Direct and high-yield chromatin isolation by SBCP unlocks superior plant proteomics and epigenomic profiling.

key messageNovel SBCP chromatin precipitation bypasses nuclear isolation to recover abundant intact chromatinproteins and enhance ChIP performance in diverse plants. Chromatin isolation remains a major technical bottleneck in plant molecular biology, often compromising studies on genome regulation. We present SBCP (Saline-Based Chromatin Precipitation), a method that directly isolates native chromatin by exploiting its differential solubility in salt solutions, thereby eliminating the need for prior nuclear purification. Compared with the traditional workflow that relies on nuclear isolation, SBCP achieves substantially higher yields (3.4-fold in poplar, 2.4-fold in Arabidopsis) and superior genomic DNA purity, while reducing chloroplast contamination by 63-73%. It efficiently enriches genuine chromatin-associated proteins, identifying 1477 such proteins in poplar-markedly more than the 967 nuclear proteins recovered by the traditional nuclear isolation workflow. Under identical sample input and reaction conditions, it also boosts general immunoprecipitation efficiency enabling robust co-immunoprecipitation assays. ChIP-seq analyses of histone modifications (H3K4me3, H3K27me3, H3K9me2) confirm that SBCP better preserves native chromatin structure, yielding higher signal-to-noise ratios, more sensitive peak detection, and broad cross-species applicability. Importantly, SBCP markedly improves chromatin immunoprecipitation (ChIP) efficiency by 5.2-fold in birch, 4.3-fold in poplar, and 3.3-fold in Arabidopsis using equivalent starting material. By integrating high efficiency, superior purity, and robustness into a streamlined workflow, SBCP provides a powerful and versatile platform for advanced research in epigenetics, transcriptional regulation, and protein-DNA interactions.