Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology.
Shuai ZhaoMo YangWenfei ZhouBaichao ZhangZhi-Qiang ChengJiaxin HuangMin ZhangZhiyou WangRui WangZhonglei ChenJinsong ZhuHaitao LiPublished in: Proceedings of the National Academy of Sciences of the United States of America (2017)
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 chip-based 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.
Keyphrases
- high throughput
- single cell
- circulating tumor
- high resolution
- dna methylation
- nucleic acid
- dna damage
- cell free
- single molecule
- circulating tumor cells
- gene expression
- protein protein
- binding protein
- oxidative stress
- amino acid
- molecular dynamics
- dna binding
- molecular dynamics simulations
- mass spectrometry
- magnetic nanoparticles