Massri Abdull Jesus, McDonald Brennan, Wray Gregory A, McClay David R
Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.
Evodevo. 2023 Jun 16;14(1):10. doi: 10.1186/s13227-023-00214-y.
The developmental gene regulatory networks (dGRNs) of two sea urchin species, Lytechinus variegatus (Lv) and Strongylocentrotus purpuratus (Sp), have remained remarkably similar despite about 50 million years since a common ancestor. Hundreds of parallel experimental perturbations of transcription factors with similar outcomes support this conclusion. A recent scRNA-seq analysis suggested that the earliest expression of several genes within the dGRNs differs between Lv and Sp. Here, we present a careful reanalysis of the dGRNs in these two species, paying close attention to timing of first expression. We find that initial expression of genes critical for cell fate specification occurs during several compressed time periods in both species. Previously unrecognized feedback circuits are inferred from the temporally corrected dGRNs. Although many of these feedbacks differ in location within the respective GRNs, the overall number is similar between species. We identify several prominent differences in timing of first expression for key developmental regulatory genes; comparison with a third species indicates that these heterochronies likely originated in an unbiased manner with respect to embryonic cell lineage and evolutionary branch. Together, these results suggest that interactions can evolve even within highly conserved dGRNs and that feedback circuits may buffer the effects of heterochronies in the expression of key regulatory genes.
尽管自共同祖先以来已经过去了大约5000万年，但两种海胆物种——多斑刺海胆（Lytechinus variegatus，Lv）和紫海胆（Strongylocentrotus purpuratus，Sp）——的发育基因调控网络（dGRNs）仍然非常相似。对转录因子进行的数百次平行实验扰动都得到了相似的结果，这支持了这一结论。最近的一项单细胞RNA测序（scRNA-seq）分析表明，dGRNs中几个基因的最早表达在Lv和Sp之间存在差异。在这里，我们对这两个物种的dGRNs进行了仔细的重新分析，特别关注首次表达的时间。我们发现，对于细胞命运特化至关重要的基因的初始表达在这两个物种的几个压缩时间段内发生。从经过时间校正的dGRNs中推断出了以前未被识别的反馈回路。尽管这些反馈中的许多在各自GRNs中的位置不同，但物种之间的总数相似。我们确定了关键发育调控基因首次表达时间的几个显著差异；与第三个物种的比较表明，这些异时性可能以一种与胚胎细胞谱系和进化分支无关的方式起源。总之，这些结果表明，即使在高度保守的dGRNs中，相互作用也可以进化，并且反馈回路可能缓冲关键调控基因表达中异时性的影响。
