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PROBER identifies proteins associated with programmable sequence-specific DNA in living cells.
Mondal, Smarajit; Ramanathan, Muthukumar; Miao, Weili; Meyers, Robin M; Rao, Deepti; Lopez-Pajares, Vanessa; Siprashvili, Zurab; Reynolds, David L; Porter, Douglas F; Ferguson, Ian; Neela, Poornima; Zhao, Yang; Meservey, Lindsey M; Guo, Margaret; Yang, Yen-Yu; Li, Lin; Wang, Yinsheng; Khavari, Paul A.
Afiliación
  • Mondal S; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Ramanathan M; Department of Pathology, Stanford University, Stanford, CA, USA.
  • Miao W; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Meyers RM; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Rao D; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Lopez-Pajares V; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Siprashvili Z; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Reynolds DL; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Porter DF; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Ferguson I; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Neela P; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Zhao Y; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Meservey LM; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Guo M; Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
  • Yang YY; Program in Biomedical Informatics, Stanford University, Stanford, CA, USA.
  • Li L; Department of Chemistry, University of California, Riverside, CA, USA.
  • Wang Y; Department of Chemistry, University of California, Riverside, CA, USA.
  • Khavari PA; Department of Chemistry, University of California, Riverside, CA, USA.
Nat Methods ; 19(8): 959-968, 2022 08.
Article en En | MEDLINE | ID: mdl-35927480
ABSTRACT
DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) in the identification and quantification of proteins associated with specific DNA sequences in living cells, we developed proximal biotinylation by episomal recruitment (PROBER). PROBER uses high-copy episomes to amplify SNR, and proximity proteomics (BioID) to identify the transcription factors and additional gene regulators associated with short DNA sequences of interest. PROBER quantified both constitutive and inducible association of transcription factors and corresponding chromatin regulators to target DNA sequences and binding quantitative trait loci due to single-nucleotide variants. PROBER identified alterations in regulator associations due to cancer hotspot mutations in the hTERT promoter, indicating that these mutations increase promoter association with specific gene activators. PROBER provides an approach to rapidly identify proteins associated with specific DNA sequences and their variants in living cells.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: ADN / Cromatina Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: ADN / Cromatina Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos