TY - JOUR
T1 - Controlling gene activation by enhancers through a drug-inducible topological insulator
AU - Tsujimura, Taro
AU - Takase, Osamu
AU - Yoshikawa, Masahiro
AU - Sano, Etsuko
AU - Hayashi, Matsuhiko
AU - Hoshi, Kazuto
AU - Takato, Tsuyoshi
AU - Toyoda, Atsushi
AU - Okano, Hideyuki
AU - Hishikawa, Keiichi
N1 - Funding Information:
We thank Prof. Shinya Yamanaka (Kyoto University) for providing us the hiPSC line. We would also like to thank Drs. Sumihiro Maeda, Kent Imaizumi, Tsukasa Sanosaka, and Tomohiko Akiyama for their scientific advice and generous supports in revising the manuscript.
PY - 2020/5
Y1 - 2020/5
N2 - While regulation of gene-enhancer interaction is intensively studied, its application remains limited. Here, we reconstituted arrays of CTCF-binding sites and devised a synthetic topological insulator with tetO for chromatin-engineering (STITCH). By coupling STITCH with tetR linked to the KRAB domain to induce heterochromatin and disable the insulation, we developed a drug-inducible system to control gene activation by enhancers. In human induced pluripotent stem cells, STITCH inserted between MYC and the enhancer down-regulated MYC. Progressive mutagenesis of STITCH led to a preferential escalation of the gene-enhancer interaction, corroborating the strong insulation ability of STITCH. STITCH also altered epigenetic states around MYC. Time-course analysis by drug induction uncovered deposition and removal of H3K27me3 repressive marks follows and reflects, but does not precede and determine, the expression change. Finally, STITCH inserted near NEUROG2 impaired the gene activation in differentiating neural progenitor cells. Thus, STITCH should be broadly useful for functional genetic studies.
AB - While regulation of gene-enhancer interaction is intensively studied, its application remains limited. Here, we reconstituted arrays of CTCF-binding sites and devised a synthetic topological insulator with tetO for chromatin-engineering (STITCH). By coupling STITCH with tetR linked to the KRAB domain to induce heterochromatin and disable the insulation, we developed a drug-inducible system to control gene activation by enhancers. In human induced pluripotent stem cells, STITCH inserted between MYC and the enhancer down-regulated MYC. Progressive mutagenesis of STITCH led to a preferential escalation of the gene-enhancer interaction, corroborating the strong insulation ability of STITCH. STITCH also altered epigenetic states around MYC. Time-course analysis by drug induction uncovered deposition and removal of H3K27me3 repressive marks follows and reflects, but does not precede and determine, the expression change. Finally, STITCH inserted near NEUROG2 impaired the gene activation in differentiating neural progenitor cells. Thus, STITCH should be broadly useful for functional genetic studies.
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U2 - 10.7554/eLife.47980
DO - 10.7554/eLife.47980
M3 - Article
C2 - 32369019
AN - SCOPUS:85084271623
VL - 9
SP - 1
EP - 37
JO - eLife
JF - eLife
SN - 2050-084X
M1 - e47980
ER -