Analysis of chromatin using a nicking enzyme
Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.
1. A method for detecting abnormal cells in or from a tissue section or biopsy wherein the abnormal cells have altered chromatin compared to normal cells, comprising:
(a) reacting the cells with a composition comprising a mixture of a nicking enzyme, four dNTPs, and at least one labeled dNTP, and a polymerase to selectively label the chromatin;
(b) incorporating the labeled dNTP into the chromatin of the cells to form labelled nucleic acid; and
(c) analyzing the pattern of labelled nucleic acid in the cells.
2. The method according to claim 1 , wherein (c) further comprises determining whether the pattern of labelled nucleic acid corresponds to a cancer diagnosis of the cells or tissues.
3. The method according to claim 1 , wherein prior to (a), making the cells permeable.
4. The method according to claim 1 , wherein the tissue section or biopsy is fixed.
5. The method according to claim 3 , wherein the tissue section or biopsy is fixed.
6. The method according to claim 1 , wherein after (b) reverse cross linking and isolating DNA from the cells.
7. The method according to claim 1 , wherein following (b), labelling nuclei from the cells with a primary antibody.
8. The method according to claim 7 , wherein after labelling with a primary antibody, labelling with a secondary antibody.
9. The method according to claim 7 , further comprising: visualizing the labelled nuclei using a fluorescent microscope.