US 11,885,814 B2
High efficiency targeted in situ genome-wide profiling
Steven Henikoff, Seattle, WA (US); Hatice Seda Kaya Okur, Redmond, WA (US); Terri Dawn Bryson, Lynnwood, WA (US); and Peter James Skene, Issaquah, WA (US)
Assigned to Fred Hutchinson Cancer Center, Seattle, WA (US)
Filed by Fred Hutchinson Cancer Research Center, Seattle, WA (US)
Filed on Jan. 26, 2022, as Appl. No. 17/585,465.
Application 17/585,465 is a continuation of application No. 16/650,179, granted, now 11,733,248, previously published as PCT/US2018/052707, filed on Sep. 25, 2018.
Claims priority of provisional application 62/562,918, filed on Sep. 25, 2017.
Prior Publication US 2022/0228203 A1, Jul. 21, 2022
Int. Cl. G01N 33/68 (2006.01); C12Q 1/6804 (2018.01); C12N 15/10 (2006.01); C12Q 1/6841 (2018.01)
CPC G01N 33/6872 (2013.01) [C12N 15/1065 (2013.01); C12Q 1/6804 (2013.01); C12Q 1/6841 (2013.01); C12Q 2522/10 (2013.01)] 32 Claims
 
1. A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell or nucleus, comprising:
contacting a permeabilized cell or nucleus immobilized on a solid surface with a first specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the first specific binding agent is coupled to a nuclease in an inactive state;
activating the nuclease and cleaving DNA bound to the chromatin-associated factor of interest to thereby excise the DNA bound to the chromatin-associated factor of interest and release it to a supernatant;
isolating the excised DNA in the supernatant; and
determining the sequence of the excised DNA, thereby mapping binding of a chromatin-associated factor of interest to a sequence of DNA in the cell or nucleus.