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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Scott Michaels

Photo of Scott Michaels
Research Images
Research photo by Scott Michaels

Wild type nuclei contain domains of highly compacted heterochromatin that are enriched in H3K27me1 (top). In atxr5/6 mutants, H3K27me1 is lost and decondensation of heterochromatin results (bottom).

Professor of Biology and Director, Center for Genomics & Bioinformatics

IU Affiliations
Center for Genomics & Bioinformatics

Contact Information
By telephone: 812-856-0302/6-0355(lab)
MY 316C / MY 359



Genome, Cell & Developmental Biology
Research Areas
  • Chromatin, Chromosomes, and Genome Integrity
  • Developmental Mechanisms and Regulation in Eukaryotic Systems
  • Plant Molecular Biology

Ph.D. University of Wisconsin-Madison
Postdoctoral Fellow, University of Wisconsin-Madison


Outstanding Junior Faculty Award

Research Description

Regulation of chromatin structure and gene expression by epigenetic modifications

Chromatin is the term used to describe DNA and associated packaging proteins (e.g. histones). Modifications of histones, such as methylation and acetylation at specific positions can cause the DNA to be packaged more tightly and become less transcriptionally active (heterochromatin), whereas other histone modifications can increase transcriptional activity by opening up the chromatin structure (euchromatin). These modifications are sometimes referred to as the "histone code" and play an important role in the regulation of gene expression in all eukaryotes. The sequences of histones, and in many cases histone-modifying enzymes, are highly conserved. Therefore, there is a high likelihood that the knowledge gained from research in model systems will have broad applications in all eukaryotes.

In our laboratory, we use two different models to study the links between histone modifications, chromatin structure, and gene expression. The first model is the constitutive heterochromatin present in Arabidopsis nuclei. In wild-type nuclei, 8-10 spots of highly compacted heterochromatin are visible (Fig 1). These spots are called chromocenters and contain repetitive sequences, transposons, and rDNA genes. Histones in chromocenters are marked by modifications that are known to repress gene expression, such as histone H3 monomethylation at lysine 27 (H3K27me1). Our laboratory has identified ATXR5 and ATXR6 as the enzymes that are responsible for H3K27me1 at chromocenters and the loss of these enzymes leads to loss of gene silencing and decondensation of heterochromatin (Fig 1). Ongoing work in our lab is elucidating the mechanisms by which the activity of ATXR5 and ATXR6 is targeted to heterochromatin and how H3K27 methylation leads to gene silencing.

The second model that we use is an epigenetic switch that is triggered by signals from the environment. To ensure that flowering occurs at a favorable time of year, many plants growing in temperate climates have adopted a biennial growth habit. These plants contain a block to flowering that is eliminated by the prolonged cold temperatures of winter; thus flowering is prevented prior to winter and promoted in the favorable conditions of spring. In biennial-like, winter-annual accessions of Arabidopsis, this block to flowering is created by the floral repressor FLOWERING LOCUS C (FLC). Prior to winter, FLC is highly expressed and prevents flowering. Cold treatment, in turn, causes a permanent epigenetic shut off of FLC expression that is mediated by repressive histone modifications at the FLC locus. Our laboratory is actively involved in determining that molecular mechanisms that control this epigenetic switch.

PhD Positions:  The Michaels lab is currently seeking PhD students to study projects related to chromatin structure and the molecular basis of flowering-time regulation in Arabidopsis.   Indiana University is an exceptional environment for plant molecular biology.  Our laboratory is housed on the third floor of Myers Hall along with four other laboratories that also use Arabidopsis as their primary model organism. This provides a thriving and vibrant environment for research.   For additional information, please contact Dr. Michaels (email).

Undergraduate job opportunity in the Michaels lab.
Our laboratory performs research on the model plant Arabidopsis and is looking for a student to help with the day-to-day maintenance of our plant growth rooms.  The work is not glamorous and can be a bit dirty: washing glassware, pots, and trays; as well as autoclaving trash, and generally preventing the place from looking like a dump.  On the upside, hours can be flexible, you get a lab coat, and there are opportunities to participate in our lab’s research program (  Experience is not required, but punctuality is (e.g. show up when you are scheduled).  Interested parties should send a brief resume and unofficial transcript to Scott Michaels (

Select Publications
Miller DF, Yan P, Fang F, Buechlein A, Kroll K, Frankhouser D, Stump C, Stump P, Ford JB, Tang H, Michaels S, Matei D, Huang TH, Chien J, Liu Y, Rusch DB, Nephew KP. 2017. Complete Transcriptome RNA-Seq. Methods Mol Biol. 2017;1513:141-162. PMID: 27807835
Christopher J. Hale, Magdalena E. Potok, Jennifer Lopez, Truman Do, Ao Liu, Javier Gallego-Bartolome, Scott D. Michaels and Steven E. Jacobsen. 2016. Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. Plos Genetics.  In press.
Wei Feng, Christopher Hale, Ryan Over, Shawn Cokus, Steven E. Jacobsen, and Scott D. Michaels. 2016. Large-scale heterochromatin remodeling linked to over replication-associated DNA damage.PNAS. In press.
Christopher J. Hale, Magdalena E. Potok, Jennifer Lopez, Truman Do, Ao Liu, Javier Gallego-Bartolome, Scott D. Michaels and Steven E. Jacobsen. 2016. Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. Plos Genetics.  PLoS Genet. 2016 Jun 2;12(6):e1006092. doi: 10.1371/journal.pgen.1006092
Wei Feng and Scott D Michaels. 2015. The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants. Annual Review of Genetics. In press.
Yannick Jacob, Elisa Bergamin, Mark T.A. Donoghue, Vanessa Mongeon, Chantal LeBlanc, Philipp Voigt, Charles J. Underwood, Joseph S. Brunzelle, Scott D. Michaels, Danny Reinberg, Jean-François Couture, and Robert A. Martienssen. 2014. Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication.  Science, 343: 1249-1253.  [article]
Ryan Over and Scott D. Michaels. 2014. Open and Closed: The Roles of Linker Histones. Molecular Plant, 7:481-491.  [article]
John T. Lovell, Thomas E. Juenger, Scott Michaels, Jesse R. Lasky, Alexander Platt, James H. Richards, Xuhong Yu, Saunak Sen and John K. McKay. (2013) Protagonistic Pleiotropy of FRIGIDA Promotes Adaptation and Positive Assortative Mating. Proceedings of the Royal Society B 280, 20131043.  [article]
Brenda J. Reinhart, Tie Liu, Nicole R. Newell, Enrico Magnani, Tengbo Huang, Randall Kerstetter, Scott Michaels and M. Kathryn Barton. 2013. Establishing a Framework for the Ad/Abaxial Regulatory Network of Arabidopsis - targets of REVOLUTA and KANADI regulation. Plant Cell, 25: 3228-49.  [article]
Lei Ding, Sang Yeol Kim, and Scott D. Michaels. (2013) FLX-family proteins regulate FLC expression in both winter-annual and rapid-cycling Arabidopsis. Plant Physiology, 163: 243-252.  [article]
Guillaume Moissiard, Shawn J. Cokus, Joshua Cary, Suhua Feng, Allison C. Billi, Hume Stroud, Dylan Husmann, Ye Zhan, Bryan R. Lajoie, Rachel P. McCord, Christopher J. Hale, Wei Feng, Scott D. Michaels, Alison R. Frand, Matteo Pellegrini, Job Dekker, John K. Kim, and Steve Jacobsen. 2012. MORC family ATPases required for heterochromatin condensation and gene silencing. Science, 336: 1448-1451.  [article]
Frederic Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Wei Feng, Hume Stroud, Steve Jacobsen, Scott Michaels, and Craig Pikaard. 2012. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes and Development, 26: 945-957.  [article]
The EPIC Planning Committee. (2012) Reading the second code: mapping epigenomes to understand plant growth, development and adaptation to the environment. Plant Cell 24 (6): 2257-61.  [article]
Hume Stroud, Christopher J. Hale, Suhua Feng, Elena Caro, Yannick Jacob, Scott D. Michaels and Steven E. Jacobsen. (2012) DNA methyltransferases are required to induce heterochromatic re-replication. PLoS Genet 8(7): e1002808.  [article]
Gu X, Jiang D, Yang W, Jacob Y, Michaels SD, and He Y. (2011) Arabidopsis Homologs of Retinoblastoma-Associated Protein 46/48 Associate with a Histone Deacetylase to Act Redundantly in Chromatin Silencing. PLoS Genet 7(11): e1002366. doi:10.1371/journal.pgen.1002366  [article]
Benjamin K. Blackman, Scott D. Michaels, and Loren H. Rieseberg. 2011. Connecting the Sun to Flowering in Sunflower Adaptation. Molecular Ecology, 20: 3503-3512.  [article]
Wei Feng, Yannick Jacob, Kira M. Veley, Lei Ding, Xuhong Yu, Goh Choe, and Scott D. Michaels. 2011. Hypomorphic alleles reveal FCA-independent roles for FY in the regulation of FLC. Plant Physiology, 155: 1425-1434.  [article]
Wei Feng and Scott D. Michaels. 2011. Dual roles for FY in the regulation of FLC. Plant Signaling & Behavior, 6: 703-705.  [article]
Benjamin K. Blackman, David A. Rasmussen, Jared L. Strasburg, Andrew R. Raduski, John M. Burke, Steven J. Knapp, Scott D. Michaels, and Loren H. Rieseberg. 2011. Contributions of Flowering Time Genes to Sunflower Domestication and Improvement. Genetics,187: 271-287.  [article]
Richard M. Amasino and Scott D. Michaels. 2010. The Timing of Flowering. Plant Physiology, 154:516-520.  [article]
Yannick Jacob, Hume Stroud, Chantal LeBlanc, Suhua Feng, Luting Zhou, Elena Caro, Christiane Hassel, Crisanto Gutierrez, Scott D. Michaels and Steven E. Jacobsen. 2010. Two histone H3 lysine 27 methyltransferases, ATXR5 and ATXR6, regulate heterochromatic DNA replication. Nature, 466: 987-991.  [article]
Benjamin K. Blackman and Scott D. Michaels. 2010. Does CO act as a transcription factor or as a co-activator? The answer may be – yes. New Phytologist, 187: 1-3.  [article]
Benjamin K. Blackman, Jared L. Strasburg, Andrew R. Raduski, Scott D. Michaels, Loren H. Rieseberg. 2010. The Role of Recently Derived FT Paralogs in Sunflower Domestication. Current Biology, 20: 629-635.  [article]
Michaels, S.D. 2010. Integration of photoperiodic timing and vernalization. In: Photoperiodism: Seasonal Time Measurement. Edited by Randy J. Nelson, David Denlinger and David Somers. Oxford University Press.  [article]
Xuhong Yu and Scott D. Michaels. 2010. The Arabidopsis Paf1c complex component CDC73 participates in the modification of FLC chromatin. Plant Physiology, 153: 1074-1084.  [article]
Jacob, Y., Feng, S., LeBlanc, C.A., Bernatavichute, Y.V., Stroud, H., Cokus, S., Johnson, L.M., Pellegrini, M., Jacobsen, S.E., and Michaels, S.D. 2009. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nature Structural and Molecular Biology, 16: 763-768.  [article]
Michaels, S.D. 2009. Flowering time regulation produces much fruit. Current Opinion in Plant Biology, 12: 75-80.  [article]
Jacob, Y. and Michaels, S.D. 2009. H3K27me1 is E(z) in animals, but not in plants. Epigenetics, 4: 266-269.  [article]
Bonnie M. Weasner, Brandon Weasner, Stephanie M. DeYoung, Scott D. Michaels and Justin P. Kumar. 2009. Transcriptional activities of the Pax6 gene eyeless regulate tissue specificity of ectopic eye formation in Drosophila. Developmental Biology, 492-502.  [article]

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