scholarly journals Predictive modelling of gene expression from transcriptional regulatory elements

2014 ◽  
Vol 16 (4) ◽  
pp. 616-628 ◽  
Author(s):  
David M. Budden ◽  
Daniel G. Hurley ◽  
Edmund J. Crampin
Keyword(s):  
Gene Expression ◽  
Predictive Modelling ◽  
Regulatory Elements ◽  
Transcriptional Regulatory Elements ◽  
Transcriptional Regulatory

scholarly journals A Unified Architecture of Transcriptional Regulatory Elements

2015 ◽  
Author(s):  
Robin Andersson ◽  
Albin Sandelin ◽  
Charles G Danko
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Transcription Initiation ◽  
Regulatory Elements ◽  
Functional Element ◽  
Gene Promoters ◽  
Single Class ◽  
Transcriptional Regulatory Elements ◽  
Transcriptional Regulatory ◽  
Transcriptional Output

Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential of enhancing transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements, and surrounding sequences, determine local transcriptional output as well as the enhancer and promoter activities of individual elements.

Identification of transcriptional elements within the long terminal repeat of Rous sarcoma virus

1983 ◽  
Vol 3 (10) ◽  
pp. 1834-1845
Author(s):  
G M Gilmartin ◽  
J T Parsons
Keyword(s):  
Long Terminal Repeat ◽  
Virus Replication ◽  
Rous Sarcoma Virus ◽  
Regulatory Elements ◽  
Terminal Repeat ◽  
Tata Box ◽  
Transcriptional Regulatory Elements ◽  
Rous Sarcoma ◽  
Transcriptional Regulatory ◽  
Sarcoma Virus

Transcriptional regulatory elements within the Rous sarcoma virus long terminal repeat were examined by the construction of a series of deletions and small insertions within the U3 region of the long terminal repeat. The analysis of these mutations in chicken embryo cells and COS cells permitted the identification of important transcriptional regulatory elements. Sequences within the region 31 to 18 base pairs upstream of the RNA cap site (-31 to -18), encompassing a TATA box-like sequence, function in the selection of the correct site of transcription initiation and, in addition, augment the efficiency of transcription. These sequences are essential for virus replication. Sequences within the region -79 to -59, overlapping a CAAT box-like sequence, are not required for virus replication and have no obvious effect on viral RNA transcription in the presence of an intact TATA box. However, in mutants lacking a functional TATA sequence, mutations in this region serve to decrease the efficiency of correct transcriptional initiation events.

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