-G di-nucleotide?
Interactions occur with the pyridime rich region of the RNA and U2 snRNP is recruited to interact correctly with the branch point A.
Why do humans have so much more complexity than C. elegans even though we only have relatively few more genes?
Humans undergo alternative splicing.
What does alternative splicing allow for?
Alternative splicing allows for one single RNA to be made into several different single proteins based on the exons kept from the pre-mRNA to the mRNA.
What are the various mRNAs that arise from alternative splicing called?
Alternative Isoforms
Briefly describe the two isoforms of the fibronectin gene?
Two important exons in the gene are EIIIB and EIIIA. They encode specific protein domains that are sticky. In fibroblasts (cells that give rise to the skin), the isoform of fibronectin that is spliced together and expressed includes both of these, which allows for the fibroblasts to adhere to other fibroblasts or other molecules. In hepatocytes in the liver, the isoform of fibronectin does not contain these exons. The fibronectin made in the liver is secreted into the blood and circulates, which is important for clotting. You wouldn’t want this fibronectin to have sticky domains as it would impede blood flow.
What is so special about the Drosophila gene Dscam?
The gene has an extraordinary number of exons that each give rise to a number of alternative mature mRNAs. Each exon region has a number of splicing alternative, and we ultimately end up with 40,000 isoforms that can theoretically be made in the cell.
Which molecular biological phenomon is sensing auditory frequencies dependent on?
Alternative Splicing
How does alternative splicing control sex determination in Drosophila?
Early in development in females (following chrosomal counting), a maternal promoter is activated for the sex-lethal (Sx1) gene. Later in development, the female-specific promoter is repressed and a different “late” sex-lethal promoter is activated in both males and females. However, only in females are the sex-lethal proteins produced since this process is based on splicing regulator. “Early” Sx1 causes exon 3 to be spliced out. Exon 3 contains a in-frame stop. As such, the “late” sex-lethal pre-mRNA and a functional Sx1 protein are generated only in the presence of an “early” Sx1 protein (which happens in females). Sx1 goes on to act similarly on Tra (transformer) transcription, meaning only females produce this protein (since males don’t splice out Tra exon 2, which contains a stop site). Tra goes on to interact with two other proteins (Tra2 and RBP1) to form a complex that acts as an SR protein for decorating specific exons. These complexes are brought to an mRNA corresponding to the double sex (Dsx) gene, which confers information on whether one will be male or female. The presence or absence of the complex will determine how Dsx is spliced and what sex is expressed.
Which enzymes change single nucleotides in the RNA?
Deaminases
What are adenosine and cytosine commonly change to by deaminase?
Adenosine to Inosine (A to I) and Cytosine to Uracil (C to U)
What process leads to changed nucleotides that show up in the cDNA but not in the genetic sequence?
RNA Editing
