Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 114, Issue 35, Pages E7245-E7254Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1704155114
Keywords
SPR imaging; epigenetic interactions; histone modifications; nucleic acid modifications; 3D-carbene chip
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Funding
- Ministry of Science and Technology of China [2016YFA0500700, 2015CB910503]
- National Natural Science Foundation of China [31470720]
- Tsinghua University Initiative Scientific Research Program
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Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate reader proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chipbased surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone reader-mark pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant.
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