Iwafuchi Lab

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; Granitto, M; Ludwig, K; Buckley, M; Koigi, S; Mirizio, G; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. Star Protocols. 2024; 5:103221.

Matsui, S; Shiley, JR; Buckley, M; Lim, HW; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. Star Protocols. 2024; 5:103233.

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, HW; Iwafuchi, M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Molecular Cell. 2024; 84:476-489.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; 52:418-427.

Iwafuchi-Doi, M. The mechanistic basis for chromatin regulation by pioneer transcription factors. WIREs Systems Biology and Medicine. 2019; 11:e1427.

Huppert, SS; Iwafuchi-Doi, M. Molecular regulation of mammalian hepatic architecture. Editor, Wellik DM. 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; 62:665-667.

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

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; 62:79-91.

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

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; Granitto, M; Ludwig, K; Buckley, M; Koigi, S; Mirizio, G; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. Star Protocols. 2024; 5:103221.

Matsui, S; Shiley, JR; Buckley, M; Lim, HW; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. Star Protocols. 2024; 5:103233.

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

Lim, HW; Iwafuchi, M. Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome. Methods in Molecular Biology. : Springer US; Springer US; 2023.

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; 40:111247.

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; 52:418-427.