Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response.
Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response.
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DOI：
10.1186/s12864-023-09714-6
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发表时间：
2023-10-18
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
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植物通过高度调节的调节网络来应对压力。虽然以前的工作从全根数据中识别出了拟南芥缺铁反应的主要调节因子，但识别在细胞水平上起作用的调节因子对于更全面地理解铁的动态平衡至关重要。在根表皮中，促进根际铁还原和吸收的复杂分子机制被认为是由bHLH转录调节因子调节的。然而，关于控制这些反应的调节机制，以及它们如何与表皮内的发育过程整合，仍然存在许多问题。在这里，我们使用转录图谱来洞察根表皮特定的调控过程。对整个根和表皮转录测量之间的差异表达基因(Deg)进行集合比较，发现器官水平和表皮特异性反应的大小和时间上的差异。利用一种独特的采样方法，结合跨时滞和非时滞窗口的互信息度量，我们识别了功能相关的差异表达基因簇之间的关系，这表明发育调控过程可能作用于众所周知的铁特异反应的上游。通过整合静态数据(DNA基序信息)和时间序列转录数据，并使用机器学习方法，特别是使用套索的Logistic回归模型，我们还识别了作为预测差异表达基因的关键特征的假定基序。已知的与这些基序结合的28个转录因子(TF)没有差异表达，表明这些转录因子可能在转录后或翻译后调节。值得注意的是，这些转录因子中的许多也在根的发育和一般的胁迫反应中发挥作用。这项工作揭示了使用完整的根数据和特定细胞的根表皮数据识别的-Fe响应的关键差异。机器学习方法与额外的静态数据相结合，确定了不能仅通过转录图谱确定的铁反应的假定调节因子，并揭示了表皮内的发育和一般应激反应如何作用于更专门的铁吸收反应的上游。网上版载有补充材料，可在10.1186/s12864-023-09714-6查阅。
Plants respond to stress through highly tuned regulatory networks. While prior works identified master regulators of iron deficiency responses in A. thaliana from whole-root data, identifying regulators that act at the cellular level is critical to a more comprehensive understanding of iron homeostasis. Within the root epidermis complex molecular mechanisms that facilitate iron reduction and uptake from the rhizosphere are known to be regulated by bHLH transcriptional regulators. However, many questions remain about the regulatory mechanisms that control these responses, and how they may integrate with developmental processes within the epidermis. Here, we use transcriptional profiling to gain insight into root epidermis-specific regulatory processes. Set comparisons of differentially expressed genes (DEGs) between whole root and epidermis transcript measurements identified differences in magnitude and timing of organ-level vs. epidermis-specific responses. Utilizing a unique sampling method combined with a mutual information metric across time-lagged and non-time-lagged windows, we identified relationships between clusters of functionally relevant differentially expressed genes suggesting that developmental regulatory processes may act upstream of well-known Fe-specific responses. By integrating static data (DNA motif information) with time-series transcriptomic data and employing machine learning approaches, specifically logistic regression models with LASSO, we also identified putative motifs that served as crucial features for predicting differentially expressed genes. Twenty-eight transcription factors (TFs) known to bind to these motifs were not differentially expressed, indicating that these TFs may be regulated post-transcriptionally or post-translationally. Notably, many of these TFs also play a role in root development and general stress response. This work uncovered key differences in -Fe response identified using whole root data vs. cell-specific root epidermal data. Machine learning approaches combined with additional static data identified putative regulators of -Fe response that would not have been identified solely through transcriptomic profiles and reveal how developmental and general stress responses within the epidermis may act upstream of more specialized -Fe responses for Fe uptake. The online version contains supplementary material available at 10.1186/s12864-023-09714-6.
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影响因子：
4.5
作者：
Bruex A;Kainkaryam RM;Wieckowski Y;Kang YH;Bernhardt C;Xia Y;Zheng X;Wang JY;Lee MM;Benfey P;Woolf PJ;Schiefelbein J
通讯作者：
Schiefelbein J
DOI：
10.1039/c7mt00136c
发表时间：
2017-07-19
期刊：
Metallomics : integrated biometal science
影响因子：
--
作者：
Connorton JM;Balk J;Rodríguez-Celma J
通讯作者：
Rodríguez-Celma J
影响因子：
4.6
作者：
Azodi CB;Lloyd JP;Shiu SH
通讯作者：
Shiu SH
影响因子：
11.6
作者：
Han, Guoliang;Wei, Xiaocen;Wang, Baoshan
通讯作者：
Wang, Baoshan
影响因子：
6.9
作者：
Derbyshire, Paul;Drea, Sinead;Dolan, Liam
通讯作者：
Dolan, Liam