High-level expression of a sweet potato sporamin gene promoter: β-glucuroidase (GUS) fusion gene in the stems of transgenic tobacco plants is conferred by multiple cell type-specific regulatory elements

1991 ◽  
Vol 225 (3) ◽  
pp. 369-378 ◽  
Author(s):  
Shozo Ohta ◽  
Tsukaho Hattori ◽  
Atsushi Morikami ◽  
Kenzo Nakamura
Keyword(s):  
Fusion Gene ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Cell Type ◽  
High Level Expression ◽  
Tobacco Plants ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
High Level ◽  
Multiple Cell Type

scholarly journals Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells

2020 ◽  
Vol 48 (7) ◽  
pp. 3513-3524 ◽  
Author(s):  
Monali NandyMazumdar ◽  
Shiyi Yin ◽  
Alekh Paranjapye ◽  
Jenny L Kerschner ◽  
Hannah Swahn ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Molecular Mechanisms ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Airway Epithelial Cells ◽  
Control Mechanisms ◽  
Airway Epithelial ◽  
Cell Type ◽  
Long Range Interactions ◽  
Cell Type Specific

Abstract The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanisms controlling its transcription are likely divergent between them. Here, we determine how two extragenic CREs that are prominent in epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at −44 and −35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here, we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter, suggesting non-redundant enhancers. The deletions also greatly reduced promoter interactions with the 5′ TAD boundary. We show substantial recruitment of RNAPII to the −35 kb element and identify CEBPβ as a key activator of airway expression of CFTR, likely through occupancy at this CRE and the gene promoter.

scholarly journals accuEnhancer: Accurate enhancer prediction by integration of multiple cell type data with deep learning

2020 ◽  
Author(s):  
Yi-An Tung ◽  
Wen-Tse Yang ◽  
Tsung-Ting Hsieh ◽  
Yu-Chuan Chang ◽  
June-Tai Wu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Cell Types ◽  
Regulatory Elements ◽  
Sequence Motifs ◽  
Cell Type ◽  
Enhancer Activity ◽  
Multiple Cell ◽  
Type Data ◽  
Different Cell Types ◽  
Multiple Cell Type

AbstractEnhancers are one class of the regulatory elements that have been shown to act as key components to assist promoters in modulating the gene expression in living cells. At present, the number of enhancers as well as their activities in different cell types are still largely unclear. Previous studies have shown that enhancer activities are associated with various functional data, such as histone modifications, sequence motifs, and chromatin accessibilities. In this study, we utilized DNase data to build a deep learning model for predicting the H3K27ac peaks as the active enhancers in a target cell type. We propose joint training of multiple cell types to boost the model performance in predicting the enhancer activities of an unstudied cell type. The results demonstrated that by incorporating more datasets across different cell types, the complex regulatory patterns could be captured by deep learning models and the prediction accuracy can be largely improved. The analyses conducted in this study demonstrated that the cell type-specific enhancer activity can be predicted by joint learning of multiple cell type data using only DNase data and the primitive sequences as the input features. This reveals the importance of cross-cell type learning, and the constructed model can be applied to investigate potential active enhancers of a novel cell type which does not have the H3K27ac modification data yet.AvailabilityThe accuEnhancer package can be freely accessed at: https://github.com/callsobing/accuEnhancer

Multiple cell-type-specific elements regulate Myc protein stability

Oncogene ◽  
2004 ◽  
Vol 23 (21) ◽  
pp. 3863-3871 ◽  
Author(s):  
Andreas Herbst ◽  
Simone E Salghetti ◽  
So Young Kim ◽  
William P Tansey
Keyword(s):  
Protein Stability ◽  
Cell Type ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Multiple Cell Type

Rabbit surfactant protein B gene: structure and functional characterization of the promoter

1996 ◽  
Vol 270 (4) ◽  
pp. L601-L612 ◽  
Author(s):  
R. K. Margana ◽  
V. Boggaram
Keyword(s):  
Functional Characterization ◽  
Surfactant Protein ◽  
Proximal Promoter ◽  
Sequence Motifs ◽  
Cell Type ◽  
High Level Expression ◽  
Surfactant Protein B ◽  
Cell Type Specific ◽  
High Level ◽  
Protein B

Surfactant protein B (SP-B) is essential for physiological function of pulmonary surfactant. In the present investigation, we isolated rabbit SP-B gene and determined its nucleotide sequence, transcription start site, and exon/intron organization. The coding region of rabbit SP-B gene is comprised of 6.8 kb of sequence and is organized into 10 introns and 11 exons. By deletion analysis we determined that a region of SP-B gene extending from -236 to +39 nucleotides is sufficient for high-level expression of CAT reporter gene in a cell type-specific manner in the pulmonary adenocarcinoma cell line NCI-H441. Deletion of 5'-flanking sequence to -140 and -71 nucleotides significantly reduced SP-B promoter activity, suggesting that the -236 to +39 region contains cis-DNA elements required for cell type-specific expression. The proximal promoter region of SP-B gene contained DNA sequence motifs for binding thyroid transcription factor 1 (TTF-1) (-113 to -97) and hepatocyte nuclear factor 3(HNF-3) (-91 to -81). Although SP-B gene sequence -140 to +39 did not support high level expression of CAT gene in NCI-H441 cells, it was capable of activation by TTF-1 in HeLa cells, suggesting that the -236 to -140 sequence plays an important role in cell type-specific activation of SP-B promoter.

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