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Formation and expression ofpseudogenes
This document discusses pseudogenes, which are dysfunctional copies of genes that have lost protein-coding ability. It covers the origin and formation of pseudogenes through DNA or RNA duplication, and describes different types like processed and unprocessed pseudogenes. The document also discusses various methods for identifying and detecting pseudogenes, databases of pseudogenes, and studies that have characterized pseudogenes in organisms like rice and Solanum plants. Finally, it explores the potential functions and utilities of pseudogenes, including their use in evolutionary studies, providing information about gene expression, and acting as competing endogenous RNAs.
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Formation and expression ofpseudogenes
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- 2. Shilpa V. Malaghan. II Ph.D (GPB) UAS, DHARWAD
- 3. Contents Introduction Origin (formation) Identification Expression Utilities 3 3
- 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 4
- 5. Central dogma ofcell biology Formation of pseudogene 5
- 6. Origin (formation) ofPseudogenes 1) Pseudogene formation after DNA- mediated gene duplication Ondrage et al., 2011 6
- 7. 2) Pseudogene formationafter RNA- mediated gene duplication (processed ψn) Ondrage et al., 2011 7
- 8. Types of Pseudogenes(ψn) Processed ψn Unprocessed ψn Unitary / disabled ψn 8
- 9. Processed ψn: Lack the promoter so “dead on arrival” Contains poly-A tail Lack intron sequence Random association with parent gene 9
- 10. Unprocessed ψn Highest structural similarity with parent gene Intact exons and introns Prevalence of ORF disrupting mutations Close association with parent gene 10
- 11. Unitary ψn No gene duplication before pseudogenization Rare in occurrence Fixed disabling mutations 11
- 12. Evidence for TE-DrivenPseudogene Formation Wicker et al., 2011 12
- 13. Detection of Pseudogenes Homology-Based Approaches: Harrison's Approach (pseudogene annotation pipeline, 2001) Sakai's Approach PPFINDER Pseudogene Finder (PSF) PseudoPipe 13
- 14. Pseudogene databases HoppsiGEN PseudoGeneQuest Pseudogene.Org University of Iowa Pseudogene Resource 14
- 15. Identification of pseudogenesin 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 15
- 16. characterization of pseudogenesin the rice gene complement Nissen et al., 2009 16
- 17. General steps fallowedin pseudogene identification Nissen et al., 2009 17
- 18. Plastid trnF(GAA) pseudogenesin four species of Solanum (Solanaceae) Peter et al., 2011 18
- 19. Manual alignment ofSolanum ψn copies Peter et al., 2011 19 5' 3'
- 20. Shared syntenic presentationof 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 21
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- 24. Analysis of miRNAtargeting the 3'-UTR of TUSC2 and pseudogene TUSC2P on chromosome Y and chromosome X. Zina et al.,2014 24
- 25. Expression analysis ofTUSC2P in cancer and non-cancer cell lines by real-time PCR and reverse transcription–PCR Zina et al.,2014 25
- 26. TUSC2P and TUSC230-UTR cloning in expression vectors Zina et al.,2014 real-time PCR results. 26
- 27. TUSC2P and TUSC230-UTR can function as competing endogenous RNAs (ceRNAs). Zina et al.,2014 27
- 28. TUSC2P/TUSC2-UTR attracts endogenousmiRNAs thus freeing TUSC2, Zina et al.,2014 TIMP2 and TIMP3 mRNAs to be translated 28
- 29. Identifying small RNAsderived from gene-pseudogene pairs or adjacent pseudogene-pseudogene pairs. Guo et al., 2009 29
- 30. The length distributionof small RNAs from four Guo et al., 2009 distinct sources. 30
- 31. Function classification ofrice pseudogenes following gene ontology terms…. Guo et al., 2009 31
- 32. Model for theevolution of B-located pseudogenes. (Banae et al., 2013) 32
- 33. Gene structure modelfor selected gene-like fragments. (Banae et al., 2013) 33
- 34. sequence comparison betweenrye B-located pseudogene-like fragments (6 to 15) and their A-located parental counterparts. (Banae et al., 2013) 34
- 35. Tissue- and Species-SpecificTranscription 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) 35 35
- 36. Accession specific expressionof Rye Pseudogenes (Banae et al., 2013) 36
- 37. Genome-Wide Distribution ofSmall RNA-Generating Loci in Arabidopsis. Kristin et al., 2007 37
- 38. Small RNA Lociin Protein-Coding Genes and Pseudogenes Kristin et al., 2007 38
- 39. Relationship between thenumbers of ψn and annotated functional genes in Pfam domain families. Zou et al., 2009 39
- 40. 40 Other utilities Evolutionary related studies Neutral substitution rate Information on splice diversity of RNA As record of fast gene expression fossils 40
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