Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
BMC Genomics. 2022 Jun 8;23(1):429. doi: 10.1186/s12864-022-08660-z.
PiRNAs prevent transposable elements wreaking havoc on the germline genome. Changes in piRNA expression over the lifetime of an individual may impact on ageing through continued suppression, or release, of transposable element expression. We identified piRNA producing clusters in the genome of Daphnia magna by a combination of bioinformatic methods, and then contrasted their expression between parthenogenetically produced eggs representing maternally-deposited germline piRNAs of young (having their 1 clutch) and old (having their 5 clutch) mothers. Results from eggs were compared to cluster expression in three generations of adults.
As for other arthropods, D. magna encodes long uni-directionally transcribed non-coding RNAs consisting of fragmented transposable elements which account for most piRNAs expressed. Egg tissues showed extensive differences between clutches from young mothers and those from old mothers, with 578 and 686 piRNA clusters upregulated, respectively. Most log fold-change differences for significant clusters were modest, however. When considering only highly expressed clusters, there was a bias towards 1 clutch eggs at 41 upregulated versus eight clusters in the eggs from older mothers. F generation differences between young and old mothers were fewer than eggs, as 179 clusters were up-regulated in young versus 170 old mothers. This dropped to 31 versus 22 piRNA clusters when comparing adults in the F generation, and no differences were detected in the F generation. Inter-generational losses of differential piRNA cluster were similar to that observed for D. magna micro-RNA expression.
Little overlap in differentially expressed clusters was found between adults containing mixed somatic and germline (ovary) tissues and germ-line representing eggs. A cluster encompassing a Tudor domain containing gene important in the piRNA pathway was upregulated in the eggs from old mothers. We hypothesise that regulation of this gene could form part of a feedback loop that reduces piRNA pathway activity explaining the reduced number of highly-expressed clusters in eggs from old mothers.
piRNA 可防止转座元件破坏生殖系基因组。个体一生中 piRNA 表达的变化可能通过持续抑制或释放转座元件的表达来影响衰老。我们通过生物信息学方法结合鉴定了大型溞基因组中的 piRNA 产生簇，然后比较了它们在代表年轻（有 1 个卵）和年老（有 5 个卵）母亲的卵中母体沉积的生殖系 piRNA 的表达。从卵中获得的结果与三代成虫中的簇表达进行了比较。
与其他节肢动物一样，大型溞编码由片段化的转座元件组成的单向转录的长非编码 RNA，这些 RNA 占表达的大多数 piRNA。卵组织在年轻母亲的卵和年老母亲的卵之间表现出广泛的差异，分别有 578 和 686 个 piRNA 簇上调。然而，大多数显著簇的对数倍变化差异较小。当仅考虑高表达的簇时，在 41 个上调的簇中，1 个卵中存在偏向，而在来自较老母亲的卵中有 8 个簇。年轻和年老母亲的 F 代差异少于卵，因为在年轻的中上调了 179 个簇，而年老的为 170 个。当比较 F 代中的成虫时，这一数字下降到 31 个与 22 个 piRNA 簇，在 F 代中未检测到差异。与大型溞微 RNA 表达观察到的情况一样，差异表达的 piRNA 簇的跨代丢失相似。
在含有混合体腔和生殖系（卵巢）组织的成虫和代表卵的生殖系之间，差异表达的簇之间几乎没有重叠。一个包含在 piRNA 途径中重要的 Tudor 结构域的基因的簇在来自年老母亲的卵中上调。我们假设该基因的调节可能构成减少来自年老母亲的卵中高表达簇数量的反馈回路的一部分。
