US 2017O 130247A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0130247 A1 DOWen et al. (43) Pub. Date: May 11, 2017 (54) COMPOSITIONS AND METHODS FOR Related U.S. Application Data ALTERING GENE EXPRESSION (60) Provisional application No. 62/234.770, filed on Sep. (71) Applicant: Whitehead Institute for Biomedical 30, 2015. Research, Cambridge, MA (US) Publication Classification (72) Inventors: Jill M. Dowen, Chapel Hill, NC (US); (51) Int. C. Zi Peng Fan, Waltham, MA (US); CI2N 15/90 (2006.01) Denes Hnisz. Cambridge, MA (US); (52) U.S. C. Tong Ihn Lee, Somerville, MA (US); CPC ........ CI2N 15/907 (2013.01); C12N 2800/80 Richard A. Young, Boston, MA (US) (2013.01) (21) Appl. No.: 15/282,905 (57) ABSTRACT Provided herein are improved compositions and methods for (22) Filed: Sep. 30, 2016 the directed control of gene expression. Patent Application Publication May 11, 2017. 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Sheet 42 of 43 US 2017/0130247 A1 Figtre i (Figare S5) ::::::::::::::::::y 8$88:a::g .3388: $3::::::::: 33;x:::::::::::::: *$88:::::::::::::38:8 ::::::::::::8& Patent Application Publication & $$$84 US 2017/O 130247 A1 May 11, 2017 COMPOSITIONS AND METHODS FOR 2012: Filippova et al., 2014; Gibcus and Dekker, 2013; ALTERING GENE EXPRESSION Naumova et al., 2013: Nora et al., 2012). 0009 TADs, also known as topological domains, are CROSS-REFERENCE TO RELATED defined by DNA-DNA interaction frequencies, and their APPLICATION(S) boundaries are regions across which relatively few DNA DNA interactions occur (Dixon et al., 2012: Nora et al., 0001. This application claims the benefit of U.S. Provi 2012). TADs average 0.8 Mb, contain approximately seven sional Application No. 62/234,770, filed Sep. 30, 2015. The protein-coding genes, and have boundaries that are shared entire teachings of the above application is incorporated by the different cell types of an organism (Dixon et al., 2012: herein by reference. Smallwood and Ren, 2013). The expression of genes within aTAD is somewhat correlated, and thus some TADs tend to GOVERNMENT SUPPORT have active genes and others tend to have repressed genes 0002 This invention was made with government support (Cavalli and Misteli, 2013; Gibcus and Dekker, 2013: Nora under Grant Number HG002668 awarded by the National et al., 2012). Institutes of Health. The government has certain rights in the 0010 Gene loops and other structures within TADs are invention. thought to reflect the activities of transcription factors (TFs), cohesin, and CTCF (Baranello et al., 2014: Gorkin et al., FIELD OF THE INVENTION 2014; Phillips-Cremins et al., 2013: Seitan et al., 2013; Zuin et al., 2014). The structures within TADs include cohesin 0003. The present invention generally relates to methods associated enhancer-promoter loops that are produced when of selectively altering gene expression within, for example, enhancer-bound TFs bind cofactors such as Mediator that, in insulated neighborhoods formed by the looping of two turn, bind RNA polymerase II at promoter sites (Lee and CTCF interaction sites occupied by cohesion.