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James Birchler

Curators Professor of Biological Sciences
PhD, 1977 Indiana University

Email: birchlerj@missouri.edu
Office: 117 Tucker Hall
Phone: 573-882-4905
Headshot of James Birchler

Research

Research summary

Chromosome evolution and function in plants and fruit fly

Research description

Our laboratory studies gene expression in multicellular eukaryotes on both the specific gene and chromosomal levels using Drosophila and maize as experimental organisms. We are interested in the mechanisms involved, how the two levels are interconnected and how they evolve.

A longstanding topic of investigation involves understanding the balance of gene regulatory mechanisms. Our results indicate that changing the stoichiometry of individual components of regulatory complexes affects target gene expression, which is manifested in chromosomal dosage series. The most common such dosage effect is an inverse correlation between the dosage of a chromosomal segment or individual regulator and the amount of target gene expression. This “inverse dosage” effect is likely to contribute to the molecular basis of aneuploid syndromes and when a regulatory dosage change is combined on the same chromosomal segment as a target gene, the target will exhibit dosage compensation. This type of dosage effect appears to be responsible for X chromosomal dosage compensation in Drosophila and potentially other species.

A second topic of study involves the role of the so-called “RNAi machinery” in transcriptional gene silencing. Small RNAs appear to act as sequence specific guides for histone modifying enzymes to regions of the genome that contain repetitive sequences such as heterochromatin, transposable elements, telomeres and other features. The modifying enzymes set up a less permissive environment for transcription. Heterchromatin formation involves the methylation of histone 3 on lysine 9 whereas cosuppression of repetitive transgenes is mediated by methylation of histone 3 on lysine 27.

Our laboratory has developed a method for chromosome painting in maize. This procedure has allowed us to examine numerous issues about the maize genome. The diversity and homogenization mechanisms of repetitive DNA elements can now be investigated. It is now possible to visualize on the maize somatic chromosomes individual gene copies, single transgenes and single copies of transposable elements such as Activator, Suppressor-mutator and RescueMu.

The structure and function of maize centromeres are under study. We have focused on the centromere of the supernumerary B chromosome because it contains a specific repeat unit that the other centromeres in the genome do not contain and thus can be examined individually. This centromere has been subjected to a deletion analysis to determine the minimum requirements for centromere function. Competition studies in heterozygotes between two different B chromosome centromeres are underway to gain an understanding of the nature of their rapid evolution. Competition between different sizes of B centromeres is also being studied in dicentric situations to examine centromere strength. Recent work has resulted in the recovery of numerous cases of inactivated centromeres. Under specific circumstances, this inactive centromeres can be reactivated. These finding illustrate the epigenetic nature of centromere activity in plants. These materials are being used to gain an understanding of how centromeres specified for activity from one cell division to the next.

Our laboratory has produced artificial chromosome platforms for maize. Such constructs should be useful for using maize as a factory for the inexpensive production of foreign proteins and as a means to introduce novel biochemical pathways to maize to confer new properties to the plant. This technology has the potential to engineer multiple new traits into crops for improved agricultural practices. From a basic standpoint, artificial constructs will allow investigators to produce designer synthetic chromosomes that will help them understand the minimum features required for function.



Select Publications

Select Publications

Zhi Gao, Fangpu Han, Tatiana V. Danilova, Jonathan C. Lamb, Patrice S. Albert and James A. Birchler, 2013. Labeling meiotic chromosomes in maize with fluorescence in situ hybridization. Methods in Molecular Biology, Plant Meiosis Protocols, Wojtek Pawlowski and Mathilde Grelon, editors.

James A. Birchler, 2013. Heterosis in Plants. Encyclopedia of Agriculture and Food Science, in press.

James A. Birchler and Reiner A. Veitia, 2013. The Gene Balance Hypothesis: Dosage effects in plants. Methods in Molecular Biology, Charles Spillane, Editor, in press.

James A. Birchler, 2013. Aneuploidy in plants and flies: the origin of studies of genomic imbalance. Seminars in Cell and Developmental Biology, in press. Rong Li, editor.

Ryan N. Douglas and James A. Birchler 2013. Plant Centromere Epigenetics. IN: Plant Centromere Biology. Edited by Jiming Jiang and James A. Birchler, Wiley-Blackwell, New York.

Robert T. Gaeta and James A. Birchler, 2013. Engineered Plant Chromosomes. IN: Plant Centromere Biology. Edited by Jiming Jiang and James A. Birchler, Wiley-Blackwell, Hoboken

James A. Birchler, 2013. Genetic Rules of Heterosis in Plants. IN: Polyploid and Hybrid Genomics. Edited by Z. Jeffrey Chen and James A. Birchler, Wiley-Blackwell, Hoboken.

Robert T. Gaeta, Rick E. Masonbrink, Lakshminarasimhan Krishnaswamy, Changzeng Zhao and James A. Birchler, 2012. Synthetic chromosome platforms in plants. Annual Review of Plant Biology 63: 307-330.

James A. Birchler and Tatiana V. Danilova, 2012. Fluorescence In Situ Hybridization and In Situ PCR. In: Plant Cytogenetics, Plant Genetics and Genomics: Crops and Models 4. H. W. Bass and J. A. Birchler, editors. Springer.

James A. Birchler, Zhi Gao and Fangpu Han, 2012. Plant Centromeres. In: Plant Cytogenetics, Plant Genetics and Genomics: Crops and Models 4. H. W. Bass and J. A. Birchler, editors. Springer.

James A. Birchler. 2012. Genetic consequences of polyploidy in plants. IN: Polyploidy and Genome Evolution. P. S. Soltis and D. E. Soltis, editors. Springer.

Shulan Fu, Zhi Gao, James A. Birchler and Fangpu Han, 2012. Dicentric chromosome formation and epigenetics of centromere formation in plants. Journal of Genetics and Genomics 39: 125-130.

James A. Birchler, 2012. Claims and counterclaims of X-chromosome compensation. Nature Structural and Molecular Biology 19: 3-5.

James A. Birchler and Gernot G. Presting, 2012. Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes and Development 26: 638-640.

James A. Birchler, 2012. Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants. Current Opinions in Plant Biology 15: 544-548.

James A. Birchler, 2012. Heterosis: What art thou? Maydica 57: 92-95.

James A. Birchler, 2012. Messing with Mendel. Developmental Cell 23: 678-679.

James A. Birchler, 2011. RNA interference: what is it? IN: RNA Interference: Application to Drug Discovery and Challenges to Pharmaceutical Development. Paul H. Johnson, Editor. Wiley-Blackwell, Hoboken, NJ, pp 3-11.

James A. Birchler, Zhi Gao, Anupma Sharma, Gernot G. Presting and Fangpu Han, 2011. Epigenetic aspects of centromere function in plants. Current Opinion in Plant Biology 14: 217-222.

Wenchao Yin, James A. Birchler and Fangpu Han, 2011. Maize centromeres: where sequence meets epigenetics. Frontiers in Biology 6: 102-108.

Ryan N. Douglas and James A. Birchler, 2011. microRNAs in Eukaryotes. Encyclopedia of Biological Chemistry, 2nd Edition.

Ryan N. Douglas and James A. Birchler, 2011. microRNAs in Eukaryotes. Encyclopedia of Biological Chemistry, 2nd Edition.

James A. Birchler, Lin Sun, Ryan Donohue, Abhijit Sanyal and Weiwu Xie, 2011. Implications of the gene balance hypothesis for dosage compensation. Frontiers in Biology 6: 118-124.

James A. Birchler and Weiwu Xie, 2011. Reflections on the inhibition of RNAi by cell death signaling. Fly 5:4 337–339.

James A. Birchler, Lin Sun, Harvey Fernandez, Ryan Donohue, Weiwu Xie, and Abhijit Sanyal, 2011. Re-evaluation of the function of the male specific lethal (MSL) complex in Drosophila. Journal of Genetics and Genomics 38: 327-332.

Reiner A. Veitia and James A. Birchler, 2011. Protein-protein and protein-DNA dosage balance and differential paralog transcription factor retention in polyploids. Frontiers in Plant Genetics and Genomics doi: 10.3389/fpls.2011.00064.

James A. Birchler, Lakshminarasimhan Krishnaswamy, Robert T. Gaeta, Rick E. Masonbrink and Changzeng Zhao, 2010. Engineered minichromosomes in plants. Critical Reviews in Plant Sciences 29: 135-147.

James A. Birchler and Reiner A. Veitia, 2010. The gene balance hypothesis: Implications for gene regulation, quantitative traits and evolution. The New Phytologist 186: 54-62.

Reiner A. Veitia and James A. Birchler, 2010. Dominance and gene dosage balance in human health and disease. Journal of Pathology 220: 174-185.

James A. Birchler, 2010. Reflections on studies of gene expression in aneuploids. Biochemical Journal 426: 119-123.

Akio Kato, Jonathan C. Lamb, Patrice S. Albert, Tatiana Danilova, Fangpu Han, Zhi Gao, Seth Findley and James A. Birchler, 2010. Chromosome Painting for Plant Biotechnology. IN: Plant Chromosome Engineering, James A. Birchler, ed. Humana Press, New York.

James A. Birchler, Hong Yao, Sivanandan Chudalayandi, Daniel Vaiman and Reiner Veitia, 2010. Heterosis. The Plant Cell 22: 2105-2112.

Honors & Awards

Selected honors and awards

Elected Fellow - AAAS 2002