Patent SG-11201807444P-A (SG)
Title: Transposase-mediated imaging of the accessible genome
Inventor: CHANG HOWARD Y
IPC: C12Q1/68
Filed: 2017-03-09
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property -, Organization 11111111011110111010101111101011111011101111101101110110011101111101111011111 International Bureau ... .1 j ..... .....!;,,, (10) International Publication Number (43) International Publication Date WO 2017/156336 Al 14 September 2017 (14.09.2017) WIP0 I PCT (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 9/22 (2006.01) Cl 2N 15/87 (2006.01) kind of national protection available): AE, AG, AL, AM, C12N 15/11 (2006.01) C12Q 1/68 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, (21) International Application Number: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US2017/021677 HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, (22) International Filing Date: KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, 9 March 2017 (09.03.2017) MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, (25) Filing Language: English RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, (26) Publication Language: English TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 62/306,504 10 March 2016 (10.03.2016) US (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant: THE BOARD OF TRUSTEES OF THE LE- GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, LAND STANFORD JUNIOR UNIVERSITY [US/US]; TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, Office of the General Counsel, Building 170, 3rd Floor, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Main Quad, P.O. Box 20386, Stanford, California 94305- DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 2038 (US). LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (72) Inventors: CHANG, Howard Y.; 269 Campus Drive, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Mail Code: 5334, Palo Alto, California 94305 (US). GW, KM, ML, MR, NE, SN, TD, TG). GREENLEAF, William J.; 279 Campus Drive West, Declarations under Rule 4.17: Room 257A, Stanford, California 94305 (US). CHEN, — of inventorship (Rule 4.17(N)) Xingqi; 269 Campus Drive, Mail Code: 5168, Palo Alto, California 94305 (US). BUENROSTRO, Jason; 3523 Published: Altamont Way, Redwood City, California 94062 (US). — with international search report (Art. 21(3)) (74) Agent: KEDDIE, James S.; 201 Redwood Shores Park- with sequence listing part of description (Rule 5.2(a)) way, Suite 200, Redwood City, California 94065 (US). (54) Title: TRANSPOSASE-MEDIATED Closed Chromatin lill) il I 4° (i 1.0 IMAGING ' ' I l la ) 410-.. OF w li 64 4, THE ACCESSIBLE GENOME I Image I Amplify & g e ,Z'- 4 , ) Sequence ,' g • II A 0 1 oft -,.. I ' ' b , fr 1-1 ,Av(p er • % tp 1 Open M Chromatin en FIG. 1 a 11 in ,—, ----. (57) : Methods for labeling and imaging the accessible genome using a transposase are disclosed. In some embodiments, a IN bifunctional transposase complex or transposome is used to insert adaptors comprising chemical tags selectively at accessible sites in C the genome where active regulatory DNA is located. Various chemical tags can be used for labeling DNA at insertion sites, includ - el ing, for example, fluorescent dyes for fluorescence imaging, metal particles for electron microscopy or magnetic manipulation of O DNA, isotopic labels, or biotin or other ligands, haptens, substrates, or inhibitors that are recognized by streptavidin, antibodies, en - ,..1: zymes, or receptors. Labeling DNA in this manner can be used to provide spatial information regarding the positioning of regulatory DNA in the genome and makes possible the imaging and sorting of cells based on the status of their regulatory DNA.