scholarly journals Genome-Wide Analyses of the Genetic Screening of C2H2-Type Zinc Finger Transcription Factors and Abiotic and Biotic Stress Responses in Tomato (Solanum lycopersicum) Based on RNA-Seq Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Tingting Zhao ◽  
Tairu Wu ◽  
Jia Zhang ◽  
Ziyu Wang ◽  
Tong Pei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Solanum Lycopersicum ◽  
Zinc Finger ◽  
Stress Responses ◽  
Biotic Stress ◽  
Genetic Screening ◽  
Rna Seq ◽  
Abiotic And Biotic Stress ◽  
Genome Wide ◽  
Biotic Stress Responses

scholarly journals Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis

2013 ◽  
Vol 73 (5) ◽  
pp. 761-775 ◽  
Author(s):  
Yusuke Nakai ◽  
Yoichi Nakahira ◽  
Hiroki Sumida ◽  
Kosuke Takebayashi ◽  
Yumiko Nagasawa ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Stress Responses ◽  
Biotic Stress ◽  
Zinc Finger Protein ◽  
Vascular Plant ◽  
Abiotic And Biotic Stress ◽  
Finger Protein ◽  
Biotic Stress Responses

scholarly journals Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

2019 ◽  
Author(s):  
Wei Wang ◽  
Gang Ren ◽  
Ni Hong ◽  
Wenfei Jin
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Cell ◽  
Zinc Finger ◽  
Ctcf Binding ◽  
Rna Seq ◽  
Expression Noise ◽  
Genome Wide ◽  
Cell Variation ◽  
Variable Genes

Abstract Background: CCCTC-Binding Factor (CTCF), also known as 11-zinc finger protein, participates in many cellular processes, including insulator activity, transcriptional regulation and organization of chromatin architecture. Based on single cell flow cytometry and single cell RNA-FISH analyses, our previous study showed that deletion of CTCF binding site led to a significantly increase of cellular variation of its target gene. However, the effect of CTCF on genome-wide landscape of cell-to-cell variation is unclear. Results: We knocked down CTCF in EL4 cells using shRNA, and conducted single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells using Fluidigm C1 system. Principal component analysis of single cell RNA-seq data showed that WT and CTCF-KD cells concentrated in two different clusters on PC1, indicating gene expression profiles of WT and CTCF-KD cells were systematically different. Interestingly, GO terms including regulation of transcription, DNA binding, Zinc finger and transcription factor binding were significantly enriched in CTCF-KD-specific highly variable genes, indicating tissue-specific genes such as transcription factors were highly sensitive to CTCF level. The dysregulation of transcription factors potentially explain why knockdown of CTCF lead to systematic change of gene expression. In contrast, housekeeping genes such as rRNA processing, DNA repair and tRNA processing were significantly enriched in WT-specific highly variable genes, potentially due to a higher cellular variation of cell activity in WT cells compared to CTCF-KD cells. We further found cellular variation-increased genes were significantly enriched in down-regulated genes, indicating CTCF knockdown simultaneously reduced the expression levels and increased the expression noise of its regulated genes. Conclusions: To our knowledge, this is the first attempt to explore genome-wide landscape of cellular variation after CTCF knockdown. Our study not only advances our understanding of CTCF function in maintaining gene expression and reducing expression noise, but also provides a framework for examining gene function.

scholarly journals Grapevine Biotechnology: Molecular Approaches Underlying Abiotic and Biotic Stress Responses

10.5772/64872 ◽  
2016 ◽  
Author(s):  
Grace Armijo ◽  
Carmen Espinoza ◽  
Rodrigo Loyola ◽  
Franko Restovic ◽  
Claudia Santibáñez ◽  
...  
Keyword(s):  
Stress Responses ◽  
Biotic Stress ◽  
Abiotic And Biotic Stress ◽  
Molecular Approaches ◽  
Biotic Stress Responses

scholarly journals Linking Autophagy to Abiotic and Biotic Stress Responses

2019 ◽  
Vol 24 (5) ◽  
pp. 413-430 ◽  
Author(s):  
Santiago Signorelli ◽  
Łukasz Paweł Tarkowski ◽  
Wim Van den Ende ◽  
Diane C. Bassham
Keyword(s):  
Stress Responses ◽  
Biotic Stress ◽  
Abiotic And Biotic Stress ◽  
Biotic Stress Responses
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