Methods and kits for isolation and analysis of a chromatin region

A method of identifying proteins including proteins comprising posttranslational modifications specifically associated with a target chromatin in a cell, the method comprising:

• (a) providing:
• i) a first cell sample comprising nucleic acid binding proteins and the target chromatin, wherein the target chromatin is tagged, and
• ii) a second cell sample comprising nucleic acid binding proteins and the target chromatin, wherein the target chromatin is not tagged,
• wherein the proteins in the first cell sample or the second cell sample are metabolically labeled,
• (b) mixing the first cell sample and the second cell sample from (a) with an affinity handle to generate a cell mixture wherein the affinity handle binds protein such that the affinity handle specifically binds the tagged target chromatin and non-specifically binds nucleic acid binding proteins,
• (c) isolating the affinity handle form the mixture in (b) wherein the affinity handle isolated consists of affinity handle bound to tagged target chromatin and affinity handle bound to nucleic acid binding proteins, wherein isolating the affinity handle isolates proteins associated with the tagged target chromatin,
• (d) identifying isolated proteins from (c),
• (e) determining whether each protein from (c) is metabolically labeled, unlabeled, or a mixture of labeled and unlabeled protein, wherein
• i) if the first cell sample from (a) is not metabolically labeled and a protein associated with the target chromatin is not metabolically labeled, then the protein is specifically associated with the tagged chromatin in the cell, and
• ii) if the first sample from (a) is metabolically labeled and a protein associated with the target chromatin is metabolically labeled, then the protein is specifically associated with the tagged chromatin in the cell.