MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma.
MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma.
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纤毛虫 Blepharisma 种系基因组中的基因组编辑可调节 MITE 感染。
DOI：
10.1073/pnas.2213985120
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发表时间：
2023-01-24
影响因子：
11.1
通讯作者：
Swart, Estienne C.
中科院分区：
文献类型：
--
作者：
Seah, Brandon K. B.;Singh, Minakshi;Emmerich, Christiane;Singh, Aditi;Woehle, Christian;Huettel, Bruno;Byerly, Adam;Stover, Naomi A.;Sugiura, Mayumi;Harumoto, Terue;Swart, Estienne C.
纤毛虫是微生物真核生物，具有独特的生命周期：它们的细胞含有两种细胞核，在发育过程中，它们会消除数千个被认为来自转座子的DNA片段。因为有显着差异，在DNA消除两个最好的研究纤毛虫群体之间，我们测序的DNA注定要消除Blepharisma，一个遥远的相关物种，其系统发育的位置，使我们能够评估哪些方面的消除可能是祖先，包括属性的消除DNA和小RNA，可能会针对他们。我们假设，截短的转座子衍生物称为MITE，这是特别丰富的消除DNA，不仅是丰富的来源，这种DNA，但也有助于延缓其产生。在有性接合后的发育过程中，纤毛虫从生殖系基因组的拷贝中切除许多内部消除序列（IES）以产生功能性体细胞基因组。大多数IES被认为起源于转座子，但假定的同源性经常被序列衰变所掩盖。为了获得关于IES和纤毛虫基因组编辑的性质的更具代表性的观点，我们组装了40，000个Blepharisma stoltei的IES，这是一个属于一个谱系（Heterotrichea）的物种，该谱系早期与深入研究的模型纤毛虫物种不同。大约四分之一的IES是短的（<115 bp），大部分是非重复的，长度上具有明显的~10 bp的周期性;其余的更长（高达7 kbp）和非周期性，并含有丰富的散布重复。与当前模型的预期相反，组装的Blepharisma种系基因组编码很少的转座酶。相反，其最丰富的重复序列（8，000个拷贝）是一个微型反向重复转座元件（MITE），显然是一个生殖系限制性Pogo家族转座子的缺失衍生物。我们假设MITE是IES的一个重要来源，IES的增殖最终是自我限制的，转座酶驯化实际上促进了垃圾DNA的积累，而不是保护种系基因组免受移动的因素的影响。
Ciliates are microbial eukaryotes with a unique life cycle: their cells contain two kinds of nuclei, and during development, they eliminate thousands of DNA segments thought to have originated from transposons. Because there are significant differences in DNA elimination between the two best-studied ciliate groups, we sequenced the DNA destined for elimination in Blepharisma, a distantly related species whose phylogenetic position allowed us to evaluate which aspects of the elimination are probably ancestral, including properties of the eliminated DNA and of small RNAs that may target them. We hypothesize that truncated transposon derivatives called MITEs, which are particularly abundant in the eliminated DNA, not only are abundant sources of this DNA but also contribute to retarding its generation. During their development following sexual conjugation, ciliates excise numerous internal eliminated sequences (IESs) from a copy of the germline genome to produce the functional somatic genome. Most IESs are thought to have originated from transposons, but the presumed homology is often obscured by sequence decay. To obtain more representative perspectives on the nature of IESs and ciliate genome editing, we assembled 40,000 IESs of Blepharisma stoltei, a species belonging to a lineage (Heterotrichea) that diverged early from those of the intensively studied model ciliate species. About a quarter of IESs were short (<115 bp), largely nonrepetitive, and with a pronounced ~10 bp periodicity in length; the remainder were longer (up to 7 kbp) and nonperiodic and contained abundant interspersed repeats. Contrary to the expectation from current models, the assembled Blepharisma germline genome encodes few transposases. Instead, its most abundant repeat (8,000 copies) is a Miniature Inverted-repeat Transposable Element (MITE), apparently a deletion derivative of a germline-limited Pogo-family transposon. We hypothesize that MITEs are an important source of IESs whose proliferation is eventually self-limiting and that rather than defending the germline genomes against mobile elements, transposase domestication actually facilitates the accumulation of junk DNA.
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