BACKGROUND: Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated. RESULTS: In this paper, we have developed a computational method to generate a genome-wide landscape of TFs and their characteristic binding DNA structures in Saccharomyces cerevisiae. We revealed DNA structural features for different TFs. The structural conservation shows positional preference in TFBSs. Structural levels of DNA sequences are correlated with TF-DNA binding affinities. CONCLUSIONS: We provided the genome-wide correspondences of TFs to DNA structures. Our findings will have implications in understanding TF regulatory mechanisms.
BACKGROUND: Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated. RESULTS: In this paper, we have developed a computational method to generate a genome-wide landscape of TFs and their characteristic binding DNA structures in Saccharomyces cerevisiae. We revealed DNA structural features for different TFs. The structural conservation shows positional preference in TFBSs. Structural levels of DNA sequences are correlated with TF-DNA binding affinities. CONCLUSIONS: We provided the genome-wide correspondences of TFs to DNA structures. Our findings will have implications in understanding TF regulatory mechanisms.
Authors: Stephen C J Parker; Loren Hansen; Hatice Ozel Abaan; Thomas D Tullius; Elliott H Margulies Journal: Science Date: 2009-03-12 Impact factor: 47.728
Authors: Gwenael Badis; Esther T Chan; Harm van Bakel; Lourdes Pena-Castillo; Desiree Tillo; Kyle Tsui; Clayton D Carlson; Andrea J Gossett; Michael J Hasinoff; Christopher L Warren; Marinella Gebbia; Shaheynoor Talukder; Ally Yang; Sanie Mnaimneh; Dimitri Terterov; David Coburn; Ai Li Yeo; Zhen Xuan Yeo; Neil D Clarke; Jason D Lieb; Aseem Z Ansari; Corey Nislow; Timothy R Hughes Journal: Mol Cell Date: 2008-12-26 Impact factor: 17.970
Authors: Cong Guo; Ian C McDowell; Michael Nodzenski; Denise M Scholtens; Andrew S Allen; William L Lowe; Timothy E Reddy Journal: BMC Genomics Date: 2017-05-19 Impact factor: 3.969