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Transcriptional milestones in Dictyostelium development
Genome Research ( IF 7 ) Pub Date : 2021-08-01 , DOI: 10.1101/gr.275496.121
Mariko Katoh-Kurasawa 1 , Karin Hrovatin 2 , Shigenori Hirose 1 , Amanda Webb 1 , Hsing-I Ho 1 , Blaž Zupan 1, 2 , Gad Shaulsky 1
Affiliation  

Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly coregulated with cell division genes, so they are expressed in mid-development although chromosomal DNA is not replicated. Our data set includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We show its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The data set is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.

中文翻译:

网柄菌发育的转录里程碑

网柄菌发育始于单细胞饥饿,终于多细胞子实体。发育形态发生伴随着广泛的转录变化,包括基因组中 13,000 个基因中的近一半。我们对野生型和 20 个突变体进行了时间序列 RNA 测序分析,以探索转录和形态发生之间的关系。这些菌株在不同阶段表现出发育停滞、加速发育或非典型形态。考虑到八个主要的形态转变,我们确定了 1371 个里程碑基因,其表达在连续转变之间急剧变化。我们还确定了 1099 个基因作为 21 个调节子的成员,这些调节子是尽管存在遗传、时间和发育扰动但仍保持协调调节的基因组。这些组中的基因注释验证了已知的转变并揭示了新的发育事件。例如,DNA 复制基因与细胞分裂基因紧密协同调节,因此它们在发育中期表达,尽管染色体 DNA 没有复制。我们的数据集包括 486 个转录谱,可以帮助识别转录和发育之间的新关系并改进基因注释。我们通过显示同种异体识别缺陷突变体中的聚集和分解循环涉及去分化来展示其效用。我们还表现出对两种常用肌动蛋白基因的遗传和发育条件的敏感性,因此它们在发育中期表达,尽管染色体 DNA 没有复制。我们的数据集包括 486 个转录谱,可以帮助识别转录和发育之间的新关系并改进基因注释。我们通过显示同种异体识别缺陷突变体中的聚集和分解循环涉及去分化来展示其效用。我们还表现出对两种常用肌动蛋白基因的遗传和发育条件的敏感性,因此它们在发育中期表达,尽管染色体 DNA 没有复制。我们的数据集包括 486 个转录谱,可以帮助识别转录和发育之间的新关系并改进基因注释。我们通过显示同种异体识别缺陷突变体中的聚集和分解循环涉及去分化来展示其效用。我们还表现出对两种常用肌动蛋白基因的遗传和发育条件的敏感性,act6act15以及coaA基因的稳健性。最后,我们建议gpdA是一种更好的 mRNA 定量标准,因为它对外部条件的敏感性低于常用标准。该数据集可通过 Web 应用程序 dictyExpress 和数据挖掘环境 Orange 进行民主化探索。
更新日期:2021-08-02
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