Gene Structure 4 Flashcards
Who came up with the intron early theory?
Walter Gilbert
What is the intron early theory?
That introns originated in prokaryotes but were lost due to genome streamlining - suggesting that eukaryotes inherited all introns from prokaryotic ancestors.
Believed introns promoted gene evolution as they permitted the shuffling of genes - produced more complex genes and larger protein collection.
What is the intron late theory?
Stated that introns were unique to eukaryotes and that new introns have been emerging throughout eukaryotic evolution - prokaryotes have never contained introns or the spliceosome.
What is the current intron theory?
Somewhere in between the early and late theory -
Group II introns originated in the mitochondrial ancestor and these invaded the host genome upon mitochondrial endosymbiosis.
(still debated).
Why can introns be a burden to a host?
3
Cell must contain spliceosome and this is a huge complex.
Also increased energy cost as RNAPII is transcribing larger sequences.
Create vulnerability - as need recognition by cis regulatory sequences to be spliced.
What are the 5 “life phases” of introns?
Genomic intron. Transcribed intron. Intron being spliced. Excised intron. Exon junction complex (EJC)-harbouring transcript.
What is the genomic intron?
Still in the DNA and is the location of the gene’s cis regulatory elements.
How are genomic introns involved in transcription initiation?
They contain enhancers, silencers and TF binding sites - mostly found in 5’ introns.
How are genomic introns involved in alternative splicing?
They contain alternative transcriptional initiation sites (promoters).
e.g. alpha-fetoprotein - cell specific expression.
How are genomic introns involved in transcriptional termination?
Intron sequences can regulate polyadenylation and cleavage.
Give an example of how genomic introns effect transcriptional termination.
Human Beta globin - protein can be soluble or membrane bound depending on where transcription is terminated and poly A tail is added.
Soluble - polyA on exon 14.
Membrane bound on exon 13.
What can genomic introns also be host to?
Nested genes - protein coding or non-coding RNA
What is the genomic design hypothesis?
Genes that need complex regulation contain more introns to accommodate their regulatory elements.
Highly expressed genes, which need low regulation have shorter introns.
What is a transcribed intron?
An intron that is present in the pre-mRNA
What is the RNAPII elongation rate and what does this mean for intron transcription?
50kb min^-1.
This means that intron may take hours to be transcribed - this explains the time delay between gene activation and translation of protein.
Give an example of how the gene activation to translation of protein time delay involved in negative feedback loops
Example - HES7 gene (transcription factor) - 19 minute delay between transcriptional initiation and full mature mRNA.
The protein produced inhibits its own transcription.
What is a spliced intron?
An intron present in mRNA - being spliced out by the spliceosome.
Which process is intron splicing linked to and how?
Transcription - linked via C-terminal domain of RNAPII.
How can splicing effect initiation of transcription?
U1-snRNP associates with and recruits TFIIH and TFIID to the 5’ splice site and stimulates phosphodiester bond formation (in mRNA).
How can splicing effect elongation of transcription?
Splicing factors and spliceosomal components can interact with transcriptional elongation factors.
U2 snRNP binding at the 3’ end of the transcript promotes the elongation using RNAP.
How can splicing effect termination of transcription?
U2 snRNP interacts with cleavage/polyA specificity factor (CSPF).
CSPF binds to polyA site and this can promote polyA tail formation and/or splicing via interaction with U2.
What is an excised intron?
An intron that has been removed from pre-mRNA by the spliceosome.
What often happens to excised intron?
They undergo debranching and degradation.
What can be expressed after an intron has been excised?
Embedded/nested genes - often miRNA and snoRNAs.
