Iwafuchi Lab
Publications

Publications

Selected Publications

Mirizio, G; Sampson, S; Iwafuchi, M. Interplay between pioneer transcription factors and epigenetic modifiers in cell reprogramming. Regenerative Therapy. 2025; 28:246-252.

Matsui, S; Shiley, JR; Buckley, M; Lim, H-W; Hu, Y-C; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. STAR Protocols. 2024; 5(3):103233.

Matsui, S; Shiley, JR; Granitto, M; Ludwig, K; Buckley, M; Koigi, S; Mirizio, G; Hu, Y-C; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. STAR Protocols. 2024; 5(3):103221.

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, H-W; Iwafuchi, M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Molecular Cell. 2024; 84(3):476-489.e10.

Iwafuchi, M; Cuesta, I; Donahue, G; Takenaka, N; Osipovich, AB; Magnuson, MA; Roder, H; Seeholzer, SH; Santisteban, P; Zaret, KS. Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nature Genetics. 2020; 52(4):418-427.

Iwafuchi-Doi, M. The mechanistic basis for chromatin regulation by pioneer transcription factors. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2019; 11(1):e1427.

Huppert, SS; Iwafuchi-Doi, M. Molecular regulation of mammalian hepatic architecture. Current Topics in Developmental Biology. 2019; 132:91-136.

Zaret, KS; Lerner, J; Iwafuchi-Doi, M. Chromatin Scanning by Dynamic Binding of Pioneer Factors. Molecular Cell. 2016; 62(5):665-667.

Iwafuchi-Doi, M; Zaret, KS. Cell fate control by pioneer transcription factors. Development. 2016; 143(11):1833-1837.

Iwafuchi-Doi, M; Donahue, G; Kakumanu, A; Watts, JA; Mahony, S; Pugh, BF; Lee, D; Kaestner, KH; Zaret, KS. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Molecular Cell. 2016; 62(1):79-91.

Iwafuchi-Doi, M; Zaret, KS. Pioneer transcription factors in cell reprogramming. Genes & Development. 2014; 28(24):2679-2692.

Chang, X; Li, W; Matsui, S; Huynh, C; Erickson, C; Guo, F; Cederquist, GY; Studer, L; Iwafuchi, M; Shillington, A; Chronis, C; Tchieu, J. ZMYND11 functions in bimodal regulation of latent genes and brain-like splicing to safeguard corticogenesis. Nature Communications. 2025; 16(1):9010.

Mirizio, G; Sampson, S; Iwafuchi, M. Interplay between pioneer transcription factors and epigenetic modifiers in cell reprogramming. Regenerative Therapy. 2025; 28:246-252.

Matsui, S; Shiley, JR; Buckley, M; Lim, H-W; Hu, Y-C; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. STAR Protocols. 2024; 5(3):103233.

Matsui, S; Shiley, JR; Granitto, M; Ludwig, K; Buckley, M; Koigi, S; Mirizio, G; Hu, Y-C; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. STAR Protocols. 2024; 5(3):103221.

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, H-W; Iwafuchi, M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Molecular Cell. 2024; 84(3):476-489.e10.

Lim, H-W; Iwafuchi, M. Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome. 2023:59-68.

Mukherjee, S; Luedeke, DM; Mccoy, L; Iwafuchi, M; Zorn, AM. SOX transcription factors direct TCF-independent WNT/β-catenin responsive transcription to govern cell fate in human pluripotent stem cells. Cell reports. 2022; 40(8):111247.

Iwafuchi, M; Cuesta, I; Donahue, G; Takenaka, N; Osipovich, AB; Magnuson, MA; Roder, H; Seeholzer, SH; Santisteban, P; Zaret, KS. Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nature Genetics. 2020; 52(4):418-427.

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