1. ProRepeat a comprehensive directory of exact tandem repeats in proteins

2. PolyQ and neurodegenerative diseases
9 diseases causes by polyQ repeats HD
DRPLA
SCA 1,2,3,6,7,17
Kennedy’s disease (SBMA)

3. Androgen receptor (AR)
Transcription factor, mediating the effect of androgens on gene expression
Gene located on the X chromosome, divided into three functional regions:
one variable, the N-terminal transregulation domain (NTD) and
two highly conserved, the DNA binding domain and the C-terminal ligand-binding domain (LBD)
Involved in differentiation between male and female phenotype
Responsible for SBMA (spinal and bulbar muscular atrophy) or Kennedy’s disease
Céline Poux, RU

4. Androgen receptor (AR)
Polymorphic polyQ repeat in the NTD
ranges between 9 and 35 residues, with an average of 20 to 25 depending on ethnic origin
Transcriptional activity depends on the intramolecular interaction between the NTD and the LBD
inversely correlated with length and flexible structure of polyQ tract
Differences in polyQ tract length can have important consequences
longer tracts : feminization syndromes
shorter tracts : prostate cancer susceptibility
repeat exceeds 40 residues : SBMA
NDT can contain other repeat tracts in mammals, such as polyP, polyG or polyQ
Céline Poux, RU

5. Androgen receptor (AR)
Transcription Factor
HORMONE BINDING
TRANSCRIPTIONAL REGULATION
DNA BINDING
NH3-
-COOH T1 T2 T3
Region 1
Region 2
Region 3
polyQ tract length has important consequences
■ shorter tracts : prostate cancer susceptibility
■ longer tracts : feminization syndromes
■ over 40 residues : SBMA (spinal and bulbar muscular atrophy) or Kennedy’s disease
9-35 residues, average of depending on ethnic origin
I will present one of these genes: the Androgen receptor gene. We chose this gene because it was one of the two polyQ genes involve in a neurodegenerative disease for which the function of the protein was known. The Androgen receptor is a transcription factor that mediates the effect on genes expression of androgens. Its action is important in the differentiation process between male and female phenotype. This protein is encoded by a gene situated on the chromosome X and divided into three main regions: the first exon encodes for the transregulation domain, the DNA binding domain and the ligand biding domain. No deleterious mutation has been recorded in the first exon except the CAG repeats domain. The length of the repeat seems modulate the activity of the protein in such a way that the shorter the track is, the stronger the effect of the protein will be. When the number of repeats increases beyond the normal length, beside feminization problems, the individuals get a great chance to develop a Spinal and Bulbar Muscular Atrophy or Kennedy disease. Few poly amino acid repeats were already known in the first exon the polyQ responsible for the disease, a polyProline and a polyGlycine at the end of the exon. After sequencing of more than 30 mammals species it turned out that the Androgen receptor is a real “slippery protein” wit a lot of repeats often short and occurring in few species, like a polyAlanine repeat in the kangaroo.

6. PolyQ in AR Collection of polyQ repeats
792 human individuals available from earlier study (Edwards, 1992)
26 armadillo individuals sequenced by CP
77 mammals and marsupials from protein database
Céline Poux, RU

7. What about repeats in other proteins?
ProRepeat database
Data sources: UniProt and RefSeq
Limited to exact tandem repeats
Standard, linear-time suffix tree algorithm
Stored in Oracle 10g
Interface in PHP5
unit length
repetitions 1
≥ 5 2
≥ 4 3
≥ 3
4 .. N
≥ 2
Maarten van den Bosch, WUR

8. DE is equivalent to ED; DEF is equivalent to EFD and FDE
Simple query syntax:
e.g. “Q” or “DE”
DE is equivalent to ED; DEF is equivalent to EFD and FDE

10. Or use ProSite syntax:
e.g. “[DE]-{P}-X(0,1).”

11. Taxonomic distributions of hits

13. Sorting/grouping options
Identifier
Repeat unit
Repetitions
Unit length
Length
Start location
End location
Protein
Taxonomy
Ontology

14. Link to DNA data
DNA coding sequences of available repeats also stored in the database
Extracted from EMBL and/or RefSeq
Hong Luo, WUR

15. Link to DNA data / errors
Approximately 3% of corresponding nucleotide sequences cannot be retrieved
Errors caused by
No links to nucleotide database (35%)
NO_ANNOTATED_CDS
No EMBL links
Annotation errors in the nucleotide database (65%)
Error type III: Join the complement of exon1, exon2, exon3 etc instead of complement the join

16. Guido Kappé, RU

17. T S Q G P A E

18. Verdeling van aminozuren in subgroepen van peptides binnen een proteoom. Bekeken zijn Single Amino Acid repeats (SAA), alle repeats minus de SAAs, en alle eiwitten (samenstelling) minus de repeats

19. Ter vergelijk, arabidopsis, waar Ser het meest abundant is in SAAs.

20. Current work Annotation of repeats versus function
Adding imperfect tandem repeats - a.k.a. approximate tandem repeats (ATR) – to the database
Offering remote access via web services (WSDL and BioMoby)
Expansion of the analysis capabilities of the interface

21. PolyQ in AR (reprise)
Impure tracts longer and more variable than pure CAG tracts (mainly CAA, CCG, and CGG)
Presence of other codons better explained by codon duplication than multiple point mutations
interrupting codons are part of elongation process, rather than hampering their dynamics as proposed previously
Negative correlation between lengths of the different CAG tracts
maximal expansion length that protein can handle without being deleterious
Céline Poux, RU

22. Acknowledgements Wageningen University and Research Centre
Maarten van den Bosch
Hong Luo
Mark Kramer
Harm Nijveen
Radboud University, Nijmegen
Guido Kappé
Céline Poux
Wilfried W. de Jong
This work was supported in part by project grants from NWO/BMI (GK, CP) and the NBIC/BioAssist program (HN)

23. Thank you for your attention!
See also our posters on phylogenetic domain visualisation (TreeDomViewer) and microarray (re)annotation at the ISMB
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