Studying Alternative Splicing Meelis Kull PhD student in the - - PowerPoint PPT Presentation

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Studying Alternative Splicing Meelis Kull PhD student in the - - PowerPoint PPT Presentation

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Studying Alternative Splicing Meelis Kull PhD student in the University of Tartu supervisor: Jaak Vilo CS Theory Days Ruge 2007 Overview Alternative splicing Its biological function Studying splicing Technology

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Studying Alternative Splicing

Meelis Kull

PhD student in the University of Tartu supervisor: Jaak Vilo CS Theory Days Rõuge 2007

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Jan 27, 2007 CS Theory Days, Rõuge 2007 2

Overview

  • Alternative splicing
  • Its biological function
  • Studying splicing

– Technology – Computational tasks

  • Tissue-specific alternative splicing
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SLIDE 3

Jan 27, 2007 CS Theory Days, Rõuge 2007 3

The Basis of Life on Earth

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Jan 27, 2007 CS Theory Days, Rõuge 2007 4

RNA Splicing

  • Folded DNA

– Unfolding

  • DNA

– Transcription

  • pre-mRNA

– Splicing

  • mRNA

– Translation

  • Poly-peptide

– Protein folding

  • Protein
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SLIDE 5

Jan 27, 2007 CS Theory Days, Rõuge 2007 5

Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU..

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SLIDE 6

Jan 27, 2007 CS Theory Days, Rõuge 2007 6

Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. (A|C)(A|U)GGU(A|G)(A|U)G(A|U) (C|U)(A|C|G|U)(C|U)U(A|C|G)A(C|U){10-20}(A|G)(C|U)AG

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SLIDE 7

Jan 27, 2007 CS Theory Days, Rõuge 2007 7

Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU..

INTRON EXON EXON I I

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Jan 27, 2007 CS Theory Days, Rõuge 2007 8

Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. .GUAUCGUGGAAGGACUCAUGACCACAGUCCAUGCCAUCACU.

INTRON I EXON EXON

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SLIDE 9

Jan 27, 2007 CS Theory Days, Rõuge 2007 9

Splicing

http://www.shenghua.sdu.edu.cn/gif/mRNA%20splicing.gif

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SLIDE 10

Jan 27, 2007 CS Theory Days, Rõuge 2007 10

Alternative Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU..

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SLIDE 11

Jan 27, 2007 CS Theory Days, Rõuge 2007 11

Alternative Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU..

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Jan 27, 2007 CS Theory Days, Rõuge 2007 12

Alternative Splicing

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. .GUAUCGUGGAAGGACUCAUGGUGGGGAGGGAGGUAGAGGGG. .UGAUGUGGGGAGUACGCUGCAGGGCCUCACUCCUUUUGCAG.

INTRON I EXON EXON

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Jan 27, 2007 CS Theory Days, Rõuge 2007 13

Alternative Splicing

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Jan 27, 2007 CS Theory Days, Rõuge 2007 14

Alternative Splicing

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Jan 27, 2007 CS Theory Days, Rõuge 2007 15

Overview

  • Alternative splicing
  • Its biological function
  • Studying splicing

– Technology – Computational tasks

  • Tissue-specific alternative splicing

✔

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Jan 27, 2007 CS Theory Days, Rõuge 2007 16

Origins of Splicing

  • Prokaryotes - splicing occurs but there

is no general machinery for performing it

  • Eukaryotes - have got spliceosome - a

protein complex specialised in carrying

  • ut splicing
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Jan 27, 2007 CS Theory Days, Rõuge 2007 17

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Jan 27, 2007 CS Theory Days, Rõuge 2007 18

Biological Function of Alternative Splicing

  • Protein Diversity - AS enables the cell

to produce more than one protein from the same gene (no need for larger genome)

  • Fast Protein Evolution - new splicing

variants emerge by replacing only a few nucleotides (DNA letters).

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Jan 27, 2007 CS Theory Days, Rõuge 2007 19

Alternative Splicing in Action

There can be different splice variants in

  • Embryos and Adults (development)
  • Brain and Muscle (anatomy)
  • Normal and Cancer (pathology)

Studying alternative splicing helps to decrypt anatomy, development, and pathology

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Jan 27, 2007 CS Theory Days, Rõuge 2007 20

Regulation of Alternative Splicing

Non-neuronal cells Neurons

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Jan 27, 2007 CS Theory Days, Rõuge 2007 21

Our Task

  • Computationally predict cases of

anatomy-, pathology-, or development- specific splicing

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Jan 27, 2007 CS Theory Days, Rõuge 2007 22

Overview

  • Alternative splicing
  • Its biological function
  • Studying splicing

– Technology – Computational tasks

  • Tissue-specific alternative splicing

✔ ✔

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Jan 27, 2007 CS Theory Days, Rõuge 2007 23

Technology

  • How was splicing performed in a cell?
  • Let us find out the final result of splicing

– Take out molecules of spliced mRNA – Find out the sequences of nucleotides

  • Compare it with the original mRNA (=DNA)

– Scan the genome to find out the matching parts

  • Matching parts - Exons,

Regions between matches - Introns

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SLIDE 24

Jan 27, 2007 CS Theory Days, Rõuge 2007 24

Example (CS Theory Days, right?)

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. GGCAGGAUUCAACAGCCCAUUCGAUCCC

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SLIDE 25

Jan 27, 2007 CS Theory Days, Rõuge 2007 25

Example

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. GGCAGGAUUCA ACAGCCCAUUCGAUCCC - 6 mismatch GGCAGGAUUCA ACAGCCCAUUCGAUCCC

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SLIDE 26

Jan 27, 2007 CS Theory Days, Rõuge 2007 26

Example

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. GGCAGGAUUCA ACAGCCCAUUCGAUCCC - 6 mismatch GGCAGGAUUCA ACAGCCCAUUCGAUCCC

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Jan 27, 2007 CS Theory Days, Rõuge 2007 27

Example

..GUAUCGUGGAAGGACUCAUGGUAUGAGAGCUGGGGAAUG.. ..GGACUGAGGCUCCCACCUUUCUCAUCCAAGACUGGCUCC.. ..UCCCUGCCGGGGCUGCGUGCAACCCUGGGGUUGGGGGUU.. ..CUGGGGACUGGCUUUCCCAUAAUUUCCUUUCAAGGUGGG.. ..GAGGGAGGUAGAGGGGUGAUGUGGGGAGUACGCUGCAGG.. ..GCCUCACUCCUUUUGCAGACCACAGUCCAUGCCAUCACU.. GGCAGGAUUCA ACAGCCCAUUCGAUCCC - 6 mismatch GGCAGGAUUCAAC AGCCCAUUCGAUCCC - 9 mismatch GGCAGGAUUCAAC AGCCCAUUCGAUCCC

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Jan 27, 2007 CS Theory Days, Rõuge 2007 28

Result of Alignment

Chromosome: 12 Gene: ENSG00000179088 (FLJ25323) Location: 102195188 - 102395213 Mapping: g(3016..3202) e(1..186) g(20522..20620) e(187..285) g(97294..97362) e(286..354) g(129971..130082) e(355..466) g(192624..192983) e(467..830)

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SLIDE 29

Jan 27, 2007 CS Theory Days, Rõuge 2007 29

Overview

  • Alternative splicing
  • Its biological function
  • Studying splicing

– Technology – Computational tasks

  • Tissue-specific alternative splicing

✔ ✔ ✔

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Jan 27, 2007 CS Theory Days, Rõuge 2007 30

Combine all mRNA produced from the same gene

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Jan 27, 2007 CS Theory Days, Rõuge 2007 31

Find all splice sites

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Jan 27, 2007 CS Theory Days, Rõuge 2007 32

Encode the mRNA alignments

1 1 1 1 1 1 . 1 1 1 1 1 1 . 1 1 1 1 1 1 1 1 .

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Jan 27, 2007 CS Theory Days, Rõuge 2007 33

Include mRNA annotation data

Anatomical site: nervous system -> central nervous system -> brain -> brain stem -> medulla oblongata Developmental stage: adult -> 27 years Pathological state: normal

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Jan 27, 2007 CS Theory Days, Rõuge 2007 34

Find alternative splicing

.000001110011110001................. dermal ...........11110001................. normal nervous .00000111001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal 0000000000001110001................. normal nervous ...................01100110110...... normal 0000000000011110001011001........... cancer nervous .000000000001110001011001........... cancer dermal 0000000000011110001011.............. normal .00000000001111000101............... normal .0000000000011100010110011.......... cancer muscle ............1010001011001101........ normal muscle .000001110011110001................. normal dermal 000000000001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal ............1010001011001........... normal nervous 0000000000001110001011.............. cancer dermal 0000000000011110001011001........... normal dermal ....................1100110110...... normal nervous ...............0001011001101........ normal nervous ........10001110001011.............. dermal .00000111001111000101............... normal dermal .000001110011110001................. cancer nervous .............................0101010 normal dermal ....................11001101........ normal nervous ........10001110001................. dermal ......................0011011010.... normal nervous

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Jan 27, 2007 CS Theory Days, Rõuge 2007 35

Find alternative splicing

.000001110011110001................. dermal ...........11110001................. normal nervous .00000111001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal 0000000000001110001................. normal nervous ...................01100110110...... normal 0000000000011110001011001........... cancer nervous .000000000001110001011001........... cancer dermal 0000000000011110001011.............. normal .00000000001111000101............... normal .0000000000011100010110011.......... cancer muscle ............1010001011001101........ normal muscle .000001110011110001................. normal dermal 000000000001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal ............1010001011001........... normal nervous 0000000000001110001011.............. cancer dermal 0000000000011110001011001........... normal dermal ....................1100110110...... normal nervous ...............0001011001101........ normal nervous ........10001110001011.............. dermal .00000111001111000101............... normal dermal .000001110011110001................. cancer nervous .............................0101010 normal dermal ....................11001101........ normal nervous ........10001110001................. dermal ......................0011011010.... normal nervous

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Jan 27, 2007 CS Theory Days, Rõuge 2007 36

Find alternative splicing

.000001110011110001................. dermal ...........11110001................. normal nervous .00000111001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal 0000000000001110001................. normal nervous ...................01100110110...... normal 0000000000011110001011001........... cancer nervous .000000000001110001011001........... cancer dermal 0000000000011110001011.............. normal .00000000001111000101............... normal .0000000000011100010110011.......... cancer muscle ............1010001011001101........ normal muscle .000001110011110001................. normal dermal 000000000001111000101............... normal dermal .0000000000011100010110011.......... cancer dermal ............1010001011001........... normal nervous 0000000000001110001011.............. cancer dermal 0000000000011110001011001........... normal dermal ....................1100110110...... normal nervous ...............0001011001101........ normal nervous ........10001110001011.............. dermal .00000111001111000101............... normal dermal .000001110011110001................. cancer nervous .............................0101010 normal dermal ....................11001101........ normal nervous ........10001110001................. dermal ......................0011011010.... normal nervous

3 6

Exon

2 6

Intron

  • ther

dermal

8 2

Exon

1 5

Intron

normal cancer

5

Exon

4

Intron

dermal normal dermal cancer

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Jan 27, 2007 CS Theory Days, Rõuge 2007 37

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Jan 27, 2007 CS Theory Days, Rõuge 2007 38

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Jan 27, 2007 CS Theory Days, Rõuge 2007 39

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Jan 27, 2007 CS Theory Days, Rõuge 2007 40

Summary

  • Alternative splicing is important for protein

diversity and evolution

  • Studying splicing involves text algorithms
  • Our contribution is a method for predicting

tissue-specific alternative splicing

  • Experiments are yet to be carried out (by
  • thers)