Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

2020 ◽  
Author(s):  
Fu-Xiang Wang ◽  
Guan-Dong Shang ◽  
Lian-Yu Wu ◽  
Geng-Zhou Xu ◽  
Xin-Yan Zhao ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Network Structure ◽  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Chromatin Accessibility ◽  
Transcriptional Regulatory

scholarly journals Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

2019 ◽  
Vol 29 (3) ◽  
pp. 449-463 ◽  
Author(s):  
Emily R. Miraldi ◽  
Maria Pokrovskii ◽  
Aaron Watters ◽  
Dayanne M. Castro ◽  
Nicholas De Veaux ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Network Inference ◽  
Transcriptional Regulatory Network ◽  
Chromatin Accessibility ◽  
T Helper ◽  
T Helper 17 ◽  
T Helper 17 Cells ◽  
Transcriptional Regulatory

scholarly journals Chromatin accessibility and translational landscapes of tea plants under chilling stress

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pengjie Wang ◽  
Shan Jin ◽  
Xuejin Chen ◽  
Liangyu Wu ◽  
Yucheng Zheng ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Chilling Stress ◽  
Chromatin Accessibility ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Limited Information ◽  
Transcriptional Regulatory ◽  
Tea Plants

AbstractPlants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.

scholarly journals Topological and causal structure of the yeast transcriptional regulatory network

10.1038/ng873 ◽  
2002 ◽  
Vol 31 (1) ◽  
pp. 60-63 ◽  
Author(s):  
Nabil Guelzim ◽  
Samuele Bottani ◽  
Paul Bourgine ◽  
François Képès
Keyword(s):  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Causal Structure ◽  
Transcriptional Regulatory

scholarly journals Screening Driving Transcription Factors in the Processing of Gastric Cancer

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Guangzhong Xu ◽  
Kai Li ◽  
Nengwei Zhang ◽  
Bin Zhu ◽  
Guosheng Feng
Keyword(s):  
Gastric Cancer ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Profiles ◽  
Functional Enrichment ◽  
Regulatory Mechanisms ◽  
Integrated Analysis ◽  
Transcriptional Regulatory

Background. Construction of the transcriptional regulatory network can provide additional clues on the regulatory mechanisms and therapeutic applications in gastric cancer.Methods. Gene expression profiles of gastric cancer were downloaded from GEO database for integrated analysis. All of DEGs were analyzed by GO enrichment and KEGG pathway enrichment. Transcription factors were further identified and then a global transcriptional regulatory network was constructed.Results. By integrated analysis of the six eligible datasets (340 cases and 43 controls), a bunch of 2327 DEGs were identified, including 2100 upregulated and 227 downregulated DEGs. Functional enrichment analysis of DEGs showed that digestion was a significantly enriched GO term for biological process. Moreover, there were two important enriched KEGG pathways: cell cycle and homologous recombination. Furthermore, a total of 70 differentially expressed TFs were identified and the transcriptional regulatory network was constructed, which consisted of 566 TF-target interactions. The top ten TFs regulating most downstream target genes were BRCA1, ARID3A, EHF, SOX10, ZNF263, FOXL1, FEV, GATA3, FOXC1, and FOXD1. Most of them were involved in the carcinogenesis of gastric cancer.Conclusion. The transcriptional regulatory network can help researchers to further clarify the underlying regulatory mechanisms of gastric cancer tumorigenesis.

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