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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Craig Pikaard

Photo of Craig Pikaard
Research Images
Research photo by Craig Pikaard

Relative locations of RNA polymerases IV (green) and II (red) in an Arabidopsis nucleus. Image by Dr. Olga Pontes.

HHMI-GBMF Investigator, Carlos O. Miller Professor, and Distinguished Professor of Biology

IU Affiliations

Contact Information
By telephone: 812-855-1874/5-2659(lab)
MY 300

Pikaard Lab website

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

Ph.D., Purdue University, 1985
Postdoctoral Research, Fred Hutchinson Cancer Research Center, Seattle


Fellow, American Association for the Advancement of Science

Research Description

My lab is interested in how genes can be selectively inactivated and how the silent state can be perpetuated through multiple rounds of cell division, and even from one generation to the next. One longstanding interest of the lab is the uniparental silencing of 45S ribosomal RNA (rRNA) genes in genetic hybrids, an epigenetic phenomenon known as nucleolar dominance. 45S rRNA genes are transcribed in the nucleolus by RNA polymerase I. There are thousands of nearly identical rRNA genes in the genome. At specific periods of development, most or all of these rRNA genes are presumably needed, but in most cell types the number of rRNA genes exceeds the physiological demands of the cell. Under these conditions, excess rRNA genes are selectively inactivated via mechanisms that involve methylation of the DNA and chemical modifications of the histone proteins that organize the DNA. My student and postdoctoral colleagues in the lab are working to understand the mechanisms responsible for selective rRNA gene silencing, focusing on new evidence that the silencing decisions are not made one rRNA gene at a time but are made on a multi-megabase, sub-chromosomal scale affecting hundreds of rRNA genes. 

A second focus of my lab is to understand the functions of RNA polymerases IV and V in the RNA-directed DNA methylation pathway. RNA polymerases IV and V are plant-specific enzymes whose subunit compositions indicate that they evolved as specialized forms of DNA-dependent RNA polymerase II, the enzyme that makes protein-coding mRNAs. Pol IV is required for the production of 24 nt small interfering RNAs (siRNAs) that direct the silencing of repeated sequences in the genome via DNA methylation. Pol V facilitates siRNA-mediated silencing by generating transcripts at the target loci to be silenced. The siRNAs bind to these Pol V transcripts in association with proteins that bring about the DNA methylation and histone modification of the associated chromatin, thus silencing genes transcribed by conventional RNA polymerases, including Pol II. New evidence indicates that specific chromatin modifications that can be perpetuated mark loci for Pol IV recruitment. We have thus proposed that epigenetic inheritance at these loci consists of at least two separable steps: the first accounting for specification and inheritance of silent locus identity and the second involving recruitment of Pol IV and the silencing machinery.

Select Publications

Todd Blevins, Frédéric Pontvianne, Ross Cocklin, Ram Podicheti, Chinmayi Chandrasekhara, Satwica Yerneni, Chris Braun, Brandon Lee, Doug Rusch, Keithanne Mockaitis, Haixu Tang and Craig S. Pikaard (2014). A two-step process for epigenetic inheritance in Arabidopsis. Molecular Cell, Mar 19. pii: S1097-2765(14)00164-6. doi: 10.1016/j.molcel.2014.02.019.

Frederic Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Iva Mozgova, Christiane Hassel, Olga M.F. Pontes, Sarah Tucker, Petr Mokros, Veronika Muchova, Jiri Fajkus, and Craig S. Pikaard (2013). Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes and Development 27:1545–1550.

Wierzbicki, A.T., Ross Cocklin, Anoop Mayampurath, Ryan Lister, M. Jordan Rowley, Brian D. Gregory, Joseph R. Ecker, Haixu Tang and Craig S. Pikaard (2012). Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs and cytosine methylation in the Arabidopsis epigenome. Genes & Development 26:1825-1836.

Jeremy R. Haag, Thomas S. Ream, Michelle Marasco, Carrie D. Nicora, Angela D. Norbeck, Ljiljana Pasa-Tolic and Craig S. Pikaard (2012). In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Molecular Cell 48:811-818.

Frédéric Pontvianne, Chinmayi Chandrasekhara, Wei Feng, Todd Blevins, Hume Stroud, Steve E. Jacobsen, Scott D. Michaels and Craig S. Pikaard (2012).  Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes & Development 26:945-957.

Ek Han Tan, Todd Blevins, Thomas Ream and Craig S. Pikaard (2012). Functional consequences of subunit diversity in RNA polymerases II and V. Cell Reports 1:208-214.

Thomas S. Ream, Jeremy R. Haag, Andrzej Wierzbicki, Carrie D. Nicora, Angela Norbeck, Jian-Kang Zhu, Gretchen Hagen, Thomas J. Guilfoyle, Ljiljana Paša-Tolić and Craig S. Pikaard (2009). Subunit compositions of the RNA silencing enzymes, Pol IV and Pol V reveal their origins as specialized forms of RNA Polymerase II. Molecular Cell 33, 192–203.

Andrzej Wierzbicki, Thomas Ream, Jeremy Haag and Craig S. Pikaard (2009). RNA Polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genetics 41:630-634.

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