Moschetti Roberta, Celauro Emanuele, Cruciani Fulvio, Caizzi Ruggiero, Dimitri Patrizio
Dipartimento di Biologia, Università degli Studi di Bari, Bari, Italy.
Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy.
PLoS One. 2014 Nov 18;9(11):e113010. doi: 10.1371/journal.pone.0113010. eCollection 2014.
Constitutive heterochromatin is a ubiquitous and still unveiled component of eukaryotic genomes, within which it comprises large portions. Although constitutive heterochromatin is generally considered to be transcriptionally silent, it contains a significant variety of sequences that are expressed, among which about 300 single-copy coding genes have been identified by genetic and genomic analyses in the last decades. Here, we report the results of the evolutionary analysis of Yeti, an essential gene of Drosophila melanogaster located in the deep pericentromeric region of chromosome 2R. By FISH, we showed that Yeti maintains a heterochromatin location in both D. simulans and D. sechellia species, closely related to D. melanogaster, while in the more distant species e.g., D. pseudoobscura and D. virilis, it is found within euchromatin, in the syntenic chromosome Muller C, that corresponds to the 2R arm of D. melanogaster chromosome 2. Thus, over evolutionary time, Yeti has been resident on the same chromosomal element, but it progressively moved closer to the pericentric regions. Moreover, in silico reconstruction of the Yeti gene structure in 19 Drosophila species and in 5 non-drosophilid dipterans shows a rather stable organization during evolution. Accordingly, by PCR analysis and sequencing, we found that the single intron of Yeti does not undergo major intraspecies or interspecies size changes, unlike the introns of other essential Drosophila heterochromatin genes, such as light and Dbp80. This implicates diverse evolutionary forces in shaping the structural organization of genes found within heterochromatin. Finally, the results of dS - dN tests show that Yeti is under negative selection both in heterochromatin and euchromatin, and indicate that the change in genomic location did not affected significantly the molecular evolution of the gene. Together, the results of this work contribute to our understanding of the evolutionary dynamics of constitutive heterochromatin in the genomes of higher eukaryotes.
组成型异染色质是真核生物基因组中普遍存在且仍未完全揭示的组成部分，在基因组中占很大比例。虽然组成型异染色质通常被认为是转录沉默的，但它包含大量表达的序列，在过去几十年中，通过遗传和基因组分析已鉴定出约300个单拷贝编码基因。在这里，我们报告了对“雪人”（Yeti）基因的进化分析结果，该基因是黑腹果蝇的一个必需基因，位于2R染色体的深着丝粒周边区域。通过荧光原位杂交（FISH），我们发现“雪人”基因在与黑腹果蝇亲缘关系密切的拟暗果蝇和塞舌尔果蝇物种中均保持异染色质定位，而在较远的物种如伪暗果蝇和粗壮果蝇中，它位于常染色质中，在与黑腹果蝇2号染色体2R臂对应的同线染色体Muller C中。因此，在进化过程中，“雪人”基因一直位于同一染色体元件上，但它逐渐向着丝粒区域靠近。此外，对19种果蝇物种和5种非果蝇双翅目昆虫的“雪人”基因结构进行的电子重建显示，该基因在进化过程中具有相当稳定的组织形式。相应地，通过PCR分析和测序，我们发现“雪人”基因的单个内含子与其他必需的果蝇异染色质基因（如light和Dbp80）的内含子不同，在种内或种间大小上没有发生重大变化。这意味着在塑造异染色质中发现的基因的结构组织方面存在多种进化力量。最后，dS - dN测试结果表明，“雪人”基因在异染色质和常染色质中均受到负选择，这表明基因组位置的变化并未显著影响该基因的分子进化。总之，这项工作的结果有助于我们理解高等真核生物基因组中组成型异染色质的进化动态。
