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 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

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 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.

Transcription factor ThWRKY4 binds to a novel WLS motif and a RAV1A element in addition to the W-box to regulate gene expression

Plant Science ◽  
2017 ◽  
Vol 261 ◽  
pp. 38-49 ◽  
Author(s):  
Hongyun Xu ◽  
Xinxin Shi ◽  
Zhibo Wang ◽  
Caiqiu Gao ◽  
Chao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Regulate Gene Expression ◽  
Regulate Gene

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.

Mutational analysis of human heat-shock transcription factor 1 reveals a regulatory role for oligomerization in DNA-binding specificity

2009 ◽  
Vol 424 (2) ◽  
pp. 253-261 ◽  
Author(s):  
Yukiko Takemori ◽  
Yasuaki Enoki ◽  
Noritaka Yamamoto ◽  
Yo Fukai ◽  
Kaori Adachi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Heat Shock ◽  
Dna Binding ◽  
Binding Domain ◽  
Heat Shock Transcription Factor ◽  
Yeast Cells ◽  
Dna Binding Domain ◽  
Regulate Gene Expression ◽  
Regulate Gene

HSF (heat-shock transcription factor) trimers bind to the HSE (heat-shock element) regulatory sequence of target genes and regulate gene expression. A typical HSE consists of at least three contiguous inverted repeats of the 5-bp sequence nGAAn. Yeast HSF is able to recognize discontinuous HSEs that contain gaps in the array of the nGAAn sequence; however, hHSF1 (human HSF1) fails to recognize such sites in vitro, in yeast and in HeLa cells. In the present study, we isolated suppressors of the temperature-sensitive growth defect of hHSF1-expressing yeast cells. Intragenic suppressors contained amino acid substitutions in the DNA-binding domain of hHSF1 that enabled hHSF1 to regulate the transcription of genes containing discontinuous HSEs. The substitutions facilitated hHSF1 oligomerization, suggesting that the DNA-binding domain is important for this conformational change. Furthermore, other oligomerization-prone derivatives of hHSF1 were capable of recognizing discontinuous HSEs. These results suggest that modulation of oligomerization is important for the HSE specificity of hHSF1 and imply that hHSF1 possesses the ability to bind to and regulate gene expression via various types of HSEs in diverse cellular processes.

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.

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