title: Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification.
abstract: The ability to map endogenous transcription factors (TFs) DNA binding activity at the proteome scale will greatly enhance our understanding of various biological processes. Here we report a highly sensitive, rapid, and high-throughput approach, transcription factor response elements on tip-mass spectrometry (TOT-MS), that allows for quantitative measurement of endogenous TFs. A total of 150 TFs from 1 μg of nuclear extracts can be quantified with single shot mass spectrometry detection in 1 h of machine time. Up to 755 TFs, which is comparable to the depth of RNA-seq, were identified by TOT coupled with on-tip small size reverse-phase liquid chromatography. We further demonstrated the capability of TOT-MS by interrogating the dynamic change of TFs in the epidermal growth factor (EGF) signaling pathway. This approach should find broad applications in elucidating the TF landscape from limited amounts of biological materials.
authors.affiliation: School of Life Sciences, Tsinghua University , Beijing 100084, China.|State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Wenhao
authors.initials: W
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.|Department of Pathogeny Biology, School of Basic Medical Sciences, North China University of Science and Technology , Tangshan 063009, Hebei, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Li
authors.affiliation: School of Life Sciences, Tsinghua University , Beijing 100084, China.|State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Song
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Mingwei
authors.initials: M
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China.
authors.forename: Yunzhi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Wanlin
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China.
authors.forename: Zhaoyu
authors.initials: Z
authors.lastname: Qin
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.
authors.forename: Bei
authors.initials: B
authors.lastname: Zhen
authors.affiliation: Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine , Houston, Texas 77030, United States.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Tsinghua University , Beijing 100084, China.|State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.|State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China.
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.|State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China.|Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine , Houston, Texas 77030, United States.
authors.forename: Jun
authors.initials: J
authors.lastname: Qin
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China.|State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Ding
mesh_terms: D002467:Cell Nucleus / Q000378:metabolism; D056148:Chromatography, Reverse-Phase; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D020218:Response Elements / Q000235:genetics*; D014157:Transcription Factors / Q000032:analysis* / Q000378:metabolism
chemical_list: D014157:Transcription Factors