scholarly journals A high‐throughput method to identify trans‐activation domains within transcription factor sequences

2018 ◽  
Vol 37 (16) ◽  
Author(s):  
Cosmas D Arnold ◽  
Filip Nemčko ◽  
Ashley R Woodfin ◽  
Sebastian Wienerroither ◽  
Anna Vlasova ◽  
...  
2020 ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf

AbstractSpear-ATAC is a modified droplet-based single-cell ATAC-seq (scATAC-seq) protocol that enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at a time. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations revealed the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles, demonstrating a high-throughput method for perturbing and evaluating dynamic single-cell epigenetic states.


Planta Medica ◽  
2016 ◽  
Vol 82 (05) ◽  
Author(s):  
C Avonto ◽  
AG Chittiboyina ◽  
D Rua ◽  
IA Khan

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.


Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1573-1581 ◽  
Author(s):  
Susanna Chou ◽  
Sukalyan Chatterjee ◽  
Mark Lee ◽  
Kevin Struhl

Abstract The general transcription factor IIA (TFIIA) forms a complex with TFIID at the TATA promoter element, and it inhibits the function of several negative regulators of the TATA-binding protein (TBP) subunit of TFIID. Biochemical experiments suggest that TFIIA is important in the response to transcriptional activators because activation domains can interact with TFIIA, increase recruitment of TFIID and TFIIA to the promoter, and promote isomerization of the TFIID-TFIIA-TATA complex. Here, we describe a double-shut-off approach to deplete yeast cells of Toa1, the large subunit of TFIIA, to <1% of the wild-type level. Interestingly, such TFIIA-depleted cells are essentially unaffected for activation by heat shock factor, Ace1, and Gal4-VP16. However, depletion of TFIIA causes a general two- to threefold decrease of transcription from most yeast promoters and a specific cell-cycle arrest at the G2-M boundary. These results indicate that transcriptional activation in vivo can occur in the absence of TFIIA.


Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1313
Author(s):  
Andreas Hoffmann ◽  
Alexander J. C. Kuehne

Carbon nanofiber nonwovens are promising materials for electrode or filtration applications; however, their utilization is obviated by a lack of high throughput production methods. In this study, we utilize a highly effective high-throughput method for the fabrication of polyacrylonitrile (PAN) nanofibers as a nonwoven on a dedicated substrate. The method employs rotational-, air pressure- and electrostatic forces to produce fibers from the inner edge of a rotating bell towards a flat collector. We investigate the impact of all above-mentioned forces on the fiber diameter, morphology, and bundling of the carbon-precursor PAN fibers. The interplay of radial forces with collector-facing forces has an influence on the uniformity of fiber deposition. Finally, the obtained PAN nanofibers are converted to carbon nonwovens by thermal treatment.


Soft Matter ◽  
2021 ◽  
Author(s):  
Tao Lin ◽  
Zhen Wang ◽  
Wen Wang ◽  
Yi Sui

We have developed a high-throughput method, by combining a hybrid neural network with a mechanistic capsule model, to predict membrane elasticity and viscosity of microcapsules from their dynamic deformation in a branched microchannel.


Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1466
Author(s):  
Lisard Iglesias-Carres ◽  
Lauren A. Essenmacher ◽  
Kathryn C. Racine ◽  
Andrew P. Neilson

Choline is metabolized by the gut microbiota into trimethylamine (TMA), the precursor of pro-atherosclerotic molecule trimethylamine N-oxide (TMAO). A reduction in TMA formation has shown cardioprotective effects, and some phytochemicals may reduce TMA formation. This study aimed to develop an optimized, high-throughput anaerobic fermentation methodology to study the inhibition of choline microbial metabolism into TMA by phenolic compounds with healthy human fecal starter. Optimal fermentation conditions were: 20% fecal slurry (1:10 in PBS), 100 µM choline, and 12 h fermentation. Additionally, 10 mM of 3,3-dimethyl-1-butanol (DMB) was defined as a positive TMA production inhibitor, achieving a ~50% reduction in TMA production. Gallic acid and chlorogenic acid reported higher TMA inhibitory potential (maximum of 80–90% TMA production inhibition), with IC50 around 5 mM. Neither DMB nor gallic acid or chlorogenic acid reduced TMA production through cytotoxic effects, indicating mechanisms such as altered TMA-lyase activity or expression.


Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 398
Author(s):  
Yusuke Aono ◽  
Yonathan Asikin ◽  
Ning Wang ◽  
Denise Tieman ◽  
Harry Klee ◽  
...  

Flavor and nutritional quality has been negatively impacted during the course of domestication and improvement of the cultivated tomato (Solanum lycopersicum). Recent emphasis on consumers has emphasized breeding strategies that focus on flavor-associated chemicals, including sugars, acids, and aroma compounds. Carotenoids indirectly affect flavor as precursors of aroma compounds, while chlorophylls contribute to sugar production through photosynthesis. However, the relationships between these pigments and flavor content are still unclear. In this study, we developed a simple and high-throughput method to quantify chlorophylls and carotenoids. This method was applied to over one hundred tomato varieties, including S. lycopersicum and its wild relatives (S. l. var. cerasiforme and S. pimpinellifolium), for quantification of these pigments in fruits. The results obtained by integrating data of the pigments, soluble solids, sugars, and aroma compounds indicate that (i) chlorophyll-abundant varieties have relatively higher sugar accumulations and (ii) prolycopene is associated with an abundance of linear carotenoid-derived aroma compounds in one of the orange-fruited varieties, “Dixie Golden Giant”. Our results suggest the importance of these pigments not only as components of fruit color but also as factors influencing flavor traits, such as sugars and aroma.


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