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Self-splicing introns:

RNA-catalysed reactions compared to spliceosomal-based


Linear intron (group 1):

- eg) protozoan rRNA genes
- these are not covalently closed


Lariate introns (group 2):

- eg) some mitochondrial genes
- Generates a lariate
- Doesn't require a snurp for splicing


Two theories of intron evolution:

- Introns evolved and proliferate early, but are being lost in some genes over time
- Introns evolved late and are proliferating, increasing in number


Comparison of intron positions in related genes in closely related species shows

- Conservation of introns in amidase genes of Aspergillus species
- A conserved intron is observed in almost all species, so there is evidence of the introns slowly being lost over time
- Single introns between species provide evidence for introns arising in sequences.


Intron evolution:

- An intron present in the cell that has been excised is reinserted into the DNA by reserve splicing, reverse transcription and recombination.
- Introns can also be lost from sequences


Intron sliding:

- Change in intron position
- An intron is spliced out, then reinserted into a different location of the gene. It has the same sequence but moves around at a slower rate


Are introns conserved?

- Intron sequences are often not conserved in sequence or length
- Intron sequences can show regions of conservation, and then we would expect some function such as a conserved regulatory site or an unsuspected coding region eg) In Drosophila, the Adh locus has another gene


Introns may code for snoRNA:

- Small nucleolar RNA that modify target RNAs, including tRNA
- Transcribed by RNAPIII
- Modify bases in rRNA and tRNA


Presumably RNA involved first then DNA evolved as it is more stable and complex. RNA is matured:

- pre-mRNA that is spliced to produce mature mRNA
- pre-rRNA is cleaved to produce a mature rRNA
- pre-tRNA is cleave to produce mature tRNA


Alternative splicing:

- Splicing of different introns and exons
- Different cell types
- Different functions
- The same DNA strip can create different products by splicing together different parts of the gene


Example of alternative splicing: SV40, simian virus 40, T antigen gene encodes two proteins (T and t)

- T: viral growth
- t: Stops cell apoptosis, so promotes viral proliferation
- From the same gene but are different splice forms and have different functions


Example of alternative splicing: Drosophila DSCAM:

- Down Syndrome Cell Adhesion Molecule
- 24 alternatively spliced exons
- 38, 016 combinations of mature mRNAs
- Can do more with the genes that you have, don't necessarily need lots and lots of genes


Transcript splicing, repression:

- This process must be controlled
- The spliceosomal complex can't see the splice site due to a protein present in some cells blocking the splice site


Transcript splicing activation:

- Splicing doesn't usually happen
- The splicosomal complex doesn't usually recognise the splice site
- A different cell type expressing an activator may recruit the splicing machinery to the splice site


RNA editing:

- Post-transcriptional modification of mRNA sequence
- DNA sequence differs from mRNA sequence
- Protein sequence differs from that predicted from DNA sequence


Two mechanisms of RNA editing:

- Nucleotide modification, site specific deamination
- Nucleotide insertion by guide RNAs


Nucleotide modification by specific enzymes:

- Cytosine deamination by cytidine deaminase (converts C to U)
- Adenine deamination by adenine deaminase (ADAR)
- Different amino acids can be inserted into the same transcript


Nucleotide insertion by guide RNAs:

- Insertion or deletion of U's
- RNA in mitochondria of some protozoans
- Insertion of U's to RNA by guideRNAs


Pre-mRNA is retained in the nucleus and must be transported out for translation:

- Mature mRNA must be exported out of the nucleus
- RNA's are bound to proteins that allows transport through the membrane into the cytoplasm