The Messing lab would like to contribute to the understanding of the expression of regulation of gene copies in plants. It is now apparent that many gene products are derived from multiple gene copies. As use of copies rapidly increases, their sequences are quite conserved or so similar that it becomes difficult to infer gene products from which the genes they produce. Therefore, it becomes necessary to sequence the genome of an organism so that one can sort gene copies in their location on chromosomes. Then one can match each RNA species quantitatively with individual gene copies.
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An important aspect of gene expression is DNA modification and chromatin structure. Maize seems to be in particular suited for this purpose because the portion of the genome representing active genes is rather small. The maize genome has an even higher percentage of repeat elements than the human genome, 85% versus 50%. Therefore, detection of such epigenetic marks in maize had to be highly enriched for a fraction of the genome. Indeed, this specific histone acetylation correlated well with transcribed genes and could be verified with many known examples of genetic loci.
Transcriptional analysis of seed development has shown that many of them are not expressed despite a normal gene structure. That has prompted us to investigate how epigenetic silencing could play a role in repressing gene expression. We applied bisulfite DNA sequencing, which can detect the methylation of DNA sequences. The methylation pattern of specific gene clusters can then be related to the transcriptional activity of them during seed development. There were several findings:
- Genes have a higher degree of methylation in non-expressing tissues, which is consistent with the observation that active genes are hypomethylated.
- The difference in methylation, however, can differ between chromosomal locations.
- Culturing endosperm, which keeps cells dividing, not only reduces DNA methylation, but also can lead to transcription of genes that were previously inactive
Dr. Joachim Messing
Joachim (Jo) Messing is the Research Director of the Waksman Institute of Microbiology and the Selman A. Waksman University Professor of Molecular Genetics at Rutgers University. Dr. Messing developed tools that helped lay the foundations of the biotechnology and genomics revolutions. He developed the first vectors for blue-white screening, single-stranded- DNA production, and universal-primer-based sequencing. He invented shotgun sequencing, developed the first programs for shotgun sequencing, and reported the first genome shotgun sequence (cauliflower mosaic virus).
Dr. Messing's 1980s-1990s work focused on the sequencing and engineering of maize storage proteins. More recently, his laboratory has used RNA interference to study the role of these proteins in seed development and molecular breeding. One of the new initiatives of his laboratory investigates the potential of sweet sorghum and duckweed as alternative bio-energy sources.
Dr. Jiaqiang Dong
Dr. Zhiyong Zhang