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The role of pre-mRNA secondary structure in gene splicing

The role of pre-mRNA secondary structure in gene splicing. Sanja Rogic Computer Science Department, UBC. Gene splicing. Splice sites consensus sequences. consensus sequences are necessary but not sufficient for splicing. R = purines (A, G) Y = pyrimidines (C, U). Motivation.

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The role of pre-mRNA secondary structure in gene splicing

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  1. The role of pre-mRNA secondary structure in gene splicing Sanja Rogic Computer Science Department, UBC

  2. Gene splicing pre-mRNA structure and splicing

  3. Splice sites consensus sequences • consensus sequences are necessary but not sufficient for splicing R = purines (A, G) Y = pyrimidines (C, U) pre-mRNA structure and splicing

  4. Motivation • splice site recognition by the spliceosome is still not well understood - new biological insights • low accuracy of computational splice site prediction is a major reason for limited accuracy of gene-finding programs - improving accuracy of gene-finding • pre-mRNA is not linear but has secondary structure • biological studies suggest that pre-mRNA secondary structure can affect splicing pre-mRNA structure and splicing

  5. Hypothesis and goal • secondary structure of pre-mRNA plays a role in splicing • characterize secondary structure elements that are additional identifiers of intronic regions Dataset – S.cerevisiae introns • 215 introns with consistent annotation between three databases: AYID, YIDB, and CYGD pre-mRNA structure and splicing

  6. Spatial architecture of yeast introns • 5’ short (~ 40 nt) introns (5’S) • 5’ long ( > 200 nt) introns (5’L) • S.cerevisiae introns have bimodal distribution of branchpoint distances 5’L introns pre-mRNA structure and splicing

  7. ‘Zipper’ stem hypothesis • 5’S introns have the optimal branchpoint distance for spliceosome assembly • 5’L introns fold into secondary structure to shorten branchpoint distance to optimal • stem/loop structures experimentally identified in several yeast introns - splicing inhibited when zipper stem disrupted zipper stem pre-mRNA structure and splicing

  8. Identification of zipper stems • computing secondary structure of introns: • secondary structures processed to identify one or more zipper stems (thermodynamical stability and loop size) • shortened branchpoint distance calculated • using programs that predict RNA secondary structure based on minimum free energy (mfold, RNAfold) • using comparative (phylogenetic) secondary structure prediction zipper stem pre-mRNA structure and splicing

  9. Branchpoint distance distribution for 5’S introns Shortened branchpoint distribution for 5’L introns Shortened length distribution for random sequences p = 0.75 p < 0.001 pre-mRNA structure and splicing

  10. Phylogenetic approach related sequences for 82 5’L introns S. cerevisiae ~10 mya S. paradoxus S. mikatae ~20 mya mLAGAN multiple sequence alignment S. bayanus Alifold find zipper stem(s) p = 0.68 calculate shortened branchpoint distance pre-mRNA structure and splicing

  11. Acknowledgements • thesis supervisors: Alan Mackworth, CS Department, UBC Holger Hoos, CS Department, UBC Francis Ouellette, UBiC • colleagues in Beta lab (Bioinformatics and Empirical & Theoretical Algorithmics) pre-mRNA structure and splicing

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