CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal.
CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, 4169 007 Porto, Portugal.
Genomics. 2020 May;112(3):2410-2417. doi: 10.1016/j.ygeno.2020.01.013. Epub 2020 Jan 22.
Described as "junk" DNA, pseudogenes are dead structures of previously active genes present in genomes. Pseudogenes are categorized into two main classes: processed pseudogenes, formed through retrotransposition, and non-processed pseudogenes, typically originated from gene decay following duplication events. The term "processed pseudogene" has changed to "retrocopy" since they are likely to evolve new functional roles and became a retrogene. Here, we surveyed 38,080 retrocopies from chimpanzee, dog, human, mouse, and rat genomes to assess their potential adaptive value. The retrocopies inserted in the same chromosome of the parental gene have higher chances of remain potentially "active" (absence of premature stop codons and frameshifts) (26.1%), while those placed into a different chromosome have a twofold decrease chance of continuing potentially "active" (7.52%). The genomic context of their placement seems associated with their expression. Retrocopies placed in intragenic regions and the same sense of the "host" gene have higher chances of being expressed relative to other genomic contexts. The proximity of retrocopies to their parental gene is associated with a lower decay rate, and their location likely influence their expression. Thus, despite their unclear role, retrocopies are probably involved in adaptive processes. Our results evidence natural selection acting in retrocopies.
被描述为“垃圾” DNA 的假基因是存在于基因组中的先前活跃基因的死亡结构。假基因分为两类：通过反转录转座形成的加工假基因和通常由基因复制后衰亡产生的非加工假基因。由于它们可能会进化出新的功能作用并成为返基因，因此术语“加工假基因”已更改为“返基因”。在这里，我们调查了来自黑猩猩、狗、人类、老鼠和大鼠基因组的 38080 个返基因，以评估它们潜在的适应价值。插入到亲本基因相同染色体上的返基因更有可能保持潜在的“活性”（没有提前终止密码子和移码）（26.1%），而那些插入到不同染色体上的返基因继续保持潜在“活性”的机会减少了两倍（7.52%）。它们插入位置的基因组背景似乎与其表达有关。插入到基因内区域且与“宿主”基因相同方向的返基因更有可能表达，而其他基因组背景的表达机会较低。返基因与其亲本基因的接近程度与较低的衰减率有关，其位置可能影响其表达。因此，尽管它们的作用尚不清楚，但返基因可能参与了适应过程。我们的结果表明，自然选择作用于返基因。
