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Shilpa V. Malaghan.

II Ph.D (GPB)

UAS, DHARWAD

Contents

Introduction

Origin (formation)

Identification

Expression

Utilities

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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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Central dogma of cell biology

Formation of pseudogene

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Origin (formation) of Pseudogenes

Ondrage et al., 2011

1) Pseudogene formation after DNA- mediated

gene duplication

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Ondrage et al., 2011

2) Pseudogene formation after RNA- mediated

gene duplication (processed ψn)

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Types of Pseudogenes (ψn)

Processed ψn

Unprocessed ψn

Unitary / disabled ψn

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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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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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Unitary ψn

No gene duplication before pseudogenization

Rare in occurrence

Fixed disabling mutations

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Evidence for TE-Driven Pseudogene

FormationWicker et al., 2011

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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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Pseudogene databases

HoppsiGEN

PseudoGeneQuest

Pseudogene.Org

University of Iowa Pseudogene Resource

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Identification of pseudogenes in the rice gene

complementNissen 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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characterization of pseudogenes in the rice gene

complement

Nissen et al., 200916

Nissen et al., 2009

General steps fallowed in pseudogene identification

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Plastid trnF(GAA) pseudogenes in four species of

Solanum (Solanaceae)

Peter et al., 201118

Manual alignment of Solanum ψn copies

Peter et al., 201119

5' 3'

Shared syntenic presentation of pseudogene

copies in four different Solanum species

Peter et al., 2011 20

Evolution of trnF (GAA) pseudogenes in cruaciferous plants

Roswitha et al., 2008

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Expression mechanism

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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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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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Zina et al.,2014

TUSC2P and TUSC2 30-UTR cloning in expression vectors

real-time PCR results.

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Zina et al.,2014

TUSC2P and TUSC2 30-UTR can function as competing

endogenous RNAs (ceRNAs).

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Zina et al.,2014

TUSC2P/TUSC2-UTR attracts endogenous miRNAs thus freeing TUSC2,

TIMP2 and TIMP3 mRNAs to be translated

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Identifying small RNAs derived from gene-pseudogene pairs or

adjacent pseudogene-pseudogene pairs.

Guo et al., 2009

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Guo et al., 2009

The length distribution of small RNAs from four

distinct sources.

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Function classification of rice pseudogenes following gene

ontology terms….Guo et al., 2009

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Model for the evolution of B-located

pseudogenes. (Banae et al., 2013)

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Gene structure model for selected gene-like

fragments.(Banae et al., 2013)

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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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Tissue- and Species-Specific Transcription of B-Located Pseudogene-Like

Fragments in Rye and Wheat.

(Banae et al., 2013)

Rye specific expression

B specific expression

Constitutive expression

Regulation of A

located gene

expression

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Accession specific expression of Rye

Pseudogenes

(Banae et al., 2013)36

Genome-Wide Distribution of Small RNA-Generating Loci in

Arabidopsis.Kristin et al., 2007

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Small RNA Loci in Protein-Coding Genes and

Pseudogenes

Kristin et al., 2007

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Relationship between the numbers of ψn and annotated

functional genes in Pfam domain families.

Zou et al., 200939

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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