Kenneth S. ZARETInstitute for Regenerative Medicine (IRM)
University of Pennsylvania, USA

Two-Parameter, Single-Molecule-Tracking Assessments
Discriminate Diverse Regulatory Factor
Behaviors in Chromatin

Contact : zaret [at sign] pennmedicine.upenn.edu
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Kenneth S. ZARETInstitute for Regenerative Medicine, University of Pennsylvania, USAResearch Interests

Our laboratory is interested in the ways that transcription factors initiate cell fate changes in embryonicTranscription factor-chromatin interactions, heterochromatin, cell reprogramming,

development, cell reprogramming, and human diseases such as cancer. We discovered that a certain class of gene
regulatory proteins, which we called "pioneer transcription factors," initiate cell fate changes by their ability totarget DNA sequences that are wrapped on a nucleosome at silent genes in cellular chromatin [1]. The initialEducation
1982
1982-1985

targeting of nucleosomal DNA by a pioneer factor causes an exposure of the underlying nucleosome [2], thus
PhD, Biophysics, University of Rochester Medical School, Rochester, NY
Postdoctoral fellowship, Biochemistry and Biophysics, University of California, San Francisco. CAallowing cooperating transcription factors, co-regulators, and ATP-dependent nucleosome remodelers to access theDNA and activate the targeted gene. Yet recent studies have shown that silent genes can exist in various states ofcompaction in chromatin, and pioneer factors have differential access to different types of silenced chromatin. To
better understand these issues, our laboratory employed HALO-tags on diverse chromosomal proteins andProfessional Career
1986- 1999

Professor, Cell, Molecular, and Developmental Biology, Brown University, RI

1999 - 2009

Senior Member, Program Leader, Cell and Dev. Biology Program, Fox Chase Cancer Ctr., PA

2009 - present

Professor and Director, IRM, Perelman School of Medicine, University of Pennsylvania, PA

transcription factors, which enabled single-molecule-tracking (SMT) of the individual molecules in real time, as themolecules diffuse in, or bind to, different chromatin domains in the nucleus of living cells. We began by using SMTof core histone proteins and quantified two parameters of molecular movement tracks over millisecond time scales[3]. We plotted the radius of confinement, which estimates the area in which the molecule performs its confined
motions, against the average displacement, representing the average distance between subsequent steps in a
motion track, over time. The two parameters, though generally positively correlated, present deviations that resolve
five mobility types for core histones with distinct subnuclear localizations. As expected, the mobility of diverse
heterochromatin proteins correlates with lower mobility chromatin, with notable differences that relate to particular

Scientific Activities
1986 - present

Signaling control of cell fate in embryonic development, cell reprogramming

1993 - present

Discovery and mechanism of action of pioneer transcription factors

2012 - present

Biophysical methods, proteomics to understand compacted heterochromatin chromatin2017 - present

Single-molecule-tracking to understand how transcription factors scan genomic chromatinbiochemical features of the proteins. Upon assessing the mobility of diverse transcription factors, we found that
pioneer factors with nucleosome binding ability can access the lowest mobility chromatin domains. Using welldefined mutations of the pioneer factor FOXA1, we found that nonspecific DNA/nucleosome binding and histoneinteractions are essential for scanning compacted chromatin. Our two-parameter SMT approach reveals how gene
regulatory proteins scan the genome during cell fate changes.

ReferencesHonors
2002

Hans Popper Basic Science Award, Amer. Assoc. for the Study of Liver Diseases, ALF

2007

Elected as a Fellow of the American Assoc. for the Adv. of Science2017

Stanley N. Cohen Biomedical Research Award, Univ. Penn.

Publications
Zaret, K.S. (2020) Pioneer transcription factors initiating gene network changes. Annual Review of Genetics, (e-pub: https://doi.org/10.1146/

1. annurev-genet-030220-015007).

[ 1 ] Zaret, K.S. (2020) Pioneer transcription factors initiating gene network changes. Annual Review of Genetics,(e-pub: https://doi.org/10.1146/annurev-genet-030220-015007).
[ 2 ] Iwafuchi, M., et al. (2020) Gene network transitions in embryos depend upon interactions between a pioneer
transcription factor and core histones. Nature Genetics 52, 418-427. PMID:32203463[ 3 ] Lerner, J., Gomez-Garcia, P.A., McCarthy, R., Liu, Z., Lakadamyali, M., and Zaret, K.S. (2020) Two-parameter
mobility assessments discriminate diverse regulatory factors behaviors in chromatin. Molecular Cell 79, 418-5427.
PMID: 32574554

Iwafuchi, M., Cuesta, I., Donahue, G, Takenaka, N. Osipovich, A.B., Magnuson, M. A., Roder, H., Seeholzer, S.H., Santisteban, P., and Zaret, K.S. (2020)

2. Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nature Genetics 52,418-427. PMID:32203463

Lerner, J., Gomez-Garcia, P.A., McCarthy, R., Liu, Z., Lakadamyali, M., and Zaret, K.S. (2020) Two-parameter mobility assessments discriminate diverse

3. regulatory factors behaviors in chromatin. Molecular Cell 79, 418-5427. PMID: 32574554
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