Transcription Factor Dynamics

Lu, Feiyue; Lionnet, Timothée

doi:10.1101/cshperspect.a040949

Cited by 52 publications

(38 citation statements)

References 191 publications

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“…We also found that cis-acting elements associated with ABA response were highly enriched in promoters of a large number of genes (Figure 5). This result is consistent with the biological identity of bZIP as a transcription factor [75]. The bZIP genes are involved in ABA signaling and ABA plays an important role in the process of plant resistance to stress [76].…”

Section: Discussionsupporting

confidence: 87%

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum)

Liang

Xia

Jiang

et al. 2022

IJMS

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The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.

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Section: Discussionsupporting

confidence: 87%

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum)

Liang

Xia

Jiang

et al. 2022

IJMS

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“…One possible, albeit speculative, explanation is that activation of transcription by distal enhancers may require prolonged enhancer-promoter contact rather than over-all contact frequency. Transcription factor binding is typically quite transient 51 , and prolonged contact might be required for proper formation of enhancer, polymerase, or mediator complexes that drive transcriptional activation. Recent work using 3D super-resolution live-cell imaging found that loops stabilized contact between anchors for 10-30 minutes 52 .…”

Section: Discussionmentioning

confidence: 99%

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

Reed

Davis

Bond

et al. 2022

Preprint

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To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation. Enhancers and genes connected by loops exhibited stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. Changes in acetylation at looped distal enhancers preceded changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, while lost loops were often accompanied by high levels of transcription with the loop boundaries themselves. Taken together, these results are consistent with a reciprocal relationship in which loops can facilitate increased transcription by connecting promoters to distal enhancers while high levels of transcription can impede loop formation.

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“…In addition to finding its best friend in the form of another transcription factor with which to dimerize, transcription factors must also recruit a party of friends to drive chromatin remodeling and/or transcriptional events. These interactions are typically driven by fuzzy binding kinetics in low complexity domains [43]. Recruitment of these machines to the appropriate region of DNA is driven by the DNA-binding activity of the transcription factor, either to remodel chromatin or to promote gene transcription.…”

Section: Party Friendsmentioning

confidence: 99%