Transcriptional milestones in Dictyostelium development.
Transcriptional milestones in Dictyostelium development.
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DOI：
10.1101/gr.275496.121
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发表时间：
2021-08
期刊：
影响因子：
7
通讯作者：
Shaulsky G
中科院分区：
文献类型：
--
作者：
Katoh-Kurasawa M;Hrovatin K;Hirose S;Webb A;Ho HI;Zupan B;Shaulsky G
Dictyosteoblasts的发展始于单细胞饥饿和多细胞子实体结束。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8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换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共调控，因此它们在发育中期表达，尽管染色体DNA不复制。我们的数据集包括486个转录谱，可以帮助确定转录和发育之间的新关系，并改善基因注释。我们显示其效用表明，在alloprynation缺陷突变体的聚集和解聚周期涉及去分化。我们还显示了两个常用的肌动蛋白基因，act6和act15，和coaA基因的鲁棒性的遗传和发育条件的敏感性。最后，我们建议，gpdA是一个更好的mRNA定量标准，因为它是较不敏感的外部条件比常用的标准。该数据集可通过网络应用程序dictyExpress和数据挖掘环境橙子进行民主化探索。
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.
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影响因子：
5.8
作者：
Gu, Zuguang;Eils, Roland;Schlesner, Matthias
通讯作者：
Schlesner, Matthias
DOI：
10.1093/bfgp/3.3.199
发表时间：
2004-11-01
期刊：
Briefings in Functional Genomics & Proteomics
影响因子：
--
作者：
Blumenthal, Thomas
通讯作者：
Blumenthal, Thomas
DOI：
10.1073/pnas.0306983101
发表时间：
2004-05-04
影响因子：
11.1
作者：
Katoh, M;Shaw, C;Shaulsky, G
通讯作者：
Shaulsky, G
影响因子：
14.9
作者：
Basu S;Fey P;Pandit Y;Dodson R;Kibbe WA;Chisholm RL
通讯作者：
Chisholm RL
影响因子：
2.7
作者：
ABE, K;YANAGISAWA, K
通讯作者：
YANAGISAWA, K