Text|Ming Yue is deceased
Editor|Bright Moon is deceased
preface
Transposable factors (TEs) are both important drivers of genomic evolution and genetic parasites with potentially significant effects on host adaptation.
Recent studies on regulatory RNAs have shown that small RNA-mediated silencing is a conserved genetic mechanism by which the host inhibits TE activity and invades the Drosophila melanogaster genome by the P element, which occurred on a historical timescale and represents an unparalleled opportunity to understand small RNA-mediated silencing to observe how TEs evolve.
Suppression of the P element translocation occurs almost simultaneously with its invasion, and recent studies have shown that this inhibition is partially achieved, possibly primarily through the Piwi-Interacting RNA (piRNA) pathway, a small RNA-mediated silencing pathway that regulates TE activity in many post-vivid species lines.
In this review, I argue that P-elemental invasion from a molecular and evolutionary genetic perspective, harmonizes the elemental regulation of the new mechanistic framework provided by the PpiRNA pathway.
The paradigm of P as piRNA-mediated silent evolution is further explored, and the findings from this system have broad taxonomic implications for the evolution of inhibition given the highly conserved role of piRNAs in regulating TEs.
P-element structure and transposition
The full-length P element consists of protein-coding genes sandwiched between multiple reverse repeats at the ends of 5' and 3', coding genes with four exons, 0, 1, 2, and 3, which alternately splice to produce two proteins.
Removing all three introns yields a transcript encoding the 87-kDa transposase, which is required for transposation, in contrast to transcripts that retain introns between exons 2 and 3 encoding 66-kDa protein, with no transposase activity.
P transposases catalyze P through a non-replicating "cut and paste" mechanism where they are excised and inserted from one genomic location to another, full-length elements transpose autonomously as they encode this enzyme.
Internally missing elements do not encode transposases, however, these non-autonomous elements can mobilize the elements they need in trans if transposases are provided by full-length elements elsewhere in the genome at the end of multiple sequences at the 5' and 3' ends.
In particular, the 10 bp common sequence at both ends of the element is P-transposase and is required for efficient transposition.
Elemental transposation occurs mainly in germlines, with estimated transposability rates of 10−1 to 10−3, in contrast, P-element activity is rare in somatic tissues, and the estimated excision rate is more than two orders of magnitude lower than that of germ cells.
Germline-specific transposa is made by p-transposase messenger RNA, and although fully spliced transposase-encoding transcripts predominate in the germline, somatic transcripts typically retain IVS3 and encode the 66-kDa protein.
Modifying P removes the elements of IVS3 enough to bring somatic excision to levels similar to those observed in germlines, consistent with the dominant role of splicing regulation in inhibiting P activity in somatic cells.
However, in vivo analysis in living organisms showed that the transgene encoding the 66-kDa protein P{Δ2-3} reduced somatic resection rates when physical activity resumed, suggesting that the protein product acts as a secondary inhibitor of somatic transposition.
Suppression of germline regulation by proteins
Although IVS3-preserving transcripts are mainly produced in somatic cells, they also appear at a lower frequency in female germlines, such as the 66-kDa repressor protein.
In addition, some internally deleted P elements encode truncated transposase proteins, similar to 66-kDa proteins, as inhibitors for transposa, unlike full-length P, however, the production of repressor proteins from internally missing elements does not rely on selective splicing.
Repressor proteins vary in structure and sequence, but are broadly divided into two categories.
Type I inhibitors including the 66-kDa protein are encoded by transcripts that include at least the first 9 nucleotides of exons 0-2 and IVS3, compared to type II inhibitors that are much shorter and encoded by transcripts containing only exon 0 and partial exon 1.
It is worth noting that elements encoding type II inhibitors have been observed in native populations, and type I repressors are known to come only from full-length elements and deletion variants resulting from mutation analysis.
Encoding type I and II inhibitors reduces the rate of excision of P elements in living organisms. Although the exact mechanism of inhibitory protein action is unknown, they are thought to be competitive inhibitors of P transcription.
The 10 bp co-sequence recognized by the P-transposase overlaps with the TATA box at the P promoter, resulting in P-transposase inhibition of transcription factor IID binding and subsequent RNA polymerase recruitment.
Site-specific binding domains for P-transposase have been identified in both type I and type II repressors, and it is known empirically that type II repressors retain binding affinity.
Thus, inhibitory proteins can also act as competitive inhibitors of transcription, and transcriptional regulation is supported by assays in living organisms.
Type II repressors reduce germline expression by active Platz reporters, and both types of inhibitors reduce burn-weak, and a P-germline expression gene-element inserted into allele scorching, further showing that type II inhibitors pass with full-length P-transposase.
The piRNA pathway strongly inhibits elements in P and other TEsD. melanogastro germlines, and similar to other RNA-mediated silencing pathways, piRNA-mediated silencing relies on small guide RNAs that target silencing and forced silencing proteins.
In addition to TE regulation, piRNA pathways perform a variety of biological functions that have been comprehensively reviewed elsewhere, however, the role of piRNA pathways in regulating TEs is particularly pronounced, with piRNA overwhelmingly derived from TE, and mutations in PIR DNA pathway components lead to significant upregulation of TE transcripts, DNA damage, and sterility.
In both male and female germlines, as well as somatic support cells in the ovaries, piRNA-mediated silencing is targeted by TE-derived antisense pi RNAs that are sequenceally complementary to TE-derived mRNAs.
Antisense piRNAs act as guides for two Piwi-Argonaute proteins, Piwi and Aubergine, which force homologous TEs, as shown in the figure below.
Piwi and Aub are different in their cell localization, germline specificity, and silencing mechanisms.
Aub is a cytoplasmic protein that is forced post-transcriptional silencing only in the germline, and Aub can be cut directly by slices of mRNA to silence target transcripts and indirectly through components that are associated with mRNA degradation mechanisms.
In contrast, Piwi, a nuclear protein that establishes transcriptional silencing in germline and ovarian somatic cell follicular cells, can mark H3K9me3 by promoting inhibitory histone methylation, and by inhibiting the deposition of the activation marker H3K4me2 at the TE site.
piRNAs are derived from specific heterochromatic loci
PiRNA regulation of a single TE family relies on the presence of at least one representative insert in a piRNA cluster, which is the one that produces PIR na, which can be particularly large and often contains inserts from multiple TE and repeat families.
These clusters are transcribed as long precursors, which are subsequently processed into mature piRNAs, most of the 142 annotated piRNA clusters D. melanodon genomes are located around centromeres and subcentromatic heterochromatin.
Most piRNA clusters are epigenetically defined by H3K9me3, a type of heterochromatin commonly associated with composition, and somewhat counterintuitively, H3K9me3 does not confer transcriptional silencing states on piRNA clusters, but rather by recruiting proteins involved in piRNA cluster transcription and precursor processing.
The role of H3K9me3 in defining piRNA clusters may explain why autosomal insertions of the TE family, silenced by piRNA transcription through the deposition of H3K9me3, sometimes behave like PIR DNA clusters; Generate abundant piRNAs from two genome strands.
Although piRNA production from a few clusters appears to be genetically hardwired, most clusters rely at least in part on maternally deposited piRNAs for PIR DNA production in the feeder germline.
Maternal deposited piRNAs were found to compound with Piwi and Aub, which are localized to the original germline in the developing embryo and thus provide a mechanism for cross-generational silencing.
The piRNA-Piwi complex targets nucleosomes that package sequences homologous to the piRNA used for H3K9me3 modification, thereby facilitating the establishment of piRNA clusters in the offspring, and since H3K9me3 is not a common chromatin marker outside constitutive heterochromatin, its piRNA-mediated deposition may be particularly important when establishing clusters in both autochromatin and facultative heterochromatin environments.
Maternal deposited piRNAs further enhance PIR na production in offspring by initiating the processing of piRNA precursor transcripts.
Specifically, matrix-deposited piRNA-Aub complexes are thought to initiate ping-pong cycles, producing germline-specific feed-forward amplification loops of both sense and antisense piRNAs.
When the antisense piRNA-Aub complex is cut by sectioning, the resulting cleavage products are further processed into righteous piRNAs, which are loaded into a third Piwi-Argonaute protein, Argonaute-3.
Senseful piRNAs complex with Ago-3 can in turn recognize and cleave antisense precursors, resulting in more antisense piRNAs that can restart the cycle.
Although piRNA biogenesis has multiple mechanisms, the ping-pong cycle produces most germline piRNAs and is essential for the regulation of many TE families.
Ping-pong amplification is thought to represent the adaptive characteristic of piRNA-mediated silencing, and piRNA production from the most transcriptionally active TEs is enhanced by using TE-derived mRNAs as ping-pong substrates, thereby increasing those most likely to transpose.
The first signs of P-element invasion appeared in the late 70s and early 80s of the 20th century, when multiple researchers reported abnormal behavior of wild-derived chromosomes, including the presence of male recombination and unexpectedly high mutation rates.
A number of offspring of intraspecific hybrids subsequently demonstrated to undergo heterogeneous developmental disorders: a germline-specific syndrome caused by P-element activity due to.
Abnormal phenotypes include male recombination and elevated mutations, but also increased female recombination, dissociation distortion, sterility, and gonadal atrophy, especially ovarian atrophy provides a simple P activity phenotypic analysis, which helps to demonstrate the propagation of P in populations around the world, and it also allows detection and genetic dissection of P-element regulation.
Heterotypal dysplasia is caused by P-element activity
The frequency of genetic abnormalities The offspring produced by a particular cross depend on the genotype of the father and the mother, and in the traditional nomenclature P element induced heterogeneous developmental disorder, there are two types of strains: M and P, when the P strain is the paternal and the M strain is the mother, the hybrid offspring are dysplasia.
However, in crosscrossing, where M-strain males mate with P-strain females, producing fully fertile, genetically defect-free offspring, the increased mutation rate in genetically abnormal germlines indicates that we found that P as an element of mobile genetic entities whose activity induces hybrid developmental disorder syndrome.
Sequence analysis of developmental disorders-induced alleles revealed that it was the insertion of DNA elements that led to the mutation, which exhibited a high degree of sequence similarity with each other.
Because these elements are abundant in the P-strain genome but rare or absent in the M-strain genome, they are called P elements.
Atypical M strains, called M', have been observed to contain the P element; however, almost all of these elements have internal deletions and are therefore immobile without autonomous copies.
Increased demonstration of β-element transcription and transposability in the transgenic lineage of P further solidifies elements of P as molecular causes of hybrid developmental disorders.
epilogue
This P-element invasion of the D. melanogastric genome advances our understanding of the evolutionary dynamics that occur between tee and their hosts, and in particular, the historical timeline of P-element invasion provides a powerful opportunity to dissect repressed evolution.
Recent discoveries of the piRNA pathway have paved the way for a deeper understanding of how host genomes respond to the invasion of new TEs by revealing molecular and genetic frameworks that inhibit evolution.
Insights into piRNA-mediated silent evolution come from the invasion of the P-element into D. melanogastric animals are likely to have universal significance beyond this particular system. piRNA-mediated TEs regulation is very conserved in metazoans.
These genomic regions provide considerable mutational targets for random insertions that invade TEs, while also avoiding the possibility that new insertions disrupt functional sequences such as protein-coding genes. If new small RNA-coding regions often emerge through epitope mutations, this will further accelerate silent evolution.
Thus, P-element invasion of D. melanogastric animals provides an opportunity to examine the simultaneous evolution of TE regulation through small RNA-dependent and independent mechanisms.