Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency
Summary: Non-genetically modified somatic cells can only be inefficiently and stochastically reprogrammed to pluripotency by exogenous expression of reprogramming factors. Low competence of natural reprogramming factors may prevent the majority of cells to successfully and synchronously reprogram. H...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004221014966 |
| _version_ | 1819261366987390976 |
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| author | Evgeniia Borisova Ken Nishimura Yuri An Miho Takami Jingyue Li Dan Song Mami Matsuo-Takasaki Dorian Luijkx Shiho Aizawa Akihiro Kuno Eiji Sugihara Taka-aki Sato Fumiaki Yumoto Tohru Terada Koji Hisatake Yohei Hayashi |
| author_facet | Evgeniia Borisova Ken Nishimura Yuri An Miho Takami Jingyue Li Dan Song Mami Matsuo-Takasaki Dorian Luijkx Shiho Aizawa Akihiro Kuno Eiji Sugihara Taka-aki Sato Fumiaki Yumoto Tohru Terada Koji Hisatake Yohei Hayashi |
| author_sort | Evgeniia Borisova |
| collection | DOAJ |
| description | Summary: Non-genetically modified somatic cells can only be inefficiently and stochastically reprogrammed to pluripotency by exogenous expression of reprogramming factors. Low competence of natural reprogramming factors may prevent the majority of cells to successfully and synchronously reprogram. Here we screened DNA-interacting amino acid residues in the zinc-finger domain of KLF4 for enhanced reprogramming efficiency using alanine-substitution scanning methods. Identified KLF4 L507A mutant accelerated and stabilized reprogramming to pluripotency in both mouse and human somatic cells. By testing all the variants of L507 position, variants with smaller amino acid residues in the KLF4 L507 position showed higher reprogramming efficiency. L507A bound more to promoters or enhancers of pluripotency genes, such as KLF5, and drove gene expression of these genes during reprogramming. Molecular dynamics simulations predicted that L507A formed additional interactions with DNA. Our study demonstrates how modifications in amino acid residues of DNA-binding domains enable next-generation reprogramming technology with engineered reprogramming factors. |
| first_indexed | 2024-12-23T19:40:40Z |
| format | Article |
| id | doaj.art-39f12cba9f554b229646605931796070 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-23T19:40:40Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-39f12cba9f554b2296466059317960702022-12-21T17:33:40ZengElsevieriScience2589-00422022-01-01251103525Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotencyEvgeniia Borisova0Ken Nishimura1Yuri An2Miho Takami3Jingyue Li4Dan Song5Mami Matsuo-Takasaki6Dorian Luijkx7Shiho Aizawa8Akihiro Kuno9Eiji Sugihara10Taka-aki Sato11Fumiaki Yumoto12Tohru Terada13Koji Hisatake14Yohei Hayashi15iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapanLaboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, JapanLaboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapanLaboratory of Animal Resource Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, JapanResearch and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba, Ibaraki 305-8550, Japan; The Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, JapanResearch and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba, Ibaraki 305-8550, JapanInstitute of Materials Structure Science, High Energy Accelerator Research Organization in Tsukuba, 1-1 Oho, Tsukuba, Ibaraki 305-0801, JapanDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, JapanLaboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, JapaniPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Corresponding authorSummary: Non-genetically modified somatic cells can only be inefficiently and stochastically reprogrammed to pluripotency by exogenous expression of reprogramming factors. Low competence of natural reprogramming factors may prevent the majority of cells to successfully and synchronously reprogram. Here we screened DNA-interacting amino acid residues in the zinc-finger domain of KLF4 for enhanced reprogramming efficiency using alanine-substitution scanning methods. Identified KLF4 L507A mutant accelerated and stabilized reprogramming to pluripotency in both mouse and human somatic cells. By testing all the variants of L507 position, variants with smaller amino acid residues in the KLF4 L507 position showed higher reprogramming efficiency. L507A bound more to promoters or enhancers of pluripotency genes, such as KLF5, and drove gene expression of these genes during reprogramming. Molecular dynamics simulations predicted that L507A formed additional interactions with DNA. Our study demonstrates how modifications in amino acid residues of DNA-binding domains enable next-generation reprogramming technology with engineered reprogramming factors.http://www.sciencedirect.com/science/article/pii/S2589004221014966Stem cell plasticityMolecular biology |
| spellingShingle | Evgeniia Borisova Ken Nishimura Yuri An Miho Takami Jingyue Li Dan Song Mami Matsuo-Takasaki Dorian Luijkx Shiho Aizawa Akihiro Kuno Eiji Sugihara Taka-aki Sato Fumiaki Yumoto Tohru Terada Koji Hisatake Yohei Hayashi Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency iScience Stem cell plasticity Molecular biology |
| title | Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency |
| title_full | Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency |
| title_fullStr | Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency |
| title_full_unstemmed | Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency |
| title_short | Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency |
| title_sort | structurally discovered klf4 variants accelerate and stabilize reprogramming to pluripotency |
| topic | Stem cell plasticity Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004221014966 |
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