Minor Introns vs Major Introns

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1 .... Minor Introns vs Major Introns Sebastian Bartschat Bioinformatics, Leipzig October 2009

2 table of content...1 introduction...2 two different types...3 classification of minor introns...4 results

3 reminder non-coding regions, interrupting two exons most genes in higher eukaryotes contain introns intron removal and ligation of 2 consecutive exons is called splicing 2 trans-esterifications carried out by the spliceosome

4 reminder non-coding regions, interrupting two exons most genes in higher eukaryotes contain introns intron removal and ligation of 2 consecutive exons is called splicing 2 trans-esterifications carried out by the spliceosome

5 major introns (U2-dependent) found in all eukaryotes excision is dependent on U2 snrna poly-pyrimidine tract upstream of 3 splice site more degenerate splice site signals GT-AG, AT-AC and GC-AG

6 minor introns (U12-dependent) found in plants and most metazoan taxa no evidence found in simple eukaryotes like S.cerevisiae, C.elegans or protists excision of minor introns is dependent on U12 snrna frequency in vertebrates in the range of % conserved splice site sequences lack of poly-pyrimidine tract GT-AG, AT-AC, other RT-AN (R is purine, N is any nucleotide)

7 comparison Steitz et al. [3]

8 Steitz et al. [3]

9 getting started focusing on T.spiralis and C.elegans using ESTs and BLAST to get possible splice sites

10 getting started focusing on T.spiralis and C.elegans using ESTs and BLAST to get possible splice sites GCAGATGAGG TGAGCTTTTA...ATTTTCAATGCAGG GCAAAGGTTT TGCAGATGAG GTGAGCTTTT...TATTTTCAATGCAG GGCAAAGGTT TTGCAGATGA GGTGAGCTTT...TTATTTTCAATGCA GGGCAAAGGT PWMs to determine the correct splice site frequency matrices were used for classification

11 intron scoring 12 P5 U ss (X ) = px i i, with U either U2 or U12 i=0 P U bps (X ) calculated for each 13nt segment in the range of (-40, -5) upstream of 3 ss

12 intron scoring 12 P5 U ss (X ) = px i i, with U either U2 or U12 i=0 Pbps U (X ) calculated for each 13nt segment in the range of (-40, -5) upstream of 3 ss computation of log-odd ratios ( ) ( P L 5 ss = log U12 5 ss 2 and L bps = log 2 P U2 5 ss P U12 bps P U2 bps transformation into z-scores S 5 ss and S bps by subtracting the sample mean an dividing by the standard deviation )

13 separation often there is no obvious cluster same importance of 5 splice site and branch site usage of a reference set of 27 minor introns [1] minimum values of their 5 ss and branch site scores as appropriate threshold

14 finding homologous introns..1 identifying the T.spiralis genes containing minor introns..2 homology search using BLASTX for detection of C.elegans proteins..3 reconstruction of genomic structure with TBLASTN..4 analysing the introns (with respect to their positions and types)

15 discrimination of introns of T.spiralis 6 4 burge (control) gt-ag type at-ac type gc-ag type branch site score splice site score

16 evolution of introns loss of intron conversion to U2 introns shift of splice sites, including a change of type

17 references C B Burge, R A Padgett, and P A Sharp. Evolutionary fates and origins of u12-type introns. Mol Cell, 2(6):773 85, Dec M Dávila López, M A Rosenblad, and T Samuelsson. Computational screen for spliceosomal rna genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res, 36(9): , May A A Patel and J A Steitz. Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol, 4(12):960 70, Dec N Sheth, X Roca, M L Hastings, T Roeder, A R Krainer, and R Sachidanandam. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res, 34(14): , 2006.

18 the end Thank you for your attention!