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US 11,198,910 B2Granted
Analysis of chromatin using a nicking enzyme
AssigneeNew England Biolabs, Inc.
InventorsChaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
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Abstract
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.
Claims11
A method for analyzing open chromatin, comprising:
- (a) obtaining a sample containing permeabilized cell nuclei, wherein the cell nuclei comprise chromatin;
- (b) reacting the cell nuclei 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;
- and
- (c) analyzing the labeled nuclei of (b) for open chromatin, wherein the analyzing is done by:
- (i) detecting an optically-detectable signal in the cell nuclei, if the at least one labeled dNTP comprises an optically detectable label;
- or
- (ii) enriching for and then sequencing labeled DNA fragments that comprise the labeled nucleotide, if the labeled nucleotide comprises an affinity tag.
4 more elements
Dependencies are inferred from the claim text.