An adenosine nucleotide switch controlling the activity of a cell type-specific transcription factor in B. subtilis

Cell ◽  
1994 ◽  
Vol 77 (2) ◽  
pp. 195-205 ◽  
Author(s):  
Scott Alper ◽  
Leonard Duncan ◽  
Richard Losick
1999 ◽  
Vol 274 (38) ◽  
pp. 26661-26667 ◽  
Author(s):  
Jianping Ye ◽  
Howard A. Young ◽  
Xiaoying Zhang ◽  
Vince Castranova ◽  
Val Vallyathan ◽  
...  

2019 ◽  
Author(s):  
Hongyang Li ◽  
Yuanfang Guan

AbstractDecoding the cell type-specific transcription factor (TF) binding landscape at single-nucleotide resolution is crucial for understanding the regulatory mechanisms underlying many fundamental biological processes and human diseases. However, limits on time and resources restrict the high-resolution experimental measurements of TF binding profiles of all possible TF-cell type combinations. Previous computational approaches either can not distinguish the cell-context-dependent TF binding profiles across diverse cell types, or only provide a relatively low-resolution prediction. Here we present a novel deep learning approach, Leopard, for predicting TF-binding sites at single-nucleotide resolution, achieving the median area under receiver operating characteristic curve (AUROC) of 0.994. Our method substantially outperformed state-of-the-art methods Anchor and FactorNet, improving the performance by 19% and 27% respectively despite evaluated at a lower resolution. Meanwhile, by leveraging a many-to-many neural network architecture, Leopard features hundred-fold to thousand-fold speedup compared to current many-to-one machine learning methods.


1995 ◽  
Vol 15 (5) ◽  
pp. 2849-2857 ◽  
Author(s):  
A P Bradford ◽  
K E Conrad ◽  
C Wasylyk ◽  
B Wasylyk ◽  
A Gutierrez-Hartmann

The mechanism by which activation of common signal transduction pathways can elicit cell-specific responses remains an important question in biology. To elucidate the molecular mechanism by which the Ras signaling pathway activates a cell-type-specific gene, we have used the pituitary-specific rat prolactin (rPRL) promoter as a target of oncogenic Ras and Raf in GH4 rat pituitary cells. Here we show that expression of either c-Ets-1 or the POU homeo-domain transcription factor GHF-1/Pit-1 enhance the Ras/Raf activation of the rPRL promoter and that coexpression of the two transcription factors results in an even greater synergistic Ras response. By contrast, the related GHF-1-dependent rat growth hormone promoter fails to respond to Ras or Raf, indicating that GHF-1 alone is insufficient to mediate the Ras/Raf effect. Using amino-terminal truncations of c-Ets-1, we have mapped the c-Ets-1 region required to mediate the optimal Ras response to a 40-amino-acid segment which contains a putative mitogen-activated protein kinase site. Finally, dominant-negative Ets and GHF constructs block Ras activation of the rPRL promoter, and each blocks the synergistic activation mediated by the other partner protein, further corroborating that a functional interaction between c-Ets-1 and GHF-1 is required for an optimal Ras response. Thus, the functional interaction of a pituitary-specific transcription factor, GHF-1, with a widely expressed nuclear proto-oncogene product, c-Ets-1, provides one important molecular mechanism by which the general Ras signaling cascade can be interpreted in a cell-type-specific manner.


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