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James Birchler

James Birchler

Curators Professor of Biological Sciences

Biological Sciences,


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. 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.

Select Publications

Yu W, Birchler JA: A green fluorescent protein-engineered haploid inducer line facilitates haploid mutant screens and doubled haploid breeding in maize. Molecular Breeding 2016, 36(1):1-12.

Feng C, Yuan J, Wang R, Liu Y, Birchler JA, Han F: Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System. Journal of Genetics and Genomics 2016, 43(1):37-43.

Birchler JA, Johnson AF, Veitia RA: Kinetics genetics: Incorporating the concept of genomic balance into an understanding of quantitative traits. Plant Science 2016, 245:128-134.

Birchler JA, Graham ND, Swyers NC, Cody JP, McCaw ME: Plant minichromosomes. Current Opinion in Biotechnology 2016, 37:135-142.

Yu, W, Yau, YY, Birchler, JA, Plant artificial chromosome technology and its potential application in genetic engineering. 2016 Plant Biotechnology Journal, 14 (5):1175-1182.

Birchler JA: Engineered minichromosome technology in plants. In: Recent Advancements in Gene Expression and Enabling Technologies in Crop Plants. 2015: 383-389.

Birchler JA: Promises and pitfalls of synthetic chromosomes in plants. Trends in Biotechnology 2015, 33(3):189-194.

Birchler JA: Engineered minichromosomes in plants. Chromosome Research 2015, 23(1):77-85.

Liu Y, Su H, Pang J, Gao Z, Wang XJ, Birchler JA, Han F: 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 2015, 112(11):E1263-E1271.

Li J, Hou J, Sun L, Wilkins JM, Lu Y, Niederhuth CE, Merideth BR, Mawhinney TP, Mossine VV, Greenlief CM et al: From gigabyte to kilobyte: A bioinformatics protocol for mining large RNA-Seq transcriptomics data. PLoS ONE 2015, 10(4).

Veitia RA, Veyrunes F, Bottani S, Birchler JA: X chromosome inactivation and active X upregulation in therian mammals: Facts, questions, and hypotheses. Journal of Molecular Cell Biology 2015, 7(1):2-11.

Veitia RA, Birchler JA: Models of buffering of dosage imbalances in protein complexes. Biology Direct 2015, 10(1).

Merchant S, Bednarek SY, Birchler JA, Coupland G, Eckardt NA, Genschik P, Greenberg J, Kieber JJ, Kliebenstein DJ, Pogson BJ et al: The Plant cell introduces breakthrough reports: A new forum for Cutting-Edge plant research. Plant Cell 2015, 27(10):2667-2668.

Lough AN, Faries KM, Koo DH, Hussain A, Roark LM, Langewisch TL, Backes T, Kremling KAG, Jiang J, Birchler JA et al: Cytogenetic and sequence analyses of mitochondrial DNA insertions in nuclear chromosomes of maize. G3: Genes, Genomes, Genetics 2015, 5(11):2229-2239.

Liu Y, Su H, Zhang J, Liu Y, Han F, Birchler JA: Dynamic epigenetic states of maize centromeres. Frontiers in Plant Science 2015, 6(OCTOBER).

Graham ND, Cody JP, Swyers NC, McCaw ME, Zhao C, Birchler JA: Engineered Minichromosomes in Plants: Structure, Function, and Applications. In: International Review of Cell and Molecular Biology. vol. 318; 2015: 63-119.

Feng C, Liu YL, Su HD, Wang HF, Birchler J, Han FP: Recent advances in plant centromere biology. Science China Life Sciences 2015, 58(3):240-245.

Ellis NA, Douglas RN, Jackson CE, Birchler JA, Dawe RK: Generation of a maize B centromere minimal map containing the central core domain. G3: Genes, Genomes, Genetics 2015, 5(12):2857-2864.

Cody JP, Swyers NC, McCaw ME, Graham ND, Zhao C, Birchler JA: Minichromosomes: Vectors for crop improvement. Agronomy 2015, 5(3):309-321.

Birchler JA: Mendel, Mechanism, Models, Marketing, and More. Cell 2015, 163(1):9-11.

Yu W, Yau YY, Birchler JA: Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnology Journal 2015.

Birchler JA: Does ectopic cell death cause somatic mutations in neighboring cells by activating transposons? Mobile Genetic Elements. 2014, 4: e28040.

Birchler JA: Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014, 123(5):459-469.

Birchler JA: Interploidy hybridization barrier of endosperm as a dosage interaction. Frontiers in Plant Science 2014, 5(JUN).

Birchler JA, Veitia RA: The gene balance hypothesis: Dosage effects in plants. In: Methods in Molecular Biology. vol. 1112; 2014: 25-32.

Zhang J, Zhang B, Su H, Birchler JA, Han F: Molecular Mechanisms of Homologous Chromosome Pairing and Segregation in Plants. Journal of Genetics and Genomics 2014, 41(3):117-123.

Zhang B, Dong Q, Su H, Birchler JA, Han F: Histone phosphorylation: Its role during cell cycle and centromere identity in plants. Cytogenetic and Genome Research 2014, 143(1-3):144-149.

Conant GC, Birchler JA, Pires JC: Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology 2014, 19:91-98.

Birchler JA: Engineered minichromosomes in plants. Current Opinion in Plant Biology 2014, 19:76-80.

Washburn JD, Birchler JA: Polyploids as a “model system” for the study of heterosis. Plant Reproduction 2014, 27(1):1-5.

Gao Z, Han F, Danilova TV, Lamb JC, Albert PS, Birchler JA: Labeling meiotic chromosomes in maize with fluorescence in situ hybridization. In: Methods in Molecular Biology. vol. 990; 2013: 35-43.

Birchler JA: Aneuploidy in plants and flies: The origin of studies of genomic imbalance. Seminars in Cell and Developmental Biology 2013, 24(4):315-319.

Douglas RN, Birchler JA: Plant Centromere Epigenetics. In: Plant Centromere Biology. 2013: 147-158.

Gaeta RT, Birchler JA: Engineered Plant Chromosomes. In: Plant Centromere Biology. 2013: 183-192.

Birchler JA: Genetic Rules of Heterosis in Plants. In: Polyploid and Hybrid Genomics. 2013: 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.

Birchler JA, Han F: Meiotic behavior of small chromosomes in maize. Frontiers in Plant Science 2013, 4(DEC).

Yao H, Gray AD, Auger DL, Birchler JA: Genomic dosage effects on heterosis in triploid maize. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(7):2665-2669.

Sun L, Johnson AF, Li J, Lambdin AS, Cheng J, Birchler JA: Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(41):16514-16519.

Kanizay LB, Albert PS, Birchler JA, Kelly Dawe R: Intragenomic conflict between the two major knob repeats of maize. Genetics 2013, 194(1):81-89.

Gaeta RT, Masonbrink RE, Zhao C, Sanyal A, Krishnaswamy L, Birchler JA: In vivo modification of a maize engineered minichromosome. Chromosoma 2013, 122(3):221-232.

Maron LG, Guimarães CT, Kirst M, Albert PS, Birchler JA, Bradbury PJ, Buckler ES, Coluccio AE, Danilova TV, Kudrna D et al: Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(13):5241-5246.

Fu S, Lv Z, Gao Z, Wu H, Pang J, Zhang B, Dong Q, Guo X, Wang XJ, Birchler JA et al: De novo centromere formation on a chromosome fragment in maize. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(15):6033-6036.

Sun L, Johnson AF, Donohue RC, Li J, Cheng J, Birchler JA: Dosage compensation and inverse effects in triple X metafemales of Drosophila. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(18):7383-7388.

Veitia RA, Bottani S, Birchler JA: Gene dosage effects: Nonlinearities, genetic interactions, and dosage compensation. Trends in Genetics 2013, 29(7):385-393.

Xie W, Donohue RC, Birchler JA: Quantitatively Increased Somatic Transposition of Transposable Elements in Drosophila Strains Compromised for RNAi. PLoS ONE 2013, 8(8).

Sun L, Fernandez HR, Donohue RC, Li J, Cheng J, Birchler JA: Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(9):E808-E817.

Murata M, Birchler JA: Arabidopsis Centromeres. In: Plant Centromere Biology. 2013: 1-14.

Masonbrink RE, Fu S, Han F, Birchler JA: Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 2013, 193(1):77-84.

Lukaszewski AJ, Birchler JA: Misdivision of Centromeres. In: Plant Centromere Biology. 2013: 111-128.

Jiang J, Birchler JA: Rice Centromeres. In: Plant Centromere Biology. 2013: 15-24.

Jiang J, Birchler JA: Preface. Plant Centromere Biology 2013:ix-x.

Jiang J, Birchler JA: Plant Centromere Biology; 2013.

Chen JZ, Birchler JA: Polyploid and Hybrid Genomics; 2013.

Birchler JA, Jeffrey Chen Z: Preface. Polyploid and Hybrid Genomics 2013:xvii-xviii.

Birchler JA, Han F: Centromere Epigenetics in Plants. Journal of Genetics and Genomics 2013, 40(5):201-204.

Birchler JA: Profile of James A. Birchler. Interview by Farooq Ahmed. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(8):2687-2689.

Gaeta RT, Masonbrink RE, Krishnaswamy L, Zhao C, Birchler JA: Synthetic chromosome platforms in plants. In: Annual Review of Plant Biology. vol. 63; 2012: 307-330.

Birchler JA: Genetic consequences of polyploidy in plants. In: Polyploidy and Genome Evolution. vol. 9783642314421; 2012: 21-32.

Fu S, Gao Z, Birchler J, Han F: Dicentric Chromosome Formation and Epigenetics of Centromere Formation in Plants. Journal of Genetics and Genomics 2012, 39(3):125-130.

Birchler JA: Claims and counterclaims of X-chromosome compensation. Nature Structural and Molecular Biology 2012, 19(1):3-5.

Birchler JA, Presting GG: Retrotransposon insertion targeting: A mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes and Development 2012, 26(7):638-640.

Birchler JA: Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants. Current Opinion in Plant Biology 2012, 15(5):544-548.

Birchler JA: Heterosis-what art thou? Maydica 2012, 57(2):92-95.

Birchler J: Messing with Mendel. Developmental Cell 2012, 23(4):678-679.

Masonbrink RE, Gaeta RT, Birchler JA: Multiple maize minichromosomes in meiosis. Chromosome Research 2012, 20(4):395-402.

Masonbrink RE, Birchler JA: Accumulation of multiple copies of maize minichromosomes. Cytogenetic and Genome Research 2012, 137(1):50-59.

Xie W, Birchler JA: Identification of inverse regulator-a (inr-a) as synonymous with pre-mRNA cleavage complex ii protein (pcf11) in drosophila. G3: Genes, Genomes, Genetics 2012, 2(6):701-706.

Yu C, Han F, Zhang J, Birchler J, Peterson T: A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice. Theoretical and Applied Genetics 2012, 125(7):1449-1462.

Birchler JA, Veitia RA: Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proceedings of the National Academy of Sciences of the United States of America 2012, 109(37):14746-14753.

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