Curators Professor of Biological Sciences
PhD, 1977 Indiana University
Chromosome evolution and function in plants and fruit fly
Research descriptionOur 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. Several examples of de novo centromeres formed over unique sequences in the absence of canonical DNA repeats have been documented. These findings illustrate the epigenetic nature of centromere activity in plants. These materials are being used to gain an understanding of how centromeres are specified.
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.
Please visit our projects website for further details.
James A. Birchler, 2015. Promises and pitfalls of synthetic chromosomes in plants. Trends in Biotechnology, 33:189-194.
James A. Birchler, 2015. Engineered minichromosomes in plants. Chromosome Research, 23:77-85.
Liu, Y., Su, H., Pang, J., Gao, Z., Wang, X.-J., James A. Birchler, Han, F., 2015. Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize. Proceedings of the National Academy of Sciences of the United States of America, 112: 1263-E1271.
Li, J., Hou, J., Sun, L., Wilkins, J.M., Lu, Y., Niederhuth, C.E., Merideth, B.R., Mawhinney, T.P., Mossine, V.V., Greenlief, C.M., Walker, J.C., Folk, W.R., Hannink, M., Lubahn, D.B., James A. Birchler, Cheng, J., 2015. From gigabyte to kilobyte: A bioinformatics protocol for mining large RNA-Seq transcriptomics data. PLoS ONE, 10: e0125000.
James A. Birchler, 2014. Engineered minichromosome technology in plants. IN: Recent Advancements in Plant Expression in Crop Plants. Edited by K. Azhakanandam, A. Silverstone, H. Daniell, M. Davey. Springer, New York.
James A. Birchler, 2014. Does ectopic cell death cause somatic mutations in neighboring cells by activating transposons? Mobile Genetic Elements 4: e28040.
James A. Birchler, 2014 Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 123: 459-469
James A. Birchler, 2014. Interploidy hybridization barrier of endosperm as a dosage interaction. Frontiers in Plant Science 5; 281: 1-4
James A. Birchler and Reiner A. Veitia, 2014. The Gene Balance Hypothesis: Dosage effects in plants. Methods in Molecular Biology 1112: 25-32. Charles Spillane, Editor.
Jing Zhang, Bing Zhang, Handong Su, James A. Birchler and Fangpu Han, 2014. Molecular mechanisms of homologous chromosome pairing and segregation in plants. Journal of Genetics and Genomics 41: 117-123.
Bing Zhang, Qianhua Dong, Handong Su, James A. Birchler and Fangpu Han, 2014. Histone phosphorylation during cell division in plants. Cytogenetics and Genome Research 143: 144-149.
Gavin C. Conant, James A. Birchler and J. Chris Pires, 2014. Dosage, Duplication and Diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology 19: 91-98.
James A. Birchler, 2014. Engineered minichromosomes in plants. Current Opinion in Plant Biology 19: 76-80.
Washburn, J.D., Birchler, J.A.(2014) Polyploids as a "model system" for the study of heterosis. Plant Reproduction, 27:1-5.
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. pp. 35-43
James A. Birchler, 2013. Heterosis in Plants. Encyclopedia of Agriculture and Food Systems.
James A. Birchler, 2013. Aneuploidy in plants and flies: the origin of studies of genomic imbalance. Seminars in Cell and Developmental Biology 24: 315-319. 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. Pp. 147-158
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. Pp. 183-192.
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. Pp. 313-321.
Rick E. Masonbrink, Shulan Fu, Fangpu Han and James A. Birchler, 2013. Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 193: 77-84.
James A. Birchler and Fangpu Han, 2013. Meiotic behavior of small chromosomes in maize. Frontiers in Plant Science, doi: 10.3389/fpls.2013.00606.
Jacob D. Washburn and James A. Birchler, 2013. Polyploids as a “model system” for the study of heterosis. Sex Plant Reproduction, doi 10.1007/s00497-013-0237-4.
Ryan N. Douglas and James A. Birchler, 2013. microRNAs in Eukaryotes. Encyclopedia of Biological Chemistry, 2nd Edition, pp 98-102.
Fangpu Han and James A. Birchler, 2013. Epigenetics of centromeres in plants. Journal of Genetics and Genomics. 40: 201-204.
Hong Yao, Anjali Dogra Gray, Donald L. Auger and James A. Birchler, 2013. Genomic dosage effects on heterosis in triploid maize. Proc. Natl. Acad. Sci., USA 110: 2665-2669.
Lin Sun, Harvey R. Fernandez, Ryan C. Donohue, Jilong Li, Jianlin Cheng and James A. Birchler, 2013. Male specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation. Proc. Natl. Acad. Sci. USA 110: E808-817.
Lisa B. Kanizay, Patrice S. Albert, James A. Birchler and R. Kelly Dawe, 2013. Evidence for intragenomic conflict between the two major knob repeats of maize. Genetics 194: 81-89.
Robert T. Gaeta, Rick E. Masonbrink, Changzeng Zhao, Abhijit Sanyal, Lakshminarasimhan Krishnaswamy and James A. Birchler, 2013. In vivo modification of a maize engineered minichromosome. Chromosoma 122: 221-232.
Lyza G. Maron, Claudia T. Guimaraes, Matias Kirst, Patrice S. Albert, James A. Birchler, Peter J. Bradbury, Edward S. Buckler, Alison E. Coluccio, Tatiana V. Danilova, David Kudrna, Jurandir V. Magalhaes, Miguel A. Pineros, Michael C. Schatz, Rod Wing and Leon V. Kochian, 2013. Aluminum tolerance in maize is associated with higher MATE1 gene copy-number. Proc. Natl. Acad. Sci., USA 110: 5241-5246.
Shulan Fu, Zhenling Lv, Zhi Gao, Huanjun Wu, Junling Pang, Bing Zhang, Qianhua Dong, Xiang Guo, Xie-Jie Wang, James A. Birchler and Gangpu Han, 2013. De novo centromere formation on a chromosome fragment in maize. Proc. Natl. Acad. Sci. USA 110: 6033-6036.
Lin Sun, Adam F. Johnson, Ryan C. Donohue, Jilong Li, Jianlin Cheng and James A. Birchler, 2013. Dosage compensation and inverse effects in triple X metafemales of Drosophila. Proc. Natl. Acad. Sci. USA 110: 7383-7388.
Reiner A. Veitia, Samuel Bottani and James A. Birchler, 2013. Gene dosage effects: non-linearities, genetic interactions and dosage compensation. Trends in Genetics 29: 385-393.
Weiwu Xie, Ryan Donohue and James A. Birchler, 2013. Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi. PLoS One 8:e72163.
Lin Sun, Adam F. Johnson, Jilong Li, Aaron S. Lambdin, Jianlin Cheng and James A. Birchler, 2013. Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila. Proc. Natl. Acad Sci. USA: 110: 16514-16519.
Robert T. Gaeta, Rick E. Masonbrink, Changzeng Zhao, Lakshminarasimhan Krishnaswamy, 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.
Rick E. Masonbrink, Robert T. Gaeta and James A. Birchler, 2012. Multiple maize minichromosomes in meiosis. Chromosome Research 20: 395-402.
Rick E. Masonbrink and James A. Birchler, 2012. Accumulation of multiple copies of maize minichromosomes. Cytogenetics and Genome Research 137: 50-59.
Weiwu Xie and James A. Birchler, 2012. Identification of Inverse regulator-a (Inr-a) as synonymous with Pre-mRNA cleavage complex II protein (Pcf11) in Drosophila. G3: Genes, Genomes, Genetics 2: 701-706.
Chuanhe Yu, Fangpu Han, Jianbo Zhang, James A. Birchler and Thomas Peterson, 2012. A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice. Theoretical and Applied Genetics 125: 1449-1462.
James A. Birchler and Reiner A. Veitia, 2012. Gene Balance Hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proc. Natl. Acad. Sci., USA 109: 14746-14753.
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.
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.
Robert T. Gaeta, Tatiana V. Danilova, Changzeng Zhao, Rick E. Masonbrink, Morgan E. McCaw and James A. Birchler, 2011. Recovery of a telomere-truncated chromosome via a compensating translocation in maize. Genome 54: 184-195.
Hong Yao, Akio Kato, Brian Mooney and James A. Birchler, 2011. Phenotypic and gene expression analysis of a ploidy series of maize inbred Oh43. Plant Molecular Biology 75: 237-251.
Dal-Hoe Koo, Fangpu Han, James A. Birchler and Jiming Jiang, 2011. Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome. Genome Research 21: 908-914.
Weiwu Xie, Chengzhi Liang and James A. Birchler, 2011. Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 188: 823-834.
Seth D. Findley, Allison L. Pappas, Yaya Cui, James A. Birchler, Reid G. Palmer and Gary Stacey, 2011. Fluorescence in situ hybridization-based karyotyping of soybean translocation lines. G3 1: 117-129.
Zhi Gao, Shulan Fu, Qianhua Dong, Fangpu Han and James A. Birchler, 2011. Inactivation of a centromere during the formation of a translocation in maize. Chromosome Research 19: 755-761
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.
Nicole C. Riddle, Hongmei Jiang, Lingling An, R.W. Doerge and James A. Birchler, 2010. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theoretical and Applied Genetics 120: 341-353.
Rick E. Masonbrink and James A. Birchler, 2010. Sporophytic nondisjunction of the maize B chromosome at high copy numbers. Journal of Genetics and Genomics. 37: 79-84
Patrice S. Albert, Zhi Gao, Tatiana V. Danilova and James A. Birchler, 2010. Diversity of chromosomal karyotypes in maize and its relatives. Cytogenetics and Genome Research 129: 6-16.
Leah M. Roark, Alice Y. Hui, Laura Donnelly, James A. Birchler and Kathleen J. Newton, 2010. Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes. Cytogenetics and Genome Research 129: 17-23
Chuanhe Yu, Tatiana V. Danilova, Jianbo Zhang, James A. Birchler, and Thomas Peterson, 2010. Constructing defined chromosome segmental duplications in maize. Cytogenectics and Genome Research 129:72-81.
Seth D. Findley, Steven Cannon, Kranthi Varala, Jianchang Du, Jianxin Ma, Matthew E. Hudson, James A. Birchler and Gary Stacey, 2010. A fluorescence in situ hybridization system for karyotyping soybean. Genetics 185: 727-744.
Honors & Awards
Selected honors and awards
Fellows Award, Academy of Science of St. Louis 2016
Faculty-Alumni Award, Mizzou Alumni Association 2015
President’s Award for Sustained Career Excellence, UM System 2015
Abraham Eisenstark Faculty Fellow Award 2015
Einstein Professor, Chinese Academy of Sciences 2014
Fellow, National Academy of Inventors 2014
Member, National Academy of Sciences 2011
Curators’ Professor, University of Missouri 2009
Award for Excellence in Academic Achievements, Northeast Normal University, Changchun, P.R. China 2007
Named one of five “Teaching Legends”, Mizzou Magazine 2003
Zeta Tau Alpha Faculty Appreciation 2003
Fellow, American Association for the Advancement of Science 2002
Outstanding Teaching Award, MU Panhellenic Council 1997
Jan. 12, 2016
Academy of Science of St. Louis honors James A. Birchler
Oct. 1, 2015
May 1, 2015
April 22, 2015
James Birchler awarded President’s Award for Sustained Career Excellence
April 9, 2015
Reviewing the potential of engineered chromosomes in plants
Dec. 18, 2014
James A. Birchler elected as a Fellow in the National Academy of Inventors
Sept. 22, 2014
Biology professor appointed associate editor of leading genetics journal
March 26, 2014
Einstein Professorship awarded to James Birchler by Chinese Academy of Sciences
Nov. 19, 2013
Two new books by Jim Birchler published
Oct. 24, 2013
New study shows global impact of genomic imbalance on gene expression in Drosophila
Jan. 28, 2013
Professor James Birchler Profiled in PNAS
Feb. 24, 2012
May 5, 2011
James Birchler Elected to National Academy of Sciences
Nov. 20, 2009
A Question of Balance
July 30, 2009
Researchers to study minichromosomes in maize with $1.9 million grant
Feb. 27, 2009
UM Curators Honor James Birchler
May 16, 2007
Researchers attach genes to minichromosomes in maize