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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. We have also found that there are extensive insertions of mitochondrial DNA into the nucleus and we are studying the nature and basis of this phenomenon. It is now possible to visualize individual copies of transposable elements such as Activator, Suppressor-mutator and RescueMu on the maize chromosomes.
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 in the endosperm and as a means to introduce novel biochemical pathways to maize to confer new properties to the plant. From a basic standpoint, artificial constructs will allow investigators to produce designer chromosomes that will help them understand the minimum features required for function.
Selected publications
James A. Birchler, Zhi Gao and Fangpu Han, 2009. A tale of two centromeres—diversity of structure but conservation of function in plants and animals. Functional and Integrative Genomics 9: 7-13.
Jianbo Zhang, Chuanhe Yu, Vinay Pulletikurti, Jonathan Lamb, Tatiana Danilova, David F. Weber, James A. Birchler and Thomas Peterson, 2009. Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize. Genes and Development 23: 755-765.
Tatiana V. Danilova and James A. Birchler, 2008. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity and banding paint development. Chromosoma 117: 345-356.
Weichang Yu, Fangpu Han, Zhi Gao, Juan M. Vega and James A. Birchler, 2007. Construction and behavior of engineered minichromosomes in maize. Proc. Natl. Acad. Sci., USA 104: 8924-8929.
Birchler, J.A. and Reiner, R.A. 2007. The gene balance hypothesis: From classical genetics to modern genomics. The Plant Cell 19: 395-402.
Selected national/international awards and honors
Elected Fellow - AAAS
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University of Missouri-Columbia
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