Year: 2017
Type: article
Abstract: // Yue Wang 1, 2 , Matthew H. Ung 2 , Tian Xia 1 , Wenqing Cheng 1 and Chao Cheng 2, 3, 4 1 School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China 2 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA 3 Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA 4 Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA Correspondence to: Wenqing Cheng, email: [email protected] Chao Cheng, email: [email protected] Keywords: transcription factor, ChIP-seq, FOXM1 reprogramming, genomic binding, breast cancer prognosis Received: April 12, 2017 Accepted: August 14, 2017 Published: August 24, 2017 ABSTRACT ChIP-seq has been commonly applied to identify genomic occupation of transcription factors (TFs) in a context-specific manner. It is generally assumed that a TF should have similar binding patterns in cells from the same or closely related tissues. Surprisingly, this assumption has not been carefully examined. To this end, we systematically compared the genomic binding of the cell cycle regulator FOXM1 in eight cell lines from seven different human tissues at binding signal, peaks and target genes levels. We found that FOXM1 binding in ER-positive breast cancer cell line MCF-7 are distinct comparing to those in not only other non-breast cell lines, but also MDA-MB-231, ER-negative breast cancer cell line. However, binding sites in MDA-MB-231 and non-breast cell lines were highly consistent. The recruitment of estrogen receptor alpha (ERα) caused the unique FOXM1 binding patterns in MCF-7. Moreover, the activity of FOXM1 in MCF-7 reflects the regulatory functions of ERα, while in MDA-MB-231 and non-breast cell lines, FOXM1 activities regulate cell proliferation. Our results suggest that tissue similarity, in some specific contexts, does not hold precedence over TF-cofactors interactions in determining transcriptional states and that the genomic binding of a TF can be dramatically affected by a particular co-factor under certain conditions.
Source: Oncotarget
Authors: Yue Wang, Matthew H. Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: diamond
OpenAlex ID: W2746435640