scholarly journals A perspective on the molecular simulation of DNA from structural and functional aspects

2021 ◽  
Author(s):  
Manas Mondal ◽  
Lijiang Yang ◽  
Zhicheng Cai ◽  
Piya Patra ◽  
Yi Qin Gao
Keyword(s):  
Gene Regulation ◽  
Environmental Factors ◽  
Protein Binding ◽  
Structural Organization ◽  
Atomistic Simulations ◽  
Dna Interactions ◽  
Structure And Dynamics ◽  
Functional Aspects ◽  
Protein Dna Interactions ◽  
Base Modifications

An overview of atomistic simulations on the effect of sequences, base modifications, environmental factors and protein binding on DNA’s hierarchical structure and dynamics in the context of protein–DNA interactions, gene regulation and structural organization of chromatin.

scholarly journals Co-expression signatures of combinatorial gene regulation

2020 ◽  
Author(s):  
Fabio Gomez-Cano ◽  
Qian Xu ◽  
Shin-Han Shiu ◽  
Arjun Krishnan ◽  
Erich Grotewold
Keyword(s):  
Gene Regulation ◽  
Regulatory Networks ◽  
Target Gene ◽  
Target Genes ◽  
Dna Interactions ◽  
Expression Studies ◽  
Gene Associations ◽  
Protein Dna Interactions ◽  
Gene Regulatory ◽  
The Impact

AbstractGene co-expression analyses provide a powerful tool to determine gene associations. The interaction of transcription factors (TFs) with their target genes is an essential step in gene regulation, yet to what extent TFs-target gene associations are recovered in co-expression studies remains unclear. Using the wealth of data available for Arabidopsis, we show here that protein-DNA interactions are overall poor indicators of TF-target co-expression, yet the inclusion of TF-TF interaction information significantly enhance co-expression signals. These results highlight the impact of combinatorial gene control on such gene association networks. We integrated this information to predict higher-order regulatory complexes, which are difficult to identify experimentally. We demonstrate that genes strongly co-expressed with a TF are also enriched in indirect targets. Our results have significant implications on the empirical understanding of complex gene regulatory networks and transcription factor function, and the significance of co-expression from the perspective of protein-protein and protein-DNA interactions.

Regulation of transcription of genes

1995 ◽  
Vol 349 (1329) ◽  
pp. 255-255
Keyword(s):  
Gene Regulation ◽  
Regulation Of Transcription ◽  
Dna Interactions ◽  
Early Stages ◽  
Genetic Switches ◽  
Protein Dna Interactions ◽  
Multiple Controls

The principles of the mechanism of gene regulation as elucidated for prokaryotes apply in outline to the eukaryotic as well. For example, the mechanisms of protein-DNA interactions are similar and in some cases highly conserved throughout evolution. It is not difficult to imagine how control elements found in prokaryotes could have been combined during evolution to render any given gene in a eukaryote subject to multiple controls. Moreover, it is now clear that the best understood case of development — that of the early stages of Drosophila - may be described as a reiteration and integration of a series of ‘genetic switches’ similar to that found in, for example, the coliphage λ.

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