Methods and kits for isolation and analysis of a chromatin region

1. 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 by contacting the target chromatin with a tag capable of specifically recognizing and binding one or more portions of the target chromatin and wherein the tag comprises an affinity handle, and

ii) a second cell sample comprising nucleic acid binding proteins and the target chromatin, where in the target chromatin is not tagged,

wherein the first cell sample and the second cell sample are lysed;

(b) performing affinity purification on each lysed cell sample in (a) using a substrate capable of binding the affinity handle, wherein affinity purification of the first cell sample results in isolation of affinity handle bound to tagged target chromatin bound to nucleic acid binding proteins and affinity purification of the second cell sample results in isolation of nucleic acid binding proteins non-specifically bound to the substrate, wherein isolating the affinity handle isolates proteins associated with the tagged target chromatin,

(c) identifying bound proteins from (b),

(d) determining the amount of each bound protein in each sample from (b), wherein bound proteins that are enriched in the first cell sample as compared to the second cell sample are specifically associated with the tagged chromatin in the first cell sample.

2. The method of claim 1 , wherein the first cell sample is lysed before tagging the target chromatin.

3. The method of claim 1 , wherein the first cell sample is lysed after tagging the target chromatin.

4. The method of claim 3 , wherein a target chromatin is tagged by expressing in a cell protein A tagged TAL protein engineered to have binding specificity for a nucleic acid sequence component of the target chromatin.

5. The method of claim 1 , wherein the proteins in the first cell sample and the second cell sample are crosslinked before lysis.

6. The method of claim 1 , wherein the chromatin in the lysed cell sample from step (a) is fragmented before isolating the tagged target nucleic acid sequence.

7. The method of claim 6 , wherein the chromatin in the lysed cell sample is fragmented to comprise nucleic acid sections comprising 500 to 1500 base pairs.

8. The method of claim 1 , wherein proteins or protein fragments associated with the target chromatin are identified using mass spectrometry.

9. The method of claim 8 , wherein the proteins or protein fragments identified using mass spectrometry are quantified and identified as enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin using label-free proteomics.

10. The method of claim 9 , wherein the label-free proteomics technique is spectral counting.

11. The method of claim 9 , wherein proteins enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin are enriched by at least 2 fold.