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Alternative Splicing Hedi Hegyi, PhD @ Institute of Enzymology, Budapest Szeged University, Biochemistry Course Oct 31, 2007. Scientific American 2005/04. Scientific American 2005/04.

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Alternative SplicingHedi Hegyi, PhD@ Institute of Enzymology, Budapest University, Biochemistry Course Oct 31, 2007


Scientific American 2005/04

  • Spring of 2000. Molecular biologists placing dollar bets: how many genes in human genome?
  • 90,000? 153,000? C.elegans:19,500, Maize:40,000
  • 35,000, 30,000,
  • a paltry 25,000!

C-value paradox: Complexity does not correlate with genome size. (C.A. Thomas, Jr, 1971)

6.7 x 1011 bp

Amoeba dubia

3.4 x 109 bp

Homo sapiens


N-value paradox: Complexity does not correlate with gene number.

~25,000 genes

~26,000 genes

~50,000 genes

discovery of alternative splicing
Discovery of Alternative Splicing
  • First predicted by Walter Gilbert in 1978
  • - First discovered for an Immunoglobulin heavy chain gene in 1980 (Edmund Choi, Michael Kuehl & Randolph Wall, Nature286, 776 - 779)
  • - Alternative splicing gives two forms of the protein with different C-termini:
    • - 1 form is shorter and secreted
    • - Other stays anchored in the plasma membrane via C-terminus

Alternative splicing of the mouse immunoglobulin μ heavy chain gene

S - signal peptide Red – untranslated region

V - variable region Green – membrane anchor

C - constant region Yellow – end of coding reg. for secreted form

splicing the spliceosome
Splicing & the spliceosome


  • 60S dynamic structure – a large complex consisting of ~ 150 proteins
  • Five small nuclear RNAs (U1, U2, U4, U5 & U6)
  • RNAs assemble with proteins to form snRNPs (“snurps”)
  • Protein splicing factors

Assembly of spliceosome requires ATP

Splicing defects

  • Estimation: 15% of all genetic diseases associated with mutated splice sites

Green globule: RNA pol

Yellow globule: spliceosome


Secondary structure of snRNAs




Orange - interaction with 5’ splice site

Green – Interaction with branch site

Blue - interaction between U2 and U6

Tan - Sm-binding site (PuAU4-6GPu)

flanked by two stem-loop structures



u1 snrna
U1 snRNA
  • Contains conserved sequence complementary to 5’ splice site of nuclear mRNA introns
  • Contains pseudouridine(y)

5’ splice site

Upstream exon




U1 snRNA

splice site recognition
Splice-site recognition

5’ splice site

3’ splice site





branch site


~ 20 – 50 nts


Branch site in yeast: often 5’- UACUAAC-3’

splice site conservation
Splice Site Conservation

Splice Junction










Donor (5’) SS

Acceptor (3’) SS

splice site conservation14
Splice Site Conservation

Splice Junction










Donor (5’) SS

Acceptor (3’) SS

splicing mechanism











Splicing mechanism

5’ splice site

branch site

3’ splice site

Exon 1 Intron Exon 2







Factors Playing a Role in Exon Recognition

1. Evolution appears to have weakened splice sites

Derived from 253, only 3% of the S. cerevisiae genes contain introns

No Alternative Splicing

Derived from 4,697 S. pombe genes; approximately 43% of all genes contain introns

Intron Retention

Derived from 49,778, nearly 100% contain introns

75% Alternative Splicing



Factors Playing a Role in Exon Recognition

Exon Recognition is complex

Exon Definition

Intron Definition

Complexity means multiple points of possible regulation and that exons could be skipped by failing to get all the pieces in place

The ability to form or disrupt these interactions is thought to play a key role in alternative splicing!!!

Nature, Vol. 418, p. 236, 2002


Intron statistics

SpeciesAverage Average Average Average % exon

exon No. intron No. length(kb) kb mRNA per gene

Yeast 1 0 1.6 1.6 100

Nematode 4 3 4.0 3.0 75

Fruit fly 4 3 11.3 2.7 24

Chicken 9 8 13.9 2.4 17

Mammals 7 6 16.6 2.2 13

Human genes


Size of internal exons 122 bp 145 bp

Number of exons 7 8.8

Size of introns 1023 bp 3356 bp


Recognizing Exons - Are Splice Sites Enough?

Most mammalian genes contain more than one intron

Extreme Examples:

Collagen Gene - 50 exons and a 40 kb precursor RNA

DMD Gene - 79 exons, 2.3 mb precursor, intron 20 is 180 kb

Neurexin - has a 0.5 mb intron!

Most genes are uninterrupted in yeast, but most genes are interrupted in flies and mammals


Support for the Exon Definition Model

Exon size is conserved in vertebrates

Intron size is not

Recognition requires a consistent target size


Additional Cis Elements and Trans-Acting Factors

- Splicing has Enhancers and Silencers

- They function to modulate spliceosome formation

Recruiting SR proteins can stabilize E complex formation

Blocking snRNP or protein interactions can prevent E complex formation

ESE - Exonic Splicing Enhancer

ESS - Exonic Splicing Silencer

ISE - Intronic Splicing Enhancer

ISS - Intronic Splicing Silencer


Models of Exon Recognition - Final Points

Trans-Factor Interaction with Exon differs from Interaction with Introns


Types of Alternative Splicing





Remaining 33%

Cell 126:37 (2006)

Nature Reviews: Genetics 5:773 (2004)

how prevalent is alternative splicing
How Prevalent is Alternative Splicing?

No one really knows for sure.

EST Database estimates between 35 - 60% of protein coding gene have alternative mRNAs

Caveat - These databases contain sequences derived from aberrant, as well as, alternative splicing, they are typically 3' and 5' end biased, and have insufficient number to infer frequency

Therefore, database mining may overestimate the rate of alternative splicing



Array-Based Numbers

Science 302, 2141-44 (2003)


Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays (Science, 2003)

10,000 multi-exon

human genes in 52


Conclusion: 74% of multi-exon human genes are alternatively spliced


Number of Splicing Isoforms per Gene by EST Comparison


Harrington et al. Nature Genetics 36:916 (2004)

regulation of by alternative splicing
Regulation of/by Alternative Splicing
  • Sex determination in Drosophila involves 3 regulatory genes that are differentially spliced in females versus males; 2 of them affect alternative splicing

1. Sxl (sex-lethal) - promotes alternative splicing of tra (exon 2 is skipped) and of its own (exon 3 is skipped) pre-mRNA

2. Tra – promotes alternative splicing of dsx (last 2 exons are excluded)

3. Dsx (double-sex) - Alternatively spliced form of dsx needed to maintain female state

Fig. 14.38


Alternative splicing in Drosophila maintains the female state

Alternative splicing

Sxl and Tra are SR proteins

Tra binds exon 4 in dsx mRNA causing it to be retained in mature mRNA.


Known Roles of Alternative SplicingStamm et al. Gene 344:1-20 (2005)

  • Introduction of stop codons -
  • 25-35% of alternative splicing events introduce stop codons that either function to produce truncated proteins or regulate mRNA stability through the nonsense mediated decay (NMD) pathway
nonsense mediated decay
Nonsense Mediated Decay
  • A surveillance mechanism that selectively degrades nonsense mRNAs
  • Regulates gene expression by alternative splicing
  • - Transcripts containing a PTC (premature termination codon) are degraded rapidly

1/3rd of alternative transcripts contain premature termination codons

Brenner, SE et al, PNAS January 7, 2003 vol. 100 no. 1 189–192


Known Roles of Alternative SplicingStamm et al. Gene 344:1-20 (2005)

  • Add new protein parts -
  • 75% of alternative splicing involves the protein coding region, in addition to truncations you can change the overall protein sequence

Known Roles of Alternative SplicingStamm et al. Gene 344:1-20 (2005)

  • Consequences of new protein parts -
  • Alter protein binding properties, eg. receptor/ligand
  • Alter intracellular localization, eg. membrane insertion
  • Alter extracellular localization, eg. secretion
  • Alter enzymatic or signaling activities, eg. TK truncations
  • Alter protein stability, eg. inclusion of cleavage sites
  • Insertion of post-translation modification domains
  • Change ion channel properties eg. slo

Known Roles of Alternative SplicingStamm et al. Gene 344:1-20 (2005)

  • Coordinated Regulation of Biological Events
  • Potassium channel activity associated with hearing (slo)
  • Muscle contraction
  • Neurite (axon or dendrite) growth
  • Cell differentiation
  • Apoptosis
  • Neuron development (Dscam) (TIBS 31:581-588, 2006)

The Power of Alternative RNA Splicing

Drosophila DSCAM gene codes for an axon guidance receptor

The final mRNA chooses 24 exons from 115 possibilities

(20 constitutive exons and 4 alternatively spliced ones)

Ig Loop 7


Ig Loop 3

Ig Loop 4

Exon 4

12 Alternatives

Exon 6

48 Alternatives

Exon 9

33 Alternatives

Exon 17

2 Alternatives

12 X 48 X 33 X 2


38,016 Possible mRNAs

Genome has only 14,800 genes!

evolutionary overview of alternative splicing
Evolutionary Overview of Alternative Splicing
  • Introns unlikely to have been derived from ancient genes
  • Multi-intron genes probably predated alternative splicing
  • Most eukaryotes have introns but alternative splicing prevalent only in multicellular organism
  • S.cerevisiae has only 253 introns (3% of its genes) and only 6 genes have 2introns
  • S. pombe: 43% of its genes have introns (usually 40-75 nt)
  • S.cerevisiae and S. pombe have NO alternative splicing

Finding Alternatively Spliced Exons

  • Compare cDNA & genomic DNA sequences
  • Compare ESTs & genomic DNA sequences
  • Compare protein & genomic sequences
large scale multiple alignment of expressed sequences
Large-scale multiple alignment of expressed sequences
  • Databases:
      • tens of thousands of mRNAs
      • millions of ESTs
  • From large-scale alignments: 60-80% of all human genes undergo alternative splicing.
alu elements
Alu elements
  • Length = ~300 bp
  • Repetitive: > 1,400,000 times in the human genome
  • Constitute >10% of the human genome
  • Found mostly in intergenic regions and introns
  • Propagate in the genome through retroposition (RNA intermediates).
alu elements can be divided into subfamilies
Alu elements can be divided into subfamilies

The subfamilies are distinguished by ~16 diagnostic positions.

alu containing exons
Alu-containing exons
  • Out of 1,182 alternatively spliced cassette exons, 62 have a significant hit to an Alu sequence.
  • Out of 4,151 constitutively spliced exons, none has a significant hit to an Alu sequence.

all Alu-containing exons are alternatively spliced.

Graur et al., Genome Res. (2002)

the minus strand of alu elements contains near splice sites
The minus strand of Alu elements contains “near” splice sites
  • The minus strand of Alu contains ~3 sites that resemble the acceptor recognition site:

Consensus acceptor site:YYYYYYNCAG/R

Alu-J: (127-114) :TTTTTTGtAG/A

  • The minus strand of Alu contains ~9 sites thatresemble the consensus donor site:

Consensus donor site: CAG/GTRAGT

Alu-J: (25-17) : CAG/GTGtGA


Alu exonization

The selection of AGs in the 3SSs of Alu-derived exons are underlined

3 genetic diseases:

1. COL4A3- Alport syndrome

2. GUSB- Sly syndrome

3. OAT- OAT deficiency

Lev-Maor G, et al, Science, 2003.


Factors Playing a Role in Exon Recognition

- Sequence features of alternatively regulated exons are different from constitutive exons.

- These features are conserved between species.

Sorek, Genome Res 14:1617 (2004)


Large-scale identification of alternative splice variants of human gene transcripts using 56,419 cDNAs

Distribution of the length difference

between the alternative

splicing variants

Takeda, J.-i. et al. Nucl. Acids Res. 2006 34:3917-3928; doi:10.1093/nar/gkl507

large scale identification of human alternative splic e variants
Large-scale identification of human alternative splice variants


(B)‘subcellular localization-changed’

(C)‘transmembrane domain-changed’


Alternative splicing databases (1,560,000 hits in google)

  • - Alternative Splicing & Transcript Diversity DbASTD
  • - SpliceMiner (querying EVDB - Evidence Viewer Database)
  • Hollywood
  • -Human Alternative Splicing Db (HASDB),
  • Putative Alternative Splicing Database,
  • PALS db,

Structure of ASTD

databases are integrated, cross-linked and are available through a variety of interface tools

ASTD data are integrated with

Ensembl genome annotation

Stamm, S. et al. Nucl. Acids Res. 2006 34:D46-D55

spliceminer ncbi
Spliceminer (NCBI)

Querying EVDB (Evidence Viewer DB). Composite of five separate interactive queries. Each query corresponds to a different Affymetrix HG-U133A Probe. The composite permitsfacile comparison of the exons that are targeted by each of the probes. For example, the probes for exons 16 and 18 uniquely identify the splice variants NM_006487 and NM_006485, respectively.


Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles (Kan, NAR, 2005)

Kan, Z. et al. Nucl. Acids Res. 2005 33:5659-5666; doi:10.1093/nar/gki834


Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles (Kan et al, NAR, 2005)

Alternative splicing events in 10818 pairs of human and mouse genes

43% (8921) of mouse alternative splices could be found in the human genome but not in human transcripts

Only 7% of human alternative splices are conserved in mouse transcripts

5 of 11 tested mouse predictions were observed in human tissues

Diverged alternative splicing is more prevalent in cancerous cell-lines

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles (Kan et al, NAR, 2005)
Microarray expression of alternatively spliced human-mouse pairs (ASP) of genes in different tissues (Kan et al, 2005)
  • level of conserved alternative splicing most elevated in brain
  • diverged alternative splicing is the most enriched in testis
functional transcripts for the brain periphery and brain and receptors

Corticotrophinreleasing hormone receptor 2 (CRHR2) alternative splices

Functional transcripts for the α,β (brain, periphery) andγ(brain) and receptors

Extracellular Domain

Cytoplasmic Domain




Catalano et al, Molecular Endocrinology. First published December 18, 2002 as doi:10.1210/me.2002-0302

the implications of alternative splicing in the encode protein complement cont d
The implications of alternative splicing in theENCODE protein complement (cont’d)

Fig. 2. The potential effect of splicing on protein structure. Four spliceisoformsmappedonto the nearest structural templates. Structures are coloredin purple where the sequence of the splice isoform is missing. (a) Hemoglobin(b) SET domain-containing protein 3, (c) Mitochondrial cysteine desulfurase(d).Eukaryoticinitiation factor 6.

how many genes and transcripts in human genome
How many genes and transcripts in human genome?
  • Ensembl NCBI 35 release (Dec, 2005): 33,869 transcripts derived from 22,218 genes
  • Ensembl NCBI 36 release (May, 2006): 48,851 transcripts derived from 23,710 genes
how many genes and transcripts in human genome cont d
How many genes and transcripts in human genome? Cont’d
  • Major source of uncertainty: nucleic acid-basedidentification of putative proteins in humans and other organisms.
  • Most proteinshave not been seen as proteins per se but their existence has been inferred fromgenomic DNA, cDNA and ESTs.
surveillance systems
Surveillance systems
  • NMD (nonsense-mediated decay) controls alternative splices that cause a premature stop codon
  • ERAD (Endoplasmic Reticulum Associated Degradation) eliminates AS (alternative splicing) isoforms with no stable 3D structure
computer modeled surveillance
Computer-modeled surveillance?
  • Selecting predicted proteins with domains of abnormal length
    • Study Pfam-A domains derived from Swissprot proteins
    • 8129 Pfam-A domain families currently in Pfam
    • How many Pfam-A families can be used for such a surveillance?
nested and truncated domains
Nested and truncated domains

Existing proteins (PFAM models)

- Matrix metalloproteinase 11

- Matrix metalloproteinase 9

Putative proteins (PFAM models)

- Glycosyl hydrolase domain

- Peptidoglycan-binding domain+DUF

computer modeled surveillance cont d
Computer-modeled surveillance? Cont´d
  • Select those predicted proteins with domains of abnormal length (>=40% of domain missing). Use for filtering:
    • 8129Pfam-A domain families currently in Pfam
    • 2752Pfam-A domain families in human Swissprot proteins
    • How many of these 2752Pfam-A families are regular enough to be used for such a surveillance? Answer: 2529
ensembl proteome coverage with regular pfam a domains
Ensembl Proteome Coverage with regular Pfam-A domains*

* Belonging to one of the 2529 regular Pfam-A families

structural studies of as

Disordered AS


Structural Studies of AS

Structured AS regions



Tumor necrosis factor


Glutathione S-transferase

parallel paradigms
Parallel Paradigms


AA seq →3-D Structure→ Function


AA seq →Disordered→Function


alternative splicing and intrinsic disorder
Alternative Splicing and Intrinsic Disorder
  • Find proteins with both ordered and disordered regions.
  • Find mRNA alternative splicing information for these proteins and map to the orderedand disordered regions.
  • For alternatively spliced regions of mRNA, do they code for ordered protein more often or do they code for disordered protein more often?

Romero PR et al. Proc Natl Acad Sci U S A. 2006 May 30;103(22):8390-5

studying the relationship intrinsic disorder as

ASED dataset:

(Alternative Splicing & Experimental Disorder)

46 proteins

74 characterized AS regions

>19,000 charaterized residues, 35% ID

Studying the Relationship Intrinsic Disorder AS


(AS Gallery)




Database of proteins with

experimentally determinedstructure and disorder

Romero PR et al. Proc Natl Acad Sci U S A. 2006 May 30;103(22):8390-5

results on ased
Results on ASED

Distribution of structurally characterized AS regions

Romero PR et al. Proc Natl Acad Sci U S A. 2006 May 30;103(22):8390-5

take home message
Take-home Message
  • Alternative splicing evolved simultaneously with multicellular organisms
  • It increases the functional diversity and complexity of an organism
  • Not all of alternative splicing is functional (e.g. Alu-exonization)
  • It is a factor in genetic diseases (cancer, etc.)
  • It is strongly associated with protein disorder
The End

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