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16. RNA Processing.pdf

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Biology (Sci)
BIOL 200
Richard Roy

Naveen Sooknanan McGill Fall 2011 RNA Processing: As we stated before, RNA polymerase II is the only one of its kinda to have a carboxyterminal domain (CTD) The CTD consists of the aa pattern YSPTSPS repeated 26 times in yeast and around 52 times in humans o Is the CTD is removed in yeast, the organism dies, and the same is assumed to happen for humans The CTD is attached to Pol II by a linker peptide which is 28nm in length The CTD is a crucial part of Pol II because it is the source of two very important phosphorylation events which essentially carry out RNA processing of class II gene transcripts. These phosphorylation events are carried out by the PNK activity of TFIIH th The first phosphorylation occurs on the 5 aa, a serine, on every repeat of the CTD. This causes a capping enzyme to bind to the CTD and install a cap onto the 5 end of the pre- mRNA as it is being transcribed o This occurs after pol II has synthesized around 25 nucleotides o This cap protects the new pre-mRNA from being digested by exonucleases o After this phosphorylation occurs, pol II becomes much more active and enters an elongation phase The second phosphorylation occurs on the 2 aa of the sequence, also a serine, at every repeat on the CTD o This occurs during elongation and recruits the splicing machinery necessary for splicing out noncoding regions of the pre-mRNA Pol I and Pol III dont have CTDs, so their gene products do not undergo capping o They do, however, undergo post transcriptional modification which will be discussed later Capping involves the addition of a 7 methylguanylate cap to the 5 end of the pre-mRNA as soon as it exits the transcription complex This ensures that the mRNA is not damaged by exonucleases and happens so quickly because to the close proximity between the 5 end of the mRNA and the capping enzyme on the CTD o This 7 MG cap comes from a GTP substrate can creates an odd 5 5 phosphodiester linkage which exonucleases cant recognize Animals and higher plants have a second security barrier in which the second base is methylated on the 2 hydroxyl group Vertebrates have a further security feature which methylates the 2 hydroxyl group of the third base Along with evasion of exonuclease digestion, the capping also allows for the recognition of various nuclear export proteins as well as translation factors in the cytoplasm 1Naveen Sooknanan McGill Fall 2011 The transition from pre-mRNA to mRNA is carried out by a mechanism called splicing. Unlike bacterial genes, most eukaryotic genes have introns which must be spliced out before the mRNA is translated. While introns were initially considered to be junk DNA, it is found that they can actually code for important regulatory functions as well as aid in alternative splicing events Splicing was discovered by hybridization events in which a finals mRNA was annealed to its corresponding gene To the scientists surprise, the mRNA was actually much smaller than the gene For example, in the hexon gene, DNA segments which coded for introns looped out of the double stranded structure because they were spliced out of the final mRNA Because of this size discrepancy, it was proved that genes pre-mRNA must undergo some splicing event to reach a mature state One important characteristic in splicing is the high level of conservation of intron borders. This helps splicing machinery know where to carry out its splicing events to form mature mRNA This is helpful for prediction of mRNA sequences from a gene without conducting the actual sequencing An AG is highly conserved at 3 end the 5 exon, followed by a GU at the 5 end of the intron
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