FSU Biology - Directories - Faculty

Department of Biological Science

at Florida State University

Biological Science Faculty Member

Dr. Karen M. McGinnis

Dr. Karen M. McGinnis

Link to maize gene coexpression network

Associate Professor
Ph.D., Arizona State University, 2000
Graduate Faculty Status

Research and Professional Interests:

My long term goal is to understand how identical genomic sequences can be interpreted to cause distinct expression patterns and phenotypes. I am particularly interested in the regulation of epigenetic modifications that heritably alter the expression of endogenous and transgenic loci in plants. These phenomena have been shown to be key elements in the growth, development, and gene regulation of a broad range of organisms; I study them predominantly in maize.

(McGinnis Lab authors in bold print below)

Selected Publications:

Schulte, L., K. Koirtyohann, and K. McGinnis (2022) Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues. G3 12: 10 pp.
(Full text PDF:) (Full text HTML:

Madzima, T., S. Vendramin, J. Lynn, P. Lemert, K. Lu, and K. McGinnis (2021) Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation. Frontiers in Plant Science 12694289: 15 pp.
(Full text PDF) (Full text HTML

Boerner, S., and K. McGinnis 2021 Computational Analysis of lncRNA from cDNA Sequences.  In  Methods in Molecular Biology: Long Non-Coding RNAs. Edited by: Zhang and Hu Humana, New York, NY. 223-241 
(Online access

Vendramin, S., J. Huang, P. A. Crisp, T. F. Madzima*, and K. M. McGinnis* (2020) Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize.. G3 .
(Available here

Huang, J., J. Zheng, H. Yuan, and K. McGinnis (2018) Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize.. BMC Plant Biology 18: 14 pp.
(available online

Stroud, K. L., and K. M. McGinnis (2017) Altered nucleosome positions in maize haplotypes and mutants of a subset of SWI/SNF-like proteins. Plant Direct 1: 17 pp.
(Full text) (PDF

Huang, J., S. Vendramin, L. Shi, and K. McGinnis (2017) Construction and Optimization of Large Gene Co-expression Network in Maize Using RNA-Seq Data. Plant Physiology 175: 568-583.
(PDF) (Full text

Huang, J., J. Lynn, L. Schulte, S. Vendramin, and K. McGinnis 2017 Epigenetic Control of Gene Expression in Maize  In  International Review of Cell and Molecular Biology Lorenzo Galluzi Elsevier 328: 25-48 

Li, Q., J. I. Gent, G. Zynda, J. Song, I. Makarevitch, C. D. Hirsch, C. N. Hirsch, R. K. Dawe, T. Madzima, K. M. McGinnis, D. Lisch, R. J. Schmitz, M. W. Vaughn, and N. M. Springer (2015) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proceedings of the National Academy of Sciences of the United States of America 112: 14728-14733.
(Full text) (PDF

Madzima, T., J. Huang, and K. M. McGinnis (2014) Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays. Epigenetics 9: 1047-1059.
(Available online

Madzima, T. F., A. E. Sloan, L. Stroud, and K. M. McGinnis 2014 Chapter 9: Epigenomics  In  Genetics, Genomics and Breeding of Maize    
(Available from CRC Press

Sloan, A. E., L. Sidorenko, and K. M. McGinnis (2014) Diverse Gene Silencing Mechanisms with Distinct Requirements for RNA Polymerase Subunits in Zea mays. Genetics 198: .
(Full text online) (PDF online

Haag, J. R., B. Brower-Toland, , E. K. Krieger, L. Sidorenko, C. D. Nicora, A. Norbeck, A. Irsigler, H. LaRue, J. Brzeski, K. McGinnis, S. Ivashuta, L. Pasa-Tolic, V. L. Chandler, and C. S. Pikaard (2014) Functional Diversification of Maize RNA Polymerase IV and V Subtypes via Alternative Catalytic Subunits. Cell Reports 9: 378-390.
(PDF online

Vera, D. L., J. Labonne, P. Alam, T. Madzima, G. G. Hoffman, S. B. Gigimurugan, J. Zhang, K. M. McGinnis, J. H. Dennis, and H. W. Bass,  (2014) Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell In press: .
(Available online

Li, Q., S. R. Eichten, P. J. Hermanson, V. Zaunbrecher, J. Song, J. Wendt, H. Rosenbaum, T. F. Madzima, A. E. Sloan, J. Huang, D. Burgess, T. Richmond, S. M. Kaeppler, K. M. McGinnis, R. Meeley, O. Danilevskaya, M. W. Vaughn, J. Jeddeloh, and N. M. Springer (2014) Genetic Perturbation of the Maize Methylome. The Plant Cell 26: 4602-4616.
(Full text) (PDF

Gent, J. I., T. F. Madzima, R. Bader, M. R. Kent, X. Zhang, M. Stam, K. M. McGinnis, and R. K. Dawe (2014) Accessible DNA and relative depletion of H3K9me2 at maize RdDM loci. The Plant Cell .
(available online

Labonne, J. D., J. E. Dorweiler, and K. M. McGinnis (2013) Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants. Epigenetics 8: 398-408.
(Available online

Fincher, J., D. Vera, D. D. Hughes, K. M. McGinnis, J. H. Dennis, and H. W. Bass (2013) Genome-wide prediction of nucleosome occupancy in maize (Zea mays L.) reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiology 162: 1127-41.
(Available online

Boerner, S. L., and K. M. McGinnis (2012) Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays. PLoS One 7: e43047.
(Available online

Eichten, S. E., N. A. Ellis, I. Makarevitsch, C. Yeh, J. I. Gent, L. Guo, K. M. McGinnis, X. Zhang, P. S. Schnable, M. W. Vaughn, R. K. Dawe, and N. M. Springer (2012) Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genetics 8: e1003127.
(Available online

Madzima, T. F., E. S. Mills, J. M. Gardiner, and K. M. McGinnis (2011) Identification of epigenetic regulators of a transcriptionally silenced transgene in maize. G3: Genes, Genomes, Genetics 1: 75-83.

Irsigler, A., and K. M. McGinnis 2011 Genetic resources for the study of epigenetic gene regulation in maize.  In  Epigenetics: A resource manual  Jeff Craig and Nick Wong Horizon Press 409-420 

McGinnis, K. M. (2010) RNAi for plant functional genomics. Briefings in Functional Genomics and Proteomics doi:10.1093/bfgp/elp052: .

McGinnis, K. M. 2009 Use of transgene induced RNAi to regulate endogenous gene expression.   In  Methods in Molecular Biology M. Paul Scott  Humana Press 91-99 

Bowler, C. A., and et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239-244.

Barbazuk, W. B., Y. Fu, and K. M. McGinnis (2008) Genome-wide analyses of alternative splicings in plants: opportunities and challenges.. Genome Research 18: 1381-1392.

McGinnis, K. M., N. Murphy, A. Carlson, A. Akula, C. Akula, H. Basinger, M. Carlson, P. Hermanson, N. Kovacevic, M. McGill, V. Seshadri, J. Yoyokie, K. Cone, H. F. Kaeppler, S. M. Kaeppler, and N. M. Springer (2007) Assessing the efficiency of RNA interference for maize functional genomics. Plant Physiology 143: 1441-1451.

McGinnis, K. M., C. Springer, Y. Lin, C. C. Carey, and V. L. Chandler (2006) Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics 173: 1637-1647.

Alleman, M. A., L. Sidorenko, K. McGinnis, J. White, V. Seshadri, J. Dorweiler, K. Sikkink, and V. Chandler (2006) An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442: 295-298.

Graduate Students:

Koirtyohann, Kathryn