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James D Forney


  • Professor of Biochemistry
  • Adjunct Professor of Biochemistry, Indiana University School of Medicine
BCHM Room 208

Area of Expertise: Regulation of differentiation in protozoa

Eukaryotic cell differentiation is generally considered a property of metazoa (multicellular organisms), yet dramatic examples of regulated cellular changes also occur in protozoa. Our laboratory is currently investigating the formation of the somatic macronucleus during sexual reproduction in ciliated protozoa.

Ciliated protozoa contain two types of nuclei, micronuclei and macronuclei, which arise from a single diploid fertilization nucleus during sexual reproduction. During the formation of the macronucleus, the germline chromosomes are amplified, fragmented and specific DNA sequences are eliminated. In Paramecium tetraurelia the coding regions of many micronuclear genes are interrupted by internal eliminated sequences (IES) that must be removed precisely to form the open reading frames in the macronuclear genome. These IESs range in size from 26 bp to over 1 kb and are always flanked by the dinucleotide 5'-TdA-3'. The isolation of mutant cell lines that are unable to remove a specific IES revealed nucleotides located within the first 6 base pairs of the eliminated sequence which are important for IES excision. Interestingly, this region contains a consensus sequence that has similarity to the termini of the mariner/Tc1 family of transposable elements. The possible relationship between this wide spread family of transposons and Paramecium IESs will require detailed knowledge of the cis and trans acting elements necessary for excision. An in vivo assay for IES excision is being used to dissect the cis acting sequences required for precise and efficient removal of these short DNA elements. With our collaborators we have shown that ligase IV and Xrcc4, proteins in the Non-Homologous End Joining (NHEJ) pathway, are required for elimination of IES in Paramecium. We also identified a novel ciliate specific protein (DIE5) that is required for IES excision in both Paramecium and the related ciliate Tetrahymena thermophila. Our focus is now turned to the role of SUMOylation in regulating critical events during formation of the macronuclear genome in Tetrahymena. 

Selected Publications

Nasir, A., Yang, Q., Chalker, D., & Forney, J. (2015). SUMOylation is developmentally regulated and required for cell pairing during conjugation in Tetrahymena thermophila. Eukaryot Cell, 14, 170-181. Retrieved from

Kapusta, A., Matsuda, A., Marmignon, A., Ku, M., Silve, A., Meyer, E., . . . Betermier, M. (2011). Highly precise and deleopmentally prongrammed genome assembly in Paramecium requires ligase IV-dependent end joining. PLoS Genetics, 7. Retrieved from

Matsuda, A., Shieh, A. Y., & Chalker, D. (2010). The conjugation-specific Die5 protein is required for development of the somatic nucleus in both Paramecium and Tetrahymena. Eukaryotic Cell, 9(7), 1087-1099. Retrieved from

Holzer, T., Mishra, K., & LeBowitz, J. (2008). Coordinate regulation of a family of promastigote-enriched RNAs by the 3' UTR PRE element in Leishma. Molecular and Biochemical Parasitology, 157, 54-64.

Cohen-Freue, G., Holzer, T., & McMaster, W. (2007). Global gene expression in Leishmania. International Journal for Parasitology, 37, 1077-1086.

Forney, J. (2006). Developmentally regulated DNA elimination in Paramecium.

Holzer, T., & McMaster, R. (2006). Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes,lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana. Molecular and Biochemical Parasitology, 146(2), 198-218.

Matsuda, A. (2006). The SUMO pathway is developmentally regulated and required for programmed DNA elimination in Paramecium tetraurelia. Eukaryotic Cell, 5(5), 806-815. Retrieved from

Matsuda, A. (2005). Analysis of Paramecium tetraurelia A-51 surface antigen gene mutants reveals positive feedback mechanisms for maintenance of expression and temperature induced activation. Eukaryotic Cell, 4(10), 1613-1619. Retrieved from

Forney, J. (2005). Developmentally regulated DNA elimination in Paramecium tetraurelia.

Awards & Honors

(2019) Book of Great Teachers. Purdue University.

(2013) Trustee Teaching Award, Indiana University. Indiana University School of Medicine.

(2010) Fellowship for Study in a Second Discipline. Purdue University.

(1998) Outstanding Teacher. Department of Biochemistry.

(1997) Top Ten Teacher in the School of Science. Purdue University.

(1995) Co-Chair, Fifth International Ciliate Molecular Biology Meeting. Federation of American Society for Experimental Biology.

(1992) Junior Faculty Award. American Cancer Society.

Department of Biochemistry, 175 South University Street, West Lafayette, IN 47907-2063 USA, (765) 494-1600

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