Genome-Wide Identification of Transcription Factor-Binding Sites in Plants Using Chromatin Immunoprecipitation Followed by Microarray (ChIP-chip) or Sequencing (ChIP-seq)

2011 ◽  
pp. 173-188 ◽  
Author(s):  
Jia-Ying Zhu ◽  
Yu Sun ◽  
Zhi-Yong Wang
Keyword(s):  
Transcription Factor ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Microarray Chip ◽  
Factor Binding ◽  
Genome Wide ◽  
Chip Chip

Genome Wide Approaches to Identify Protein-DNA Interactions

2020 ◽  
Vol 26 (42) ◽  
pp. 7641-7654 ◽  
Author(s):  
Tao Ma ◽  
Zhenqing Ye ◽  
Liguo Wang
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Target Genes ◽  
Rapid Development ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Computational Approaches ◽  
Factor Binding ◽  
Genome Wide ◽  
Chip Chip

Background: Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites. Objective: This review aims to provide an overview of these three techniques including their experiment procedures, computational approaches, and popular analytic tools. Conclusion: ChIP-chip, ChIP-seq, and ChIP-exo have been the major techniques to study genome- wide in vivo protein-DNA interaction. Due to the rapid development of next-generation sequencing technology, array-based ChIP-chip is deprecated and ChIP-seq has become the most widely used technique to identify transcription factor binding sites in genome-wide. The newly developed ChIP-exo further improves the spatial resolution to single nucleotide. Numerous tools have been developed to analyze ChIP-chip, ChIP-seq and ChIP-exo data. However, different programs may employ different mechanisms or underlying algorithms thus each will inherently include its own set of statistical assumption and bias. So choosing the most appropriate analytic program for a given experiment needs careful considerations. Moreover, most programs only have command line interface so their installation and usage will require basic computation expertise in Unix/Linux.

scholarly journals Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7526 ◽  
Author(s):  
Alfredo Mendoza-Vargas ◽  
Leticia Olvera ◽  
Maricela Olvera ◽  
Ricardo Grande ◽  
Leticia Vega-Alvarado ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
E Coli ◽  
Factor Binding ◽  
Genome Wide

scholarly journals Mapping genome-wide transcription factor binding sites in frozen tissues

2013 ◽  
Vol 6 (1) ◽  
pp. 30 ◽  
Author(s):  
Daniel Savic ◽  
Jason Gertz ◽  
Preti Jain ◽  
Gregory M Cooper ◽  
Richard M Myers
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Genome Wide
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