Ferro Diana, Lepennetier Gildas, Catania Francesco
Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany.
Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany
Nucleic Acids Res. 2015 Sep 30;43(17):8157-68. doi: 10.1093/nar/gkv843. Epub 2015 Aug 24.
In Paramecium, the regeneration of a functional somatic genome at each sexual event relies on the elimination of thousands of germline DNA sequences, known as Internal Eliminated Sequences (IESs), from the zygotic nuclear DNA. Here, we provide evidence that IESs' length and sub-terminal bases jointly modulate IES excision by affecting DNA conformation in P. tetraurelia. Our study reveals an excess of complementary base pairing between IESs' sub-terminal and contiguous sites, suggesting that IESs may form DNA loops prior to cleavage. The degree of complementary base pairing between IESs' sub-terminal sites (termed Cin-score) is positively associated with IES length and is shaped by natural selection. Moreover, it escalates abruptly when IES length exceeds 45 nucleotides (nt), indicating that only sufficiently large IESs may form loops. Finally, we find that IESs smaller than 46 nt are favored targets of the cellular surveillance systems, presumably because of their relatively inefficient excision. Our findings extend the repertoire of cis-acting determinants for IES recognition/excision and provide unprecedented insights into the distinct selective pressures that operate on IESs and somatic DNA regions. This information potentially moves current models of IES evolution and of mechanisms of IES recognition/excision forward.
在草履虫中，每次有性生殖事件中功能性体细胞基因组的再生依赖于从合子核DNA中消除数千个生殖系DNA序列，即内部消除序列（IESs）。在此，我们提供证据表明，IESs的长度和亚末端碱基通过影响四膜虫的DNA构象共同调节IES切除。我们的研究揭示了IESs亚末端与相邻位点之间存在过量的互补碱基配对，这表明IESs在切割前可能形成DNA环。IESs亚末端位点之间的互补碱基配对程度（称为Cin评分）与IES长度呈正相关，并受自然选择影响。此外，当IES长度超过45个核苷酸（nt）时，它会突然升高，这表明只有足够大的IESs才可能形成环。最后，我们发现小于46 nt的IESs是细胞监测系统的优先靶向目标，可能是因为它们的切除效率相对较低。我们的研究结果扩展了IES识别/切除的顺式作用决定因素的范围，并为作用于IESs和体细胞DNA区域的不同选择压力提供了前所未有的见解。这些信息可能推动当前IES进化模型以及IES识别/切除机制向前发展。
