James A. Birchler
Division of Biological Sciences
E-mail: birchlerj at missouri dot edu
Office address: 117 Tucker Hall
Office phone: 573-882-4905
Lab address: 573-882-4871
We are studying the implications of dosage dependent regulatory hierarchies for their impact on the phenotype and evolutionary processes. This is being studied via gene expression in aneuploid plants. We have also generated tetraploid derivatives of diverse inbred lines and are using these in conjunction with microarray analysis to understand how regulatory gene dosage effects the phenotype with particular reference to hybrid vigor.
Our laboratory has recently developed a chromosome painting protocol for maize chromosomes that allows each member of the karyotype to be distinguished from the others. We are using this procedure to study chromosome structure and behavior, the nature of organellar genome insertions into the nucleus and the distribution of various types of transposabe elements in the genome. The technique is also useful for identifying chromosomal aberrations and locating transgenes to chromosomal position.
The structure and evolution of abnormal chromosomes in maize are also being investigated. These supernumerary B chromosomes are inactive and nondisjoin at certain mitoses in the life cycle. We have cloned sequences from the maize B chromosome in an effort to understand its behavior and evolution on the molecular level. These sequences include the centromere of the B chromosome, which we are analyzing to understand the organization and function of this critical chromosomal structure. The major effort is to use derivatives of the B chromosome of maize to develop an artificial chromosome vector that can be used to accept multiple genes. In this way, it may become possible to add whole biochemical pathways to confer new properties to maize or to use maize as a factory for the production of foreign proteins of interest.
- MU plant genome research receives $3 million boost from National Science Foundation (Nov 2010)
- ASPB members lead new plant genome research program awards (Nov 2010)
- Curators honor three MU professors. Columbia Daily Tribune(Feb 2009)
- Pennisi E. A question of balance. Science 2009;326(5956):1059
- James Birchler Appointed Curators' Professor (Feb 2009)
- "IPG member Jim Birchler constructs artificial chromosomes for corn" (2008)
- Petite Performer: miniature chromosomes pack a big punch (fall 2007)
- Researchers attach minichromosomes in maize (2007)
- Research to target genetics in corn. Columbia Daily Tribune (July 2007)
- Cane A. Corn supremacy. Financial Times (May 26, 2007)
- Breakthrough research helps identify chromosomes in corn (Sep 2004)
- UGA named recipient of $5.6 million grant from NSF for corn improvement (Jul 2004)
- Elected Fellow, American Association for the Advancement of Science (2002)
- Last Series Lecturer, MU Residence Hall Association (2002)
- Named one of five "Teaching Legends", Mizzou Magazine (2003)
- Zeta Tau Alpha Faculty Appreciation (2003)
- Honors Convocation, Faculty Mentor (2003)
- Award for Excellence in Academic Achievements, Northeast Normal University, Changchun, P. R. China (2007)
- Appointed Curators' Professor of Biological Sciences, University of Missouri (2009)
Birchler J, Sun L, Fernandez H, Donohue R, Xie W, and Sanyal A. Re-evaluation of the function of the male specific lethal complex in Drosophila. Journal of Genetics and Genomics, Article in Press.
Xie W, Liang C, and Birchler JA. Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 2011;188(4):823-834.
Koo DH, Han F, Birchler JA, and Jiang J. Distinct DNA methylation patterns associated with active and nactive centromeres of the maize B chromosome. Genome Research 2011, 21(6):908-914.
Kato A, Lamb JC, Albert PS, Danilova T, Han F, Gao Z, Findley S, and Birchler JA. Chromosome painting for plant biotechnology. Methods in Molecular Biology 2011 (Clifton, N.J.);701:67-96.
Yao H, Kato A, Mooney B, and Birchler JA. Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43. Plant Molecular Biology 2011;75(3):237-251.
Birchler JA, Gao Z, Sharma A, Presting GG, and Han F. Epigenetic aspects of centromere function in plants. Current Opinion in Plant Biology 2011;14(2):217-222.
Gaeta RT, Danilova TV, Zhao C, Masonbrink RE, McCaw ME, and Birchler JA. Recovery of a telomere-truncated chromosome via a compensating translocation in maize. Genome 2011;54(3):184-195.
Yu C, Danilova T, Zhang J, Birchler J and Peterson T. Constructing defined chromosome segmental duplications in maize. Cytogenetic and Genome Research 2010;129(1-3):72-81.
Veitia RA and Birchler JA. Dominance and gene dosage balance in health and disease: Why levels matter! Journal of Pathology 2010;220(2):174-185.
Roark LM, Hui AY, Donnelly L, Birchler JA and Newton KJ. Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes. Cytogenetic and Genome Research 2010;129(1-3):17-23.
Riddle NC, Jiang H, An L, Doerge RW and Birchler JA. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theoretical and Applied Genetics 2010;120(2):341-353.
Masonbrink RE and Birchler JA. Sporophytic nondisjunction of the maize B chromosome at high copy numbers. Journal of Genetics and Genomics 2010;37(1):79-84.
Masonbrink RE and Birchler JA. Sporophytic nondisjunction of the maize B chromosome at high copy numbers. Journal of Genetics and Genomics 2010;37(1):79-84.
Birchler JA, Yao H, Chudalayandi S, Vaiman D and Veitia RA. Heterosis. Plant Cell 2010;22(7):2105-2112.
Birchler JA and Veitia RA. The gene balance hypothesis: Implications for gene regulation, quantitative traits and evolution. New Phytologist 2010;186(1):54-62.
Birchler JA and Pires JC. Cytogenetic and Genome Research: Preface. Cytogenetic and Genome Research 2010;129(1-3):5.
Birchler JA and Pires JC. Advances in plant cytogenetics. Preface. Cytogenetic and Genome Research 2010;129(1-3):5.
Birchler JA, Krishnaswamy L, Gaeta RT, Masonbrink RE and Zhao C. Engineered minichromosomes in plants. Critical Reviews in Plant Sciences 2010;29(3):135-147.
Birchler JA, Gao Z and Han F. Pairing in plants: Import is important. Proceedings of the National Academy of Sciences of the United States of America 2010;106(47):19751-19752.
Birchler JA. Reflections on studies of gene expression in aneuploids. Biochemical Journal 2010;426(2):119-123.
Albert PS, Gao Z, Danilova TV and Birchler JA. Diversity of chromosomal karyotypes in maize and its relatives. Cytogenetic and Genome Research 2010;129(1-3):6-16.
Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, Shi J, Gao Z, Han F, Lee H, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK and Presting GG. Maize centromere structure and evolution: Sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genetics 2009;5(11):art. no. e1000743.
Sun X and Birchler JA. Studies on the short range spreading of the male specific lethal (MSL) complex on the X chromosome in Drosophila. Cytogenetic and Genome Research 2009;124(2):158-169.
Sun X and Birchler JA. Interaction study of the male specific lethal (MSL) complex and trans-acting dosage effects in metafemales of drosophila melanogaster. Cytogenetic and Genome Research 2009;124(3-4):298-311.
Riddle NC, Jiang H, An L, Doerge RW and Birchler JA. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theoretical and Applied Genetics 2009;120(2):341-353.
Kavi H and Birchler J. Drosophila KDM2 is a H3K4me3 demethylase regulating nucleolar organization. BMC Research Notes 2009;2.
Han F, Gao Z and Birchler JA. Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. Plant Cell 2009;21(7): 1929-1939.
Birchler JA and Han F. Maize centromeres: structure, function, epigenetics. Annual Review of Genetics 2009;43:287-303.
Birchler JA, Gao Z and Han F. Pairing in plants: Import is important. Proceedings of the National Academy of Sciences of the United States of America 2009;106(47):19751-19752.
Birchler JA, Gao Z and Han F. A tale of two centromeres - Diversity of structure but conservation of function in plants and animals. Functional and Integrative Genomics 2009;9(1):7-13.
Birchler JA. Dosage compensation for the birds. Heredity 2009;102(5):423-424.
Veitia RA, Bottani S and Birchler JA. Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends in Genetics 2008.
Vega JM, Yu W, Han F, Kato A, Peters EM, Zhang ZJ and Birchler JA. Agrobacterium-mediated transformation of maize (Zea mays) with Cre-lox site specific recombination cassettes in BIBAC vectors. Plant Molecular Biology 2008;66(6):587-598.
Riddle NC and Birchler JA. Comparative analysis of inbred and hybrid maize at the diploid and tetraploid levels. Theoretical and Applied Genetics 2008;116(4):563-576.
Lough AN, Roark LM, Kato A, Ream TS, Lamb JC, Birchler JA and Newton KJ. Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize. Genetics 2008;178(1):47-55.
Jin W, Lamb JC, Zhang W, Kolano B, Birchler JA and Jiang J. Histone modifications associated with both A and B chromosomes of maize. Chromosome Research 2008;16(8):1203-1214.
Danilova TV and Birchler JA. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: Resolution, sensitivity, and banding paint development. Chromosoma 2008;117(4):345-356.
Birchler JA, Yu W and Han F. Plant engineered minichromosomes and artificial chromosome platforms. Cytogenetic and Genome Research 2008;120(3-4):228-232.
Birchler JA and Kavi HH. Molecular biology: Slicing and dicing for small RNAs. Science 2008;320(5879):1023-1024.
Yu W, Lamb JC, Han F and Birchler JA. Cytological visualization of DNA transposons and their transposition pattern in somatic cells of maize. Genetics 2007;175(1):31-39.
Yu W, Han F, Gao Z, Vega JM and Birchler JA. Construction and behavior of engineered minichromosomes in maize. Proceedings of the National Academy of Sciences of the United States of America 2007;104(21):8924-8929.
Yu W, Han F and Birchler JA. Engineered minichromosomes in plants. Current Opinion in Biotechnology 2007;18(5):425-431.
Lamb JC, Yu W, Han F and Birchler JA. Plant chromosomes from end to end: telomeres, heterochromatin and centromeres. Current Opinion in Plant Biology 2007;10(2):116-122.
Lamb JC, Riddle NC, Cheng YM, Theuri J and Birchler JA. Localization and transcription of a retrotransposon-derived element on the maize B chromosome. Chromosome Research 2007;15(3):383-398.
Lamb JC, Meyer JM, Corcoran B, Kato A, Han F and Birchler JA. Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Research 2007;15(1):33-49.
Lamb JC, Meyer JM and Birchler JA. A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region. Chromosoma 2007;116(3):237-247.
Lamb JC, Danilova T, Bauer MJ, Meyer UM, Holland JJ, Jensen MD and Birchler JA. Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 2007;175(3):1047-1058.
Han F, Lamb JC, Yu W, Gao Z and Birchler JA. Centromere function and nondisjunction are independent components of the maize B chromosome accumulation mechanism. Plant Cell 2007;19(2):524-533.
Han F, Gao Z, Yu W and Birchler JA. Minichromosome analysis of chromosome pairing, disjunction, and sister chromatid cohesion in maize. Plant Cell 2007;19(12):3853-3863.
Birchler JA, Yao H and Chudalayandi S. Biological consequences of dosage dependent gene regulatory systems. Biochimica et Biophysica Acta - Gene Structure and Expression 2007;1769(5-6):422-428.
Birchler JA and Veitia RA. The gene balance hypothesis: From classical genetics to modern genomics. Plant Cell 2007;19(2):395-402.
Yu W, Lamb JC, Han F and Birchler JA. Telomere-mediated chromosomal truncation in maize. Proceedings of the National Academy of Sciences of the United States of America 2006;103(46):17331-17336.
Yu W, Han F, Kato A and Birchler JA. Characterization of a maize isochromosome 8S-8S. Genome 2006;49(6):700-706.
Riddle NC, Kato A and Birchler JA. Genetic variation for the response to ploidy change in Zea mays L. Theoretical and Applied Genetics 2006;114(1):101-111.
Lamb JC and Birchler JA. Retroelement genome painting: Cytological visualization of retroelement expansions in the genera zea and tripsacum. Genetics 2006;173(2):1007-1021.
Kavi HH, Fernandez HR, Xie W and Birchler JA. Polycomb, pairing and PIWI - RNA silencing and nuclear interactions. Trends in Biochemical Sciences 2006;31(9):485-487.
Kato A and Birchler JA. Induction of tetraploid derivatives of maize inbred lines by nitrous oxide gas treatment. Journal of Heredity 2006;97(1):39-44.
Kato A, Albert PS, Vega JM and Birchler JA. Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotechnic and Histochemistry 2006;81(2-3):71-78.
Han F, Lamb JC and Birchler JA. High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize. Proceedings of the National Academy of Sciences of the United States of America 2006;103(9):3238-3243.
Birchler JA, Yao H and Chudalayandi S. Unraveling the genetic basis of hybrid vigor. Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):12957-12958.
Birchler JA, Fernandez HR and Kavi HH. Commonalities in compensation. BioEssays 2006;28(6):565-568.
Bhadra MP, Bhadra U and Birchler JA. Misregulation of sex-lethal and disruption of male-specific lethal complex localization in drosophila species hybrids. Genetics 2006;174(3):1151-1159.
Bauer MJ and Birchler JA. Organization of endoreduplicated chromosomes in the endosperm of Zea mays L. Chromosoma 2006;115(5):383-394.
Theuri J, Phelps-Durr T, Mathews S and Birchler J. A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize. Cytogenetic and Genome Research 2005;110(1-4):203-208.
Ream TS, Strobel J, Roller B, Auger DL, Kato A, Halbrook C, Peters EM, Theuri J, Bauer MJ, Addae P, Dioh W, Staub JM, Gilbertson LA and Birchler JA. A test for ectopic exchange catalyzed by Cre recombinase in maize. Theoretical and Applied Genetics 2005;111(2):378-385.
Matzke MA and Birchler JA. RNAi-mediated pathways in the nucleus. Nature Reviews Genetics 2005;6(1):24-35.
Lamb JC, Kato A and Birchler JA. Sequences associated with A chromosome centromeres are present throughout the maize B chromosome. Chromosoma 2005;113(7):337-349.
Kavi HH, Xie W, Fernandez HR and Birchler JA. Global analysis of siRNA-mediated transcriptional gene silencing. BioEssays 2005;27(12):1209-1212.
Kavi HH, Fernandez HR, Xie W and Birchler JA. RNA silencing in Drosophila. FEBS Letters 2005;579(26):5940-5949.
Kato A, Zheng YZ, Auger DL, Phelps-Durr T, Bauer MJ, Lamb JC and Birchler JA. Minichromosomes derived from the B chromosome of maize. Cytogenetic and Genome Research 2005;109(1-3):156-165.
Kato A, Vega JM, Han F, Lamb JC and Birchler JA. Advances in plant chromosome identification and cytogenetic techniques. Current Opinion in Plant Biology 2005;8(2):148-154.
Kato A, Lamb JC, Han F, Vega J and Birchler JA. Molecular analysis of maize chromosomes. Maydica 2005;50(3-4):311-320.
Jin W, Lamb JC, Vega JM, Dawe RK, Birchler JA and Jiang J. Molecular and functional dissection of the maize B chromosome centromere. Plant Cell 2005;17(5):1412-1423.
Fernandez HR, Kavi HH, Xie W and Birchler JA. Heterochromatin: On the ADAR radar? Current Biology 2005;15(4):
Della Vedova CB, Lorbiecke R, Kirsch H, Schulte MB, Scheets K, Borchert LM, Scheffler BE, Wienand U, Cone KC and Birchler JA. The dominant inhibitory chalcone synthase allele C2-Idf (inhibitor diffuse) from Zea mays (L.) acts via an endogenous RNA silencing mechanism. Genetics 2005;170(4):1989-2002.
Birchler JA, Riddle NC, Auger DL and Veitia RA. Dosage balance in gene regulation: Biological implications. Trends in Genetics 2005;21(4):219-226.
Bhadra MP, Bhadra U, Kundu J and Birchler JA. Gene expression analysis of the function of the male-specific lethal complex in drosophila. Genetics 2005;169(4):2061-2074.
Auger DL, Peters EM and Birchler JA. A genetic test of bioactive gibberellins as regulators of heterosis in maize. Journal of Heredity 2005;96(5):614-617.
Auger DL, Gray AD, Ream TS, Kato A, Coe Jr EH and Birchler JA. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 2005;169(1):389-397.
Phelps-Durr TL and Birchler JA. An asymptotic determination of minimum centromere size for the maize B chromosome. Cytogenetic and Genome Research 2004;106(2-4):309-313.
Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, Birchler JA and Elgin SCR. Heterochromatic silencing and HP1 localization in drosophila are dependent on the RNAi machinery. Science 2004;303(5658):669-672.
Lamb JC, Theuri J and Birchler JA. What's in a centromere? Genome Biology 2004;5(9):
Kato A, Lamb JC and Birchler JA. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proceedings of the National Academy of Sciences of the United States of America 2004;101(37):13554-13559.
Birchler JA and Newton KJ. Discovering the seeds of diversity in plant genomes. Genome Biology 2004;5(5):
Birchler JA, Kavi HH and Fernandez HR. Heterochromatin: RNA points the way. Current Biology 2004;14(18):
Auger DL, Ream TS and Birchler JA. A test for a metastable epigenetic component of heterosis using haploid induction in maize. Theoretical and Applied Genetics 2004;108(6):1017-1023.
Riddle NC and Birchler JA. Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends in Genetics 2003;19(11):597-600.
Osborn TC, Chris Pires J, Birchler JA, Auger DL, Chen ZJ, Lee HS, Comai L, Madlung A, Doerge RW, Colot V and Martienssen RA. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 2003;19(3):141-147.
Lamb JC and Birchler JA. The role of DNA sequence in centromere formation. Genome Biology 2003;4(5):
Jiang J, Birchler JA, Parrott WA and Dawe RK. A molecular view of plant centromeres. Trends in Plant Science 2003;8(12):570-575.
Birchler JA, Pal-Bhadra M and Bhadra U. Dosage dependent gene regulation and the compensation of the X chromosome in Drosophila males. Genetica 2003;117(2-3):179-190.
Birchler JA, Kelly Dawe R and Doebley JF. Marcus Rhoades, preferential segregation and meiotic drive. Genetics 2003;164(3):835-841.
Birchler JA, Auger DL and Riddle NC. In search of the molecular basis of heterosis. Plant Cell 2003;15(10):2236-2239.
Xiaoyan Zhong C, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J and Dawe RK. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 2002;14(11):2825-2836.
Pal-Bhadra M, Bhadra U and Birchler JA. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Molecular Cell 2002;9(2):315-327.
Kaszas E, Kato A and Birchler JA. Cytological and molecular analysis of centromere misdivision in maize. Genome 2002;45(4):759-768.
Auger DL and Birchler JA. Maize tertiary trisomic stocks derived from B-A translocations. Journal of Heredity 2002;93(1):42-47.
Page BT, Wanous MK and Birchler JA. Characterization of a maize chromosome 4 centromeric sequence: Evidence for an evolutionary relationship with the B chromosome centromere. Genetics 2001;159(1):291-302.
Frolov MV, Benevolenskaya EV and Birchler JA. Molecular analysis of a novel Drosophila diacylglycerol kinase, DGKŒµ. Biochimica et Biophysica Acta - Molecular Cell Research 2001;1538(2-3):339-352.
Cooper JL and Birchler JA. Developmental impact on trans-acting dosage effects in maize aneuploids. Genesis 2001;31(2):64-71.
Birchler JA, Bhadra U, Bhadra MP and Auger DL. Dosage-dependent gene regulation in multicellular eukaryotes: Implications for dosage compensation, aneuploid syndromes, and quantitative traits. Developmental Biology 2001;234(2):275-288.
Auger DL, Newton KJ and Birchler JA. Nuclear gene dosage effects upon the expression of maize mitochondrial genes. Genetics 2001;157(4):1711-1721.
Frolov MV, Benevolenskaya EV and Birchler JA. The oxen gene of drosophila encodes a homolog of subunit 9 of yeast ubiquinol-cytochrome c oxidoreductase complex: Evidence for modulation of gene expression in response to mitochondrial activity. Genetics 2000;156(4):1727-1736.
Birchler JA, Pal Bhadra M and Bhadra U. Making noise about silence: Repression of repeated genes in animals. Current Opinion in Genetics and Development 2000;10(2):211-216.
Bhadra U, Pal-Bhadra M and Birchler JA. Histone acetylation and gene expression analysis of Sex lethal mutants in drosophila. Genetics 2000;155(2):753-763.
Benevolenskaya EV, Frolov MV and Birchler JA. Kruppel homolog (Kr h) is a dosage-dependent modifier of gene expression in Drosophila. Genetical Research 2000;75(2):137-142.