20.01.14 Pseudogenes and clinical relevance Flashcards
1
Q
What is a pseudogene
A
- a DNA sequence that shows a high degree of sequence homology to a functional gene.
- 10-20,000 in human genome.
2
Q
Why are pseudogenes common
A
- Gene duplication events may be evolutionary advantageous (create new functional gene variants with a selective advantage)
- they are functional and evolutionarily conserved.
3
Q
What are the subclasses of pseudogenes
A
- Non-processed (duplicated)
- Processed (retrotransposed)
- Unitary (solitary)
- RNA
- Mitochondrial
4
Q
What is a non-processed pseudogene
A
- A defective gene arising from a copy of genomic DNA sequences. Arise via tandem duplication (unequal crossover between homologous chromosomes or sister chromatid exchange within the same chromosome).
- Often close to functional gene counterparts
- Examples: SMN1/2, CYP21A2/CYP21A1P, PMS2.
- ALthough some pseudogenes can be dispersed due to recombination, e.g. NF1
5
Q
What is a processed (retrotransposed) pseudogene
A
- A defective gene arising from copying at the cDNA level (contains exonic sequences only)
- Arise via retrotransposition: where cellular reverse transcriptases use processed gene transcripts (e.g. mRNA) that can then integrate into the genome at a new location.
- Some examples of where function is retained and they are called retrogenes.
- Examples= UTP14a/c
6
Q
What is a unitary (solitary) pseudogene
A
- Arise through spontaneous mutations in protein-coding genes.
- Different to other pseudogenes in that they are not duplicated before becoming inactive.
- Very rare.
7
Q
What are RNA pseudogenes
A
- Hard to identify as pseudogenes as they have no reading frame and often lack introns
- example U6 snRNA
- Alu repeat arose from copying of 7SL RNA transcripts
8
Q
What are mitochondrial pseudogenes
A
- A defective copy of a mitochondrial gene but found in nuclear genome.
- Mitochondrial pseudogenes are more abundant than the actual mitochondrial genome.
9
Q
Mechanisms of action of pseudogenes at a DNA level
A
- Due to sequence similarity to parental gene, can elicit function by gene conversion/recombination.
- Upstream regulatory sequences of pseudogene may affect transcription of parental gene
- Insertion into other gene altering their sequence and thus transcriptional activities.
- pseudogenes may acquire additional exons, modifying their function
10
Q
Example of a pseudogene acting at a DNA level
A
- gene conversion between PMS2 and pseudogene leads to inactivation of PM2
- Homologous recombination between BRCA1 and pseudogenes leads to deletion of BRCA1 promoter
11
Q
Mechanisms of action of pseudogenes at an RNA level
A
- Pseudogene RNAs compete with parental mRNAs, thus increasing expression
- Antisense pseudogene transcripts repress parental gene transcription or form endo-siRNAs that inhibit expression of parental gene at posttranscriptional level.
- Pseudogenes function as IncRNAs and affect other genes (unrelated to parental gene)
- Pseudogenes encode microRNA precursors
- Pseudogene RNAs comptete for microRNAs that target parental or unrelated genes. Increases expression of microRNA targets.
12
Q
Example of a pseudogene acting at a RNA level
A
-PTENP1 (pseudogene of PTEN) acts as a miRNA decoy, by binding to miRNA and allowing PTEN to escape miRNA-mediated silencing. PTENP1 is deleted in several types of cancer (breast, colon and melanoma). Reduced PTENP1 expression leads to increased miRNA-mediated silencing of PTEN and loss of function of the tumour suppressor.
13
Q
Mechanisms of action of pseudogenes at a protein level
A
- Translation of pseudogenes into a truncated or mutated protein with novel functionality
- Pseudogenic proteins have the same function as parental proteins but function in different tissues or cellular compartments.
- Partially functional pseudogenic proteins affect the activity of parental proteins
- Short pseudogenic open reading frames generate antigenic peptides that are exposed on cell surface.
14
Q
Example of a pseudogene acting at a protein level
A
- Ha-RAS2 is the pseudogene of HRAS. Has Gly12 and Lu63 mutations leading it to be constitutively active.
- BRAFP1 is the pseudogene of BRAF. Selectively overexpressed in tumours leading to activation of ERK signalling
15
Q
Clinically relevant non-processed pseudo genes.
1. Spinal muscular atrophy (SMA)
A
- SMA region at 5q13, consists of a 500kb inverted duplication.
- 4 genes, 2 copies of each.
- SMN1 (active, telomeric), SMN2 (pseudogene, centromeric) relevant for SMA
- SMN1 and 2 can only be distinguished by single nucleotide substitutions in exon 7 and 8 (synonymous).
- SMA individuals lack a functional copy of SMN1 (98% mutations involve dels/ gene conversions of at least exon 7 of SMN1)
- SMN2 retains partial functionality so the number of SMN2 copies can act as a dose-dependent disease modifier (more copies, milder phenotype and increased life expectancy)
