Developmental Biology
Iwafuchi Lab

Iwafuchi Research Lab

The long-term goal of the Iwafuchi lab is to reveal gene and chromatin regulatory principles underlying dramatic cell fate changing events that occur in embryonic development, tissue repair (physiological reprogramming), and diseases, and ultimately to utilize this knowledge to precisely engineer cell fates.  

Although more than 200 transcription factors are expressed in each cell, only a small number of transcription factors are necessary to elicit dramatic cell fate changes. Within these key transcription factors, a subset called “pioneer factors” have a remarkable ability to change chromatin landscape, thereby imparting a competence for cell-type-specific gene expression.  

We focus on deciphering the chromatin-level regulation in cell fate changes and understanding how different families of pioneer factors impact such regulation. We are building a team to tackle these questions, combining developmental biology and human stem cells and organoid culture systems with genetics and genomics/bioinformatics.

Training in the Lab

The Iwafuchi Lab provides training for postdoctoral fellows and graduate students.  If you are interested in joining the lab, please send your CV including the names of 3 references, along with a brief statement of your research interests to Maki (makiko.iwafuchi@cchmc.org).  We look forward to hearing from you!

Publications

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, H; 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. Wiley Interdisciplinary Reviews-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.

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, H; 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.

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. Wiley Interdisciplinary Reviews-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.

Makino Iwafuchki-Doi

Makiko Iwafuchi, Ph.D.
Assistant Professor

Division of Developmental Biology

Center for Stem Cell & Organoid Medicine (CuSTOM)

Cincinnati Children’s Hospital Medical Center
University of Cincinnati College of Medicine
3333 Burnet Avenue, Location S3.244

Shipping Address:

240 Albert Sabin Way, MLC 7007
Cincinnati, OH 45229-3039

513-636-0882 (office)
513-633-4449 (lab)

makiko.iwafuchi@cchmc.org