A photo of Makiko Iwafuchi.

Makiko Iwafuchi, PhD

  • Assistant Professor, UC Department of Pediatrics



My research focuses on deciphering the chromatin-level regulation in cell fate changes and understanding how different families of pioneer factors and cellular microenvironments impact on such regulation. Our team tackles these questions by combining the developmental biology of human stem cells and organoid culture systems with genomics, bioinformatics and super-resolution imaging.

The long-term goal of my lab is to reveal gene and chromatin regulatory principles underlying dramatic cell fate changing events that occur in embryonic development, tissue repair and disease. My ultimate goal is to utilize this knowledge to precisely control cell fates.

During my education and career, I was honored to receive fellowships from the Japan Society for the Promotion of Sciences (JSPS), the Naito Foundation, the Astellas Foundation and the Uehara Memorial Foundation.

BSc: Kitasato University, Japan.

PhD: Osaka University, Japan.

Postdoctoral Fellow: University of Pennsylvania, Philadelphia, PA.


Chromatin regulation; pioneer transcription factors; cell programming and reprogramming

Research Areas

Developmental Biology



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


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


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


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


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


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


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

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

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

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

From the Blog

How ‘Pioneers’ Blaze the One Trail that Determines Cell Fate
Genomics and Development

How ‘Pioneers’ Blaze the One Trail that Determines Cell Fate

Makiko Iwafuchi, PhD, Hee Woong Lim, PhD1/10/2024