scholarly journals Transcription Factor ANAC074 Binds to NRS1, NRS2, or MybSt1 Element in Addition to the NACRS to Regulate Gene Expression

2018 ◽  
Vol 19 (10) ◽  
pp. 3271
Author(s):  
Lin He ◽  
Jingyu Xu ◽  
Yucheng Wang ◽  
Kejun Yang
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Biological Processes ◽  
Regulate Gene Expression ◽  
Cis Element ◽  
Stress Responsive Genes ◽  
Regulate Gene ◽  
Gus Assays

NAC (NAM, ATAF1/2, and CUC2) transcription factors play important roles in many biological processes, and mainly bind to the NACRS with core sequences “CACG” or “CATGTG” to regulate gene expression. However, whether NAC proteins can bind to other motifs without these core sequences remains unknown. In this study, we employed a Transcription Factor-Centered Yeast one Hybrid (TF-Centered Y1H) screen to study the motifs recognized by ANAC074. In addition to the NACRS core cis-element, we identified that ANAC074 could bind to MybSt1, NRS1, and NRS2. Y1H and GUS assays showed that ANAC074 could bind the promoters of ethylene responsive genes and stress responsive genes via the NRS1, NRS2, or MybSt1 element. ChIP study further confirmed that the bindings of ANAC074 to MybSt1, NRS1, and NRS2 actually occurred in Arabidopsis. Furthermore, ten NAC proteins from different NAC subfamilies in Arabidopsis thaliana were selected and confirmed to bind to the MybSt1, NRS1, and NRS2 motifs, indicating that they are recognized commonly by NACs. These findings will help us to further reveal the functions of NAC proteins.

scholarly journals Challenges of Decoding Transcription Factor Dynamics in Terms of Gene Regulation

Cells ◽  
2018 ◽  
Vol 7 (9) ◽  
pp. 132 ◽  
Author(s):  
Erik Martin ◽  
Myong-Hee Sung
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Cell Biology ◽  
Extrinsic Factors ◽  
Regulate Gene Expression ◽  
Technological Advances ◽  
Experimental Approaches ◽  
Intrinsic And Extrinsic Factors ◽  
Regulate Gene

Technological advances are continually improving our ability to obtain more accurate views about the inner workings of biological systems. One such rapidly evolving area is single cell biology, and in particular gene expression and its regulation by transcription factors in response to intrinsic and extrinsic factors. Regarding the study of transcription factors, we discuss some of the promises and pitfalls associated with investigating how individual cells regulate gene expression through modulation of transcription factor activities. Specifically, we discuss four leading experimental approaches, the data that can be obtained from each, and important considerations that investigators should be aware of when drawing conclusions from such data.

scholarly journals Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

2019 ◽  
Vol 70 (19) ◽  
pp. 5355-5374 ◽  
Author(s):  
Dandan Zang ◽  
Jingxin Wang ◽  
Xin Zhang ◽  
Zhujun Liu ◽  
Yucheng Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Heat Shock ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Ion Homeostasis ◽  
Cellulose Synthase ◽  
Regulate Gene Expression ◽  
E Box ◽  
Regulate Gene

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

scholarly journals Dietary microRNA—A Novel Functional Component of Food

2019 ◽  
Vol 10 (4) ◽  
pp. 711-721 ◽  
Author(s):  
Lin Zhang ◽  
Ting Chen ◽  
Yulong Yin ◽  
Chen-Yu Zhang ◽  
Yong-Liang Zhang
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Biological Significance ◽  
Circulatory System ◽  
Physiological Effects ◽  
Biological Processes ◽  
Regulate Gene Expression ◽  
Functional Component ◽  
Health And Disease ◽  
Regulate Gene

ABSTRACT MicroRNAs are a class of small RNAs that play essential roles in various biological processes by silencing genes. Evidence emerging in recent years suggests that microRNAs in food can be absorbed into the circulatory system and organs of humans and other animals, where they regulate gene expression and biological processes. These food-derived dietary microRNAs may serve as a novel functional component of food, a role that has been neglected to date. However, a significant amount of evidence challenges this new concept. The absorption, stability, and physiological effects of dietary microRNA in recipients, especially in mammals, are currently under heavy debate. In this review, we summarize our current understanding of the unique characteristics of dietary microRNAs and concerns about both the mechanistic and methodological basis for studying the biological significance of dietary microRNAs. Such efforts will benefit continuing investigations and offer new perspectives for the interpretation of the roles of dietary microRNA with respect to the health and disease of humans and animals.

scholarly journals Nkx3.1 Functions as Para-transcription Factor to Regulate Gene Expression and Cell Proliferation in Non-cell Autonomous Manner

2012 ◽  
Vol 287 (21) ◽  
pp. 17248-17256 ◽  
Author(s):  
Jian Zhou ◽  
Li Qin ◽  
Jean Ching-Yi Tien ◽  
Li Gao ◽  
Xian Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Transcription Factor ◽  
Regulate Gene Expression ◽  
Regulate Gene

Identification of Gsr1 in Arabidopsis thaliana: A locus inferred to regulate gene expression in response to exogenous glutamine

Euphytica ◽  
2006 ◽  
Vol 151 (3) ◽  
pp. 291-302 ◽  
Author(s):  
R. Meyer ◽  
J. Yuan ◽  
J. Afzal ◽  
M. J. Iqbal ◽  
Mengxia Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals TFAP2 paralogs pioneer chromatin access for MITF and directly inhibit genes associated with cell migration

2021 ◽  
Author(s):  
Colin Kenny ◽  
Ramile Dilshat ◽  
Hannah Seberg ◽  
Eric Van Otterloo ◽  
Gregory Bonde ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Wild Type ◽  
Regulate Gene Expression ◽  
Enhancer Binding Protein ◽  
Pioneer Factors ◽  
Regulate Gene ◽  
Do So

Transcription factors in the Activating-enhancer-binding Protein 2 (TFAP2) family redundantly regulate gene expression in melanocytes and melanoma. Previous ChIP-seq experiments indicate that TFAP2A and Microphthalmia-associated Transcription Factor (MITF), a master regulator in these cell types, co-activate enhancers of genes promoting pigmentation. Evidence that TFAP2 paralogs can serve as pioneer factors supports the possibility that TFAP2 facilitates MITF binding at co-bound enhancers, although this model has not been tested. In addition, while MITF and TFAP2 paralogs both appear to repress genes that promote invasion, whether they do so by co-repressing enhancers is unknown. To address these questions we evaluated gene expression, chromatin accessibility, TFAP2A and MITF binding, and chromatin marks characteristic of active enhancers in SK-MEL-28 melanoma cells that were wild-type or deleted of the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C (i.e., TFAP2-KO cells). Integrated analyses revealed distinct subsets of enhancers bound by TFAP2A in WT cells that are inactivated and activated, respectively, in TFAP2-KO cells. At enhancers bound by both MITF and TFAP2A, MITF is generally lost in TFAP2A/TFAP2C double mutants, but not vice versa, implying TFAP2 pioneers chromatin access for MITF. There is a strong correlation between the sets of genes inhibited by MITF and TFAP2, although we did not find evidence that TFAP2 and MITF inhibit enhancers cooperatively. The findings imply that MITF and TFAP2 paralogs cooperatively affect the melanoma phenotype.

scholarly journals The Clock Protein CCA1 and the bZIP Transcription Factor HY5 Physically Interact to Regulate Gene Expression in Arabidopsis

2008 ◽  
Vol 1 (1) ◽  
pp. 58-67 ◽  
Author(s):  
Christos Andronis ◽  
Simon Barak ◽  
Stephen M. Knowles ◽  
Shoji Sugano ◽  
Elaine M. Tobin
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Bzip Transcription Factor ◽  
Regulate Gene Expression ◽  
Clock Protein ◽  
Regulate Gene

scholarly journals Interaction of OIP5-AS1 with MEF2C mRNA promotes myogenic gene expression

2020 ◽  
Vol 48 (22) ◽  
pp. 12943-12956
Author(s):  
Jen-Hao Yang ◽  
Ming-Wen Chang ◽  
Poonam R Pandey ◽  
Dimitrios Tsitsipatis ◽  
Xiaoling Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Muscle Regeneration ◽  
Muscle Development ◽  
Rna Binding ◽  
Myogenic Differentiation ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Regulate Gene Expression ◽  
Regulate Gene

Abstract Long noncoding (lnc)RNAs potently regulate gene expression programs in physiology and disease. Here, we describe a key function for lncRNA OIP5-AS1 in myogenesis, the process whereby myoblasts differentiate into myotubes during muscle development and muscle regeneration after injury. In human myoblasts, OIP5-AS1 levels increased robustly early in myogenesis, and its loss attenuated myogenic differentiation and potently reduced the levels of the myogenic transcription factor MEF2C. This effect relied upon the partial complementarity of OIP5-AS1 with MEF2C mRNA and the presence of HuR, an RNA-binding protein (RBP) with affinity for both transcripts. Remarkably, HuR binding to MEF2C mRNA, which stabilized MEF2C mRNA and increased MEF2C abundance, was lost after OIP5-AS1 silencing, suggesting that OIP5-AS1 might serve as a scaffold to enhance HuR binding to MEF2C mRNA, in turn increasing MEF2C production. These results highlight a mechanism whereby a lncRNA promotes myogenesis by enhancing the interaction of an RBP and a myogenic mRNA.

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