Research progress of piRNA evolution. Xuedong Pan 2012-3-28. What is piRNA. Small RNAs: piRNA , siRNA , miRNA . piRNA : derive from repetitive genomic element, interact with PIWI. AGO family protein. RISC(RNA induced silencing complex). Guide RNA. Germline -specific AGO .
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Research progress ofpiRNA evolution
AGO family protein
RISC(RNA induced silencing complex)
piRISC: recognize and silence complementary RNA
PIWI family( PIWI,AUB, AGO3)
Proved; 5’U and 10 A
Long precursor can generate a lot of piRNAs, thus is piRNA cluster
Not only piwi. Piwi interact with Tudor-domain proteins directly. Tudor-domain proteins methylatearginine in piwi, which differs piwi with other AGOs. Piwi also needs Armi.
In drosophila testis, AT-chrX code piR, piR interact with AUB, and little AGO3, to suppress vasa
In drosophila testis, if Su on ChrY do not work, Ste on ChrX is deprepressed, which leads to infertility.
Piwi expression driven by TJ. piR from 3’UTR of tj together with piwi suppress Fas3.
Failure of nos mRNA deadenylation and translational repression by piR
Conclusion: different developmental stage, different protein and piR
piR enriched in TE. Binds MILI and MIWI2
Pachytene: cross over happens
piR not enriched in TE. Binds MIWI and MILI
TDR: tudor domain containing proteins. Bind piwi directly.
Piwi family in mouse: MIWI2, MIWI, MILI
1) 43% of all rodent piR clusters arose after rodent-primate divergence. While the highest known expansion rate for olfactory receptors is 33%.
2) Olfactory receptors and miRNAs are lost at the same rate with which they are acquired. However, not a single cluster loss was observed for piRNA.
Architecture of a typical cluster-harboring genomic region. Intergenic region between two protein-coding genes piRNA cluster. The inserted segment is depicted in brackets.
The inserted segment is scanned against the genome to locate the source paralog.
Similarity between cluster- and source paralog-harboring regions includes preceding REs
Double-stranded break, leads to extension and reannealing of the broken strand
1) quantified expression levels of 32 TE families
2) in ovaries of one wild-type and three piRNA mutants
piRNA repress TEs in RNA level
IR/DR: inverted/direct repeats bind by transposases
Reverse transcription in cytoplasm, integration in nucleus by integrases
LTR: long terminal repeat
GAG protein: form virus-like particles
ORF1 and ORF2 have reverse transcriptase domain
mRNAs are integrated into genome by target-primed reverse transcription
Selection: fitness is exponential quadratic, decreasing function of TE copy number.
recombination: uniform distribution of crossover positions
transposition and excision(Poisson process throughout genome)
For 15000 generations
b = 5e-6
1) piRNAs have no repression effect: u1 = u2
2) 3) 4) piRNAs can reduce retrotransposition rates to 10%, 1% and 0.1%(u2 = 0.1u1, 0.01u1, 0.001u1)
Number of retrotransposons
Fitness costs to the host
* scenario1,2,3,4: piRNA’s repressing capabilities increases
Proportion(%) of all retrotransposons that are piRTs
Scaled parameters: Ne = 500, a = 0.001, b= 0.0005, r = 2.5e-8, u1 = 0.01, v = 0
Frequency spectra of piRT insertions:
When piRNA takes effect, piRTs have a higher probability to be fixed
Frequency spectra of targetRT insertions
Also has a higher probability to be fixed, because their deleterious effects are alleviated by piRNAs
C vs. D: subset of A vs. B, recombination occured
A vs. B: TE longer than 500bp
No recombination occured
Combination of 2 datasets
** piRNA also enriches in centromeric and telomeric region. TelomericlacZ insertion produces abundant piRNAs. Telomere is a picluster?
Recombination rate = 2.5e-8
Recombination rate = 0
human piR sequences(Girard et al. 2006)
mouse piR sequences(Lau et al. 2006)
Hapmap phase3 data
methods: derived allele frequency spectrum; BWA tool, mapping reads
piR flanking region (1000bp each side of piR);
nucleotide substitution between human and chimp is not significantly different between piR region and piR flanking region
Selective constraint in Africans is consistent with a much higher rate of transposon insertions in African compared with non-African populations(Ewing A, Kazazian H, Genome Res, 2010)
Younger TEs are more active, so more piRNAs which target them remain in current human genome; the pattern is the same for mouse
The pattern is the same in our data
L1-ORF2 functions as reverse transcriptase
Red line: number of G/C-nucleotides per base on L1 mRNA
Blue line: density of sense piRNA matches to L1
Green line: density of antisense piRNA matches to L1