Khrameeva Ekaterina E, Fudenberg Geoffrey, Gelfand Mikhail S, Mirny Leonid A
1 Institute for Information Transmission, Problems (the Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, Moscow 127051, Russian Federation.
2 Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, build. 3, Moscow 143026, Russian Federation.
J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.
Three-dimensional (3D) organization of genomes affects critical cellular processes such as transcription, replication, and deoxyribo nucleic acid (DNA) repair. While previous studies have investigated the natural role, the 3D organization plays in limiting a possible set of genomic rearrangements following DNA repair, the influence of specific organizational principles on this process, particularly over longer evolutionary time scales, remains relatively unexplored. In budding yeast S.cerevisiae, chromosomes are organized into a Rabl-like configuration, with clustered centromeres and telomeres tethered to the nuclear periphery. Hi-C data for S.cerevisiae show that a consequence of this Rabl-like organization is that regions equally distant from centromeres are more frequently in contact with each other, between arms of both the same and different chromosomes. Here, we detect rearrangement events in Saccharomyces species using an automatic approach, and observe increased rearrangement frequency between regions with higher contact frequencies. Together, our results underscore how specific principles of 3D chromosomal organization can influence evolutionary events.
基因组的三维（3D）组织影响着关键的细胞过程，如转录、复制和脱氧核糖核酸（DNA）修复。虽然先前的研究已经探讨了3D组织在限制DNA修复后可能出现的一系列基因组重排中所起的自然作用，但特定组织原则对这一过程的影响，尤其是在更长的进化时间尺度上，仍相对未被探索。在芽殖酵母酿酒酵母中，染色体被组织成一种类似拉布尔（Rabl）的构型，着丝粒和端粒聚集并附着在核膜上。酿酒酵母的Hi-C数据表明，这种类似拉布尔的组织形式的一个结果是，在同一条和不同染色体的臂之间，与着丝粒等距的区域彼此更频繁地接触。在这里，我们使用一种自动方法检测了酿酒酵母属物种中的重排事件，并观察到接触频率较高的区域之间重排频率增加。总之，我们的结果强调了3D染色体组织的特定原则如何能够影响进化事件。
