small understanding of cell biology.............

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2. Shilpa V. Malaghan.
II Ph.D (GPB)
UAS, DHARWAD

3. Contents
 Introduction
 Origin (formation)
 Identification
 Expression
 Utilities
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4. Introduction
The word ‘pseudogene’ was first used by Jacq et
al., 1977.
Pseudogenes are dysfunctional relatives of genes
that have lost their protein-coding ability or are
otherwise no longer expressed in the cell.
Charecteristic features,
• Highest homology to parental functional gene
• Presence of disablements to prevent its expression
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5. Central dogma of cell biology
Formation of pseudogene
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6. Origin (formation) of Pseudogenes
1) Pseudogene formation after DNA- mediated
gene duplication
Ondrage et al., 2011
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7. 2) Pseudogene formation after RNA- mediated
gene duplication (processed ψn)
Ondrage et al., 2011
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8. Types of Pseudogenes (ψn)
Processed ψn
Unprocessed ψn
Unitary / disabled ψn
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9. Processed ψn:
 Lack the promoter so “dead on arrival”
 Contains poly-A tail
 Lack intron sequence
 Random association with parent gene
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10. Unprocessed ψn
 Highest structural similarity with parent gene
 Intact exons and introns
 Prevalence of ORF disrupting mutations
 Close association with parent gene
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11. Unitary ψn
 No gene duplication before pseudogenization
 Rare in occurrence
 Fixed disabling mutations
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12. Evidence for TE-Driven Pseudogene
Formation
Wicker et al., 2011
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13. Detection of Pseudogenes
Homology-Based Approaches:
 Harrison's Approach
(pseudogene annotation pipeline, 2001)
 Sakai's Approach
 PPFINDER
 Pseudogene Finder (PSF)
 PseudoPipe
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14. Pseudogene databases
 HoppsiGEN
 PseudoGeneQuest
 Pseudogene.Org
 University of Iowa Pseudogene Resource
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15. Identification of pseudogenes in the rice gene
complement
Nissen et al., 2009
1 Pseudogenes (with parent gene and at least one frameshift or premature stop codon)
2 GPFs not supported by cDNA or EST evidence
3 The UTRs of the GPFs are longer than mean + 2 standard deviations
4 The CDS of the GPFs are shorter than 50 amino acids
5 The GPFs contain a stretch of 18 adenines in a 20-base window, within -200 to 400 bases from the end of the
annotated UTR, or within 600 bases of the stop codon if no UTR is annotated
6 The GPFs have a significantly smaller number of exons
7 The GPFs contain a single exon and are within a segmentally duplicated region but have no paralog in the duplicated
region
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16. characterization of pseudogenes in the rice gene
complement
Nissen et al., 2009
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17. General steps fallowed in pseudogene identification
Nissen et al., 2009
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18. Plastid trnF(GAA) pseudogenes in four species of
Solanum (Solanaceae)
Peter et al., 2011
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19. Manual alignment of Solanum ψn copies
Peter et al., 2011
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5' 3'

20. Shared syntenic presentation of pseudogene
copies in four different Solanum species
Peter et al., 2011 20

21. Evolution of trnF (GAA) pseudogenes in cruaciferous plants
Roswitha et al., 2008
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23. Expression mechanism
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24. Analysis of miRNA targeting the 3'-UTR of TUSC2 and pseudogene TUSC2P
on chromosome Y and chromosome X.
Zina et al.,2014
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25. Expression analysis of TUSC2P in cancer and non-cancer
cell lines by real-time PCR and reverse transcription–PCR
Zina et al.,2014
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26. TUSC2P and TUSC2 30-UTR cloning in expression vectors
Zina et al.,2014
real-time PCR results.
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27. TUSC2P and TUSC2 30-UTR can function as competing
endogenous RNAs (ceRNAs).
Zina et al.,2014
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28. TUSC2P/TUSC2-UTR attracts endogenous miRNAs thus freeing TUSC2,
Zina et al.,2014
TIMP2 and TIMP3 mRNAs to be translated
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29. Identifying small RNAs derived from gene-pseudogene pairs or
adjacent pseudogene-pseudogene pairs.
Guo et al., 2009
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30. The length distribution of small RNAs from four
Guo et al., 2009
distinct sources.
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31. Function classification of rice pseudogenes following gene
ontology terms….
Guo et al., 2009
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32. Model for the evolution of B-located
pseudogenes. (Banae et al., 2013)
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33. Gene structure model for selected gene-like
fragments.
(Banae et al., 2013)
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34. sequence comparison between rye B-located pseudogene-like
fragments (6 to 15) and their A-located parental
counterparts.
(Banae et al., 2013)
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35. Tissue- and Species-Specific Transcription of B-Located Pseudogene-Like
Fragments in Rye and Wheat.
B specific expression
Rye specific expression
Constitutive expression
Regulation of A
located gene
expression
(Banae et al., 2013)
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36. Accession specific expression of Rye
Pseudogenes
(Banae et al., 2013)
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37. Genome-Wide Distribution of Small RNA-Generating Loci in
Arabidopsis.
Kristin et al., 2007
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38. Small RNA Loci in Protein-Coding Genes and
Pseudogenes
Kristin et al., 2007
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39. Relationship between the numbers of ψn and annotated
functional genes in Pfam domain families.
Zou et al., 2009 39

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Other utilities
 Evolutionary related studies
 Neutral substitution rate
 Information on splice diversity of RNA
 As record of fast gene expression fossils
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