Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax
Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax
复制标题
DOI：
10.1016/j.jtbi.2016.08.038
复制
发表时间：
2016-12-07
影响因子：
2
通讯作者：
Jonoska, Natasa
中科院分区：
文献类型：
--
作者：
Burns, Jonathan;Kukushkin, Denys;Jonoska, Natasa
一些纤毛虫属，例如尖毛虫属和柱甲虫属，在发育过程中经历了大规模的基因组重组，并为研究 DNA 重排提供了模式生物。这些纤毛虫的一个共同特征是存在两种类型的细胞核：种系微核和转录活性体细胞大核，其中含有超过 16,000 个基因大小的“纳米染色体”。在接合过程中，旧的亲本大核分解，并从合子微核的副本形成新的大核。在此过程中，大核染色体通过 DNA 加工事件进行组装，删除了微核 90-98% 的 DNA 含量。这包括删除中断微核中前体 DNA 区域的非编码 DNA 片段，以及转座子和其他种系限制的 DNA。每个大核基因座可以作为几个不连续的、排列的和/或倒转的DNA片段存在于微核中。在这里，我们研究了全基因组范围的乱序基因结构，这些结构描述了三毛尖毛虫（第一个完全测序的乱序基因组）中的所有前体-产物关系。我们发现，在乱序微核前体片段组中，五种常见的、重复出现的模式可以描述超过 80% 的尖毛虫乱序基因。其中包括易位和倒位的情况，以及以连续奇数和偶数 DNA 片段交替延伸为特征的其他特定模式。此外，我们发现奇偶片段交替的迭代模式最多四次可以描述超过 96% 的乱序前体基因座。这些高度结构化的遗传结构在乱序基因中的重复出现可能反映了反复发生的进化事件，这些事件在种系基因组中产生了超过 3000 个乱序基因座。 (C) 2016 Elsevier Ltd. 保留所有权利。
Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally active somatic macronucleus containing over 16,000 gene sized "nano-chromosomes". During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt precursor DNA regions in the micronucleus, as well as transposons and other germline-limited DNA. Each macronuclear locus may be present in the micronucleus as several nonconsecutive, permuted, and/or inverted DNA segments. Here we investigate the genome-wide range of scrambled gene architectures that describe all precursor-product relationships in Oxytricha trifallax, the first completely sequenced scrambled genome. We find that five general, recurrent patterns in the sets of scrambled micronuclear precursor pieces can describe over 80% of Oxytricha's scrambled genes. These include instances of translocations and inversions, and other specific patterns characterized by alternating stretches of consecutive odd and even DNA segments. Moreover, we find that iterating patterns of alternating odd even segments up to four times can describe over 96% of the scrambled precursor loci. Recurrence of these highly structured genetic architectures within scrambled genes presumably reflects recurrent evolutionary events that gave rise to over 3000 of scrambled loci in the germline genome. (C) 2016 Elsevier Ltd. All rights reserved.