The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters.
The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters.
复制标题
DOI：
10.7554/elife.80067
复制
发表时间：
2022-10-04
期刊：
影响因子：
7.7
通讯作者：
Brennecke J
中科院分区：
文献类型：
--
作者：
Baumgartner L;Handler D;Platzer SW;Yu C;Duchek P;Brennecke J
RNA 干扰系统依赖于小 RNA 前体的合成，其序列定义了这些沉默途径的目标谱。果蝇异染色质蛋白 1 (HP1) 变体 Rhino 允许在种系细胞中富含转座子的异染色质位点内转录 PIWI 相互作用 RNA (piRNA) 前体。目前的模型提出，Rhino 在 piRNA 源位点上的特定染色质占据是由组蛋白标记和母系遗传的 piRNA 决定的，但也暗示存在其他未发现的特异性线索。在这里，我们鉴定出锌指相关结构域 (ZAD)-C2H2 锌指蛋白多样化家族的成员 Kipferl，作为卵巢中关键的犀牛辅助因子。通过与富含鸟苷的 DNA 基序结合并与 Rhino 染色结构域相互作用，Kipferl 将 Rhino 招募到特定位点并将其稳定在染色质上。在 kipferl 突变果蝇中，Rhino 的大部分目标染色质位点丢失，而是在着丝粒周围卫星阵列上积累，导致针对 piRNA 的转座子水平降低并损害生育能力。我们的研究结果表明，除了 H3K9me3 标记之外，DNA 序列还决定了 piRNA 源基因座的身份，并提供了有关 Rhino 如何陷入遗传冲突交火的见解。我们 DNA 中的基因编码了我们身体计划的要素以及如何完成体内的每项任务。然而，我们的基因组还包含许多不编码功能基因的 DNA 重复区域。其中一些区域是被称为转座子的遗传寄生虫，它们试图在宿主的 DNA 周围繁殖和传播。为了防止转座子 DNA 干扰身体的运作方式，人类和其他动物进化出了复杂的防御机制来识别转座子并防止其繁殖。在一种称为 piRNA 途径的机制中，宿主产生称为 piRNA 的小分子，其序列与转座子的序列互补，并充当沉默转座子的向导。制造这些 piRNA 的指令以转座子片段的形式存储在宿主 DNA 的专用区域（称为 piRNA 簇）中。因此，这些簇充当遗传记忆，允许宿主识别并沉默宿主基因组内其他位置的特定转座子。在果蝇中，一种名为 Rhino 的蛋白质与紧密堆积的 piRNA 簇结合，从而可以制造 piRNA。然而，目前尚不清楚Rhino如何能够识别并结合piRNA簇，但不能识别其他类似的密集DNA区域。鲍姆加特纳等人。使用遗传、基因组和成像方法相结合来研究犀牛如何在果蝇基因组中找到自己的方式。他们发现另一种名为 Kipferl 的蛋白质与 Rhino 相互作用，并且是 Rhino 与几乎所有 piRNA 簇结合所必需的。由于 Kipferl 本身可以与 Rhino 需要找到的序列结合，因此结果表明 Kipferl 的作用是在密集的 piRNA 簇内招募并启动 Rhino 结合。进一步的实验发现，在缺乏 Kipferl 的果蝇中，Rhino 与称为卫星重复序列的 DNA 区域结合，暗示这些自私的序列可能会为了自身利益而竞争 Rhino。 Kipferl 和 Rhino 共同定义 piRNA 通路记忆系统的发现极大地促进了我们对如何建立基于小 RNA 的序列特异性防御系统的理解。
RNA interference systems depend on the synthesis of small RNA precursors whose sequences define the target spectrum of these silencing pathways. The Drosophila Heterochromatin Protein 1 (HP1) variant Rhino permits transcription of PIWI-interacting RNA (piRNA) precursors within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhino’s specific chromatin occupancy at piRNA source loci is determined by histone marks and maternally inherited piRNAs, but also imply the existence of other, undiscovered specificity cues. Here, we identify a member of the diverse family of zinc finger associated domain (ZAD)-C2H2 zinc finger proteins, Kipferl, as critical Rhino cofactor in ovaries. By binding to guanosine-rich DNA motifs and interacting with the Rhino chromodomain, Kipferl recruits Rhino to specific loci and stabilizes it on chromatin. In kipferl mutant flies, Rhino is lost from most of its target chromatin loci and instead accumulates on pericentromeric Satellite arrays, resulting in decreased levels of transposon targeting piRNAs and impaired fertility. Our findings reveal that DNA sequence, in addition to the H3K9me3 mark, determines the identity of piRNA source loci and provide insight into how Rhino might be caught in the crossfire of genetic conflicts. The genes within our DNA encode the essentials of our body plan and how each task in the body is achieved. However, our genome also contains many repetitive regions of DNA that do not encode functional genes. Some of these regions are genetic parasites known as transposons that try to multiply and spread around the DNA of their host. To prevent transposon DNA from interfering with the way the body operates, humans and other animals have evolved elaborate defense mechanisms to identify transposons and prevent them from multiplying. In one such mechanism, known as the piRNA pathway, the host makes small molecules known as piRNAs that have sequences complementary to those of transposons, and act as guides to silence the transposons. The instructions to make these piRNAs are stored in the form of transposon fragments in dedicated regions of host DNA called piRNA clusters. These clusters thereby act as genetic memory, allowing the host to recognize and silence specific transposons in other locations within the host’s genome. In fruit flies, a protein called Rhino binds to piRNA clusters that are densely packed to allow piRNAs to be made. However, it remained unclear how Rhino is able to identify and bind to piRNA clusters, but not to other similarly densely packed regions of DNA. Baumgartner et al. used a combination of genetic, genomic, and imaging approaches to study how Rhino finds its way in the fruit fly genome. They found that another protein called Kipferl interacts with Rhino and is required for Rhino to bind to nearly all piRNA clusters. Since Kipferl can by itself bind to the sequences that Rhino needs to find, the results suggest that Kipferl acts to recruit and initiate Rhino binding within densely packed piRNA clusters. Further experiments found that, in flies lacking Kipferl, Rhino binds to regions of DNA called Satellite repeats, hinting that these selfish sequences may compete for Rhino for their own benefit. The finding that Kipferl and Rhino work together to define the memory system of the piRNA pathway strongly advances our understanding of how a sequence-specific defense system based on small RNAs can be established.