scholarly journals Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

2007 ◽  
Vol 17 (6) ◽  
pp. 898-909 ◽  
Author(s):  
G. M. Euskirchen ◽  
J. S. Rozowsky ◽  
C.-L. Wei ◽  
W. H. Lee ◽  
Z. D. Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Mammalian Cells ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Binding Regions

scholarly journals Discovering a less-is-more effect to select transcription factor binding sites informative for motif inference

2020 ◽  
Author(s):  
Jinrui Xu ◽  
Jiahao Gao ◽  
Mark Gerstein
Keyword(s):  
Transcription Factor ◽  
Statistical Methods ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Less Is More ◽  
Factor Binding ◽  
Strong Binding ◽  
Binding Regions

ABSTRACTMany statistical methods have been developed to infer the binding motifs of a transcription factor (TF) from a subset of its numerous binding regions in the genome. We refer to such regions, e.g. detected by ChIP-seq, as binding sites. The sites with strong binding signals are selected for motif inference. However, binding signals do not necessarily indicate the existence of target motifs. Moreover, even strong binding signals can be spurious due to experimental artifacts. Here, we observe that such uninformative sites without target motifs tend to be “crowded” -- i.e. have many other TF binding sites present nearby. In addition, we find that even if a crowded site contains recognizable target motifs, it can still be uninformative for motif inference due to the presence of interfering motifs from other TFs. We propose using less crowded and shorter binding sites in motif interference and develop specific recommendations for carrying this out. We find our recommendations substantially improve the resulting motifs in various contexts by 30%-70%, implying a “less-is-more” effect.

scholarly journals Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

2013 ◽  
Vol 10 (5) ◽  
pp. 421-426 ◽  
Author(s):  
J Christof M Gebhardt ◽  
David M Suter ◽  
Rahul Roy ◽  
Ziqing W Zhao ◽  
Alec R Chapman ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Transcription Factor Binding ◽  
Single Molecule Imaging ◽  
Factor Binding

scholarly journals miR-2478 inhibits TGFβ1 expression by targeting the transcriptional activation region downstream of the TGFβ1 promoter in dairy goats

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Zhuanjian Li ◽  
Xianyong Lan ◽  
Ruili Han ◽  
Jing Wang ◽  
Yongzhen Huang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Mammary Gland ◽  
Mammary Gland Development ◽  
Target Genes ◽  
Transcription Factor Binding ◽  
Luciferase Reporter ◽  
Dairy Goats ◽  
Factor Binding ◽  
Binding Regions ◽  
Gland Development

Abstract In a previous study, miR-2478 was demonstrated to be up-regulated in dairy goat mammary glands during peak lactation compared with the dry period. However, the detailed mechanisms by which miR-2478 regulates physiological lactation and mammary gland development in dairy goats remain unclear. In this study, we used bioinformatics analysis and homologous cloning to predict the target genes of miR-2478 and selected INSR, FBXO11, TGFβ1 and ING4 as candidate target genes of miR-2478. Subsequently, by targeting the 5′UTR of the TGFβ1 gene, we verified that miR-2478 significantly inhibited TGFβ1 transcription and the Pearson’s correlation coefficient between miR-2478 expression and TGFβ1 expression was −0.98. Furthermore, we identified the potential promoter and transcription factor binding regions of TGFβ1 and analyzed the potential mechanisms of interaction between miR-2478 and TGFβ1. Dual-luciferase reporter assays revealed that two regions, spanning from −904 to −690 bp and from −79 to +197 bp, were transcription factor binding regions of TGFβ1. Interesting, the miR-2478 binding sequence was determined to span from +123 to +142 bp in the TGFβ1 gene promoter. Thus, our results have demonstrated that miR-2478 binds to the core region of the TGFβ1 promoter and that it affects goat mammary gland development by inhibiting TGFβ1 transcription.

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