scholarly journals In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yaping Fang ◽  
Yunlong Wang ◽  
Qin Zhu ◽  
Jia Wang ◽  
Guoliang Li
Keyword(s):  
Transcription Factor ◽  
In Silico ◽  
Transcription Factor Binding ◽  
Binding Motif ◽  
Transcription Factor Binding Motif ◽  
Factor Binding ◽  
In Silico Identification

scholarly journals Rational gRNA Design Based on Transcription Factor Binding Data

2021 ◽  
Author(s):  
David Bergenholm ◽  
Yasaman Dabirian ◽  
Raphael Ferreira ◽  
Verena Siewers ◽  
Florian David ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Genome Engineering ◽  
Transcription Factor Binding ◽  
Central Carbon Metabolism ◽  
Binding Motif ◽  
Transcription Factor Binding Motif ◽  
Factor Binding ◽  
Transcription Factor Motif ◽  
Binding Data ◽  
Genes Encoding

Abstract The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has become a standard tool in many genome engineering endeavors. The endonuclease-deficient version of Cas9 (dCas9) is also a powerful programmable tool for gene regulation. In this study, we made use of Saccharomyces cerevisiae transcription factor binding data to obtain a better understanding of the interplay between transcription factor binding and binding of dCas9 fused to an activator domain, VPR. More specifically, we targeted dCas9-VPR towards binding sites of Gcr1-Gcr2 and Tye7 present in several promoters of genes encoding enzymes engaged in the central carbon metabolism. From our data, we observed an upregulation of gene expression when dCas9-VPR was targeted next to a transcription factor binding motif, whereas downregulation or no change was observed when dCas9 was bound on a transcription factor motif. This suggests a steric competition between dCas9 and the specific transcription factor. Integrating transcription factor binding data, therefore, proved to be useful for designing gRNAs for CRISPRi/a applications.

scholarly journals RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

2017 ◽  
Vol 45 (13) ◽  
pp. e119-e119 ◽  
Author(s):  
Jaime Abraham Castro-Mondragon ◽  
Sébastien Jaeger ◽  
Denis Thieffry ◽  
Morgane Thomas-Chollier ◽  
Jacques van Helden
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Motif ◽  
Transcription Factor Binding Motif ◽  
Factor Binding ◽  
Redundancy Reduction

scholarly journals Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Giovanna Ambrosini ◽  
Ilya Vorontsov ◽  
Dmitry Penzar ◽  
Romain Groux ◽  
Oriol Fornes ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Motif ◽  
Transcription Factor Binding Motif ◽  
Factor Binding

In-silico Evidences of Regulatory Roles of WT1 Transcription Factor Binding Sites on the Intervening Sequences of the Human Bcl-2 Gene

2018 ◽  
Vol 13 (3) ◽  
pp. 260-272
Author(s):  
Gholampour-Faroji Nazanin ◽  
Haddad-Mashadrizeh Aliakbar ◽  
Mirahmadi Mahdi ◽  
Monhemi Hassan ◽  
Shahreki-Mojahed Safoora ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
In Silico ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Intervening Sequences
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