scholarly journals Internal telomeric repeats and ‘TCP domain’ protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells

2003 ◽  
Vol 33 (6) ◽  
pp. 957-966 ◽  
Author(s):  
Dominique Trémousaygue ◽  
Lionel Garnier ◽  
Claude Bardet ◽  
Patrick Dabos ◽  
Christine Hervé ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Protein Binding ◽  
Binding Sites ◽  
Telomeric Repeats ◽  
Regulate Gene Expression ◽  
Protein Binding Sites ◽  
Domain Protein ◽  
Regulate Gene

Multiple proteins interact with the fushi tarazu proximal enhancer

1993 ◽  
Vol 13 (9) ◽  
pp. 5549-5559
Author(s):  
W Han ◽  
Y Yu ◽  
N Altan ◽  
L Pick
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Protein Binding ◽  
Binding Sites ◽  
Fusion Gene ◽  
Drosophila Embryo ◽  
Fushi Tarazu ◽  
Stripe Pattern ◽  
Enhancer Element ◽  
Protein Binding Sites

The expression of the Drosophila segmentation gene fushi tarazu (ftz) is controlled at the level of transcription. The proximal enhancer, located approximately 3.4 kb upstream of the transcription start site, directs lacZ fusion gene expression in a ftz-like seven-stripe pattern in transgenic fly embryos. We have taken a biochemical approach to identify DNA-binding proteins that regulate ftz gene expression through the proximal enhancer. DNase I footprinting and methylation interference experiments with staged Drosophila embryo nuclear extracts identified nine protein binding sites in the proximal enhancer. Ten different sequence-specific DNA-binding complexes that interact with eight of these sites were identified. Some interact with multiple sites, while others bind to single sites in the enhancer. Two of the complexes that interact with multiple sites appear to contain the previously described ftz regulators, FTZ-F1 and TTK/FTZ-F2. These in vitro studies allowed us to narrow down the proximal enhancer to a 323-bp DNA fragment that contains all of the protein binding sites. Expression directed by this minimal enhancer element in seven ftz-like stripes in transgenic embryos is identical to that directed by the full-length enhancer. Internal deletions of several sites abolish reporter gene expression in vivo. Thus, the ftz proximal enhancer, like other cell-type-specific eukaryotic enhancers, interacts with an array of proteins that are expected to mediate the establishment, maintenance, and repression of transcription of the ftz gene in seven stripes in the developing embryo.

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 Multiple proteins interact with the fushi tarazu proximal enhancer.

1993 ◽  
Vol 13 (9) ◽  
pp. 5549-5559 ◽  
Author(s):  
W Han ◽  
Y Yu ◽  
N Altan ◽  
L Pick
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Protein Binding ◽  
Binding Sites ◽  
Fusion Gene ◽  
Drosophila Embryo ◽  
Fushi Tarazu ◽  
Stripe Pattern ◽  
Enhancer Element ◽  
Protein Binding Sites

The expression of the Drosophila segmentation gene fushi tarazu (ftz) is controlled at the level of transcription. The proximal enhancer, located approximately 3.4 kb upstream of the transcription start site, directs lacZ fusion gene expression in a ftz-like seven-stripe pattern in transgenic fly embryos. We have taken a biochemical approach to identify DNA-binding proteins that regulate ftz gene expression through the proximal enhancer. DNase I footprinting and methylation interference experiments with staged Drosophila embryo nuclear extracts identified nine protein binding sites in the proximal enhancer. Ten different sequence-specific DNA-binding complexes that interact with eight of these sites were identified. Some interact with multiple sites, while others bind to single sites in the enhancer. Two of the complexes that interact with multiple sites appear to contain the previously described ftz regulators, FTZ-F1 and TTK/FTZ-F2. These in vitro studies allowed us to narrow down the proximal enhancer to a 323-bp DNA fragment that contains all of the protein binding sites. Expression directed by this minimal enhancer element in seven ftz-like stripes in transgenic embryos is identical to that directed by the full-length enhancer. Internal deletions of several sites abolish reporter gene expression in vivo. Thus, the ftz proximal enhancer, like other cell-type-specific eukaryotic enhancers, interacts with an array of proteins that are expected to mediate the establishment, maintenance, and repression of transcription of the ftz gene in seven stripes in the developing embryo.

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 The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana

PLoS Genetics ◽  
2020 ◽  
Vol 16 (4) ◽  
pp. e1008324
Author(s):  
Melody Nicolau ◽  
Nathalie Picault ◽  
Julie Descombin ◽  
Yasaman Jami-Alahmadi ◽  
Suhua Feng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transposable Elements ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases

2021 ◽  
Vol 22 (8) ◽  
pp. 4187
Author(s):  
Chia-Chun Tseng ◽  
Man-Chun Wong ◽  
Wei-Ting Liao ◽  
Chung-Jen Chen ◽  
Su-Chen Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Natural Selection ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Current Evidence ◽  
Regulate Gene Expression ◽  
Factor Binding ◽  
Regulate Gene

Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.

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