BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes.
Zhe WengFengying RuanWeitian ChenZhichao ChenYeming XieMeng LuoZhe XieChen ZhangJuan WangYuxin SunYitong FangMei GuoChen TanWenfang ChenYiqin TongYaning LiHongqi WangChong TangPublished in: Genome biology (2023)
Epigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin state. Here we describe BIND&MODIFY, a method using long-read sequencing for profiling histone modifications and transcription factors on individual DNA fibers. We use recombinant fused protein A-M.EcoGII to tether methyltransferase M.EcoGII to protein binding sites to label neighboring regions by methylation. Aggregated BIND&MODIFY signal matches bulk ChIP-seq and CUT&TAG. BIND&MODIFY can simultaneously measure histone modification status, transcription factor binding, and CpG 5mC methylation at single-molecule resolution and also quantifies correlation between local and distal elements.
Keyphrases
- single molecule
- transcription factor
- dna methylation
- genome wide
- gene expression
- dna binding
- single cell
- atomic force microscopy
- living cells
- protein protein
- binding protein
- dna damage
- high throughput
- rna seq
- small molecule
- high resolution
- high density
- circulating tumor cells
- cell free
- oxidative stress
- mass spectrometry
- circulating tumor