Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Elife. 2022 Apr 11;11:e73225. doi: 10.7554/eLife.73225.
Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was studied in a few cases only. To provide a genome-scale view, we considered the set of budding yeast TFs classified as whole-genome duplication (WGD)-retained paralogs (~35% of all specific TFs). Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA-binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed uneven splitting of ancestral preferences between duplicates, and the preferential acquiring of new targets by the least conserved paralog (biased neo/sub-functionalization). Interactions between paralogs were rare, and, when present, occurred through weak competition for DNA-binding or dependency between dimer-forming paralogs. We discuss the implications of our findings for the evolutionary design of transcriptional networks.
在进化过程中，新的转录因子 (TF) 通过基因复制出现，促进转录网络的生长和重布线。只有少数情况下研究了 TF 副本如何发生分歧。为了提供基因组规模的视图，我们考虑了一组被分类为全基因组复制 (WGD) 保留的同源基因 (约占所有特定 TF 的 35%)。使用高分辨率分析，我们发现约 60%的同源基因进化出了不同的结合偏好。我们表明，这种分歧主要源于 DNA 结合域 (DBD) 之外的变异，而 DBD 偏好仍然基本保持不变。对非 WGD 同源基因的分析表明，在复制之间，祖先偏好的不均匀分裂，以及最保守的同源基因 (偏向新/亚功能化) 优先获得新的靶标。同源基因之间的相互作用很少见，而且当存在时，通过 DNA 结合的弱竞争或二聚体形成同源基因之间的依赖性发生。我们讨论了我们的发现对转录网络进化设计的影响。
