A photo of Makiko Iwafuchi.

Assistant Professor, UC Department of Pediatrics


Biography & Affiliation


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.

Research Interests

Chromatin regulation; pioneer transcription factors; cell programming and reprogramming

Academic Affiliation

Assistant Professor, UC Department of Pediatrics

Research Divisions

Developmental Biology


BSc: Kitasato University, Japan.

PhD: Osaka University, Japan.

Postdoctoral Fellow: University of Pennsylvania, Philadelphia, PA.


Selected Publication

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.

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

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

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.

Enhancer Analyses Using Chicken Embryo Electroporation. Uchikawa, M; Nishimura, N; Iwafuchi-Doi, M; Kondoh, H. Methods in Molecular Biology. 2017; 1650:191-202.