Studies on genome structure, homologous meiotic recombination, and functional genomics in maize. The Dooner lab has observed that rather than adhering to a rigid plan, the genomes of many organisms, like maize and humans, comprise mobile, gene-coding DNA elements. Dr. Dooner sees these as small islands of gene-coding regions in a vast sea of highly repeated sequences. In maize, these "islands" shift positions along or between chromosomes, yet remain intact and functional in the process. With chromosomal exchanges limited to the sequences between gene-coding regions, genes remain unscathed in different neighborhoods. The result is functional genes in multiple neighborhoods, concluding that this picture is one of a protective evolutionary adaptation.
Transposons Transposons are the main consitutents of the maize genome. We study their structures and interactions and use them as genetic tools to elucidate the function of genes. We have identified several new genetically active transposons, including Jittery, Mx, and TED, which are new autonomous members of the Mutator and hAT superfamilies. Maize appears to have several noninteracting elements in each superfamily, suggesting that new transposon specificities have arisen frequently. In our functional genomics project, we have generated an Ac insertion library which yielded many new interesting phenotypes, such as defective pollen grains with corkscrew pollen tube and seedings unable to produce volatile chemicals to defend themselves against insects. We are currently optimizing the use of Ac-Ds transposons as gene-searching engines in maize. We are developing a set of transgenic lines carrying a uniquely marked Ds element which should integrate at multiple locations in the genome and greatly facilitate the isolation of the interrupted gene and generating thousands of sequence-indexed single gene knockouts for use by the maize community.
Genome variability Maize is the most variable plant species known. This variability manifests itself at all levels, ranging from variations in plant shape to polymorphisms in restriction enzyme sites. We recently discovered that allelic regions of the genome can vary by as much as 70% of their DNA, including the presence or absence of certain genes. This finding may help to explain the phenomena of hybrid vigor and inbreeding depression. We are presently characterizing two specific regions in the genome of different inbreds, land races, and wild relatives of maize in order to further document the extent of this variability.
Homologous recombination We have previously found that meitoic recombination in maize is restricted to genes, which comprise only 5% or less of the genome. We continue to use the bronze locus of maize, a uniquely advantageous system, to attempt to obtain answers to basic questions regarding the process of homologous meiotic recombination in plants. A main question that we are addressing is the effect of sequence diversity on the outcome of recombination events in maize. Most recombination events between pairs of highly polymorphic maize alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover (NCO) gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. We have recently found that NCO gene conversion at the bz locus exhibits a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene.
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Polarized gene conversion at the bz locus of maize.
Dooner, HK, He L. 2014. Polarized gene conversion at the bz locus of maize.. Proc Natl Acad Sci USA. 111(38):13918-23.
Nucleotide diversity is greater in maize than in most organisms studied to date, so allelic pairs in a hybrid tend to be highly polymorphic. Most recombination events between such pairs of maize polymorphic alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. To investigate whether gene conversion at the bz locus is polarized, two large diallel crossing matrices involving mutant sites spread across the bz gene were performed and more than 2,500 intragenic recombinants were scored. In both diallels, around 90% of recombinants could be accounted for by gene conversion. Furthermore, conversion exhibited a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene. The implications of these findings are discussed with reference to recent data from genome-wide studies in other plants.
Variation in allelic expression associated with a recombination hotspot in Zea mays.
Hawkins, JS, Delgado V, Feng L, Carlise M, Dooner HK, Bennetzen JL. 2014. Variation in allelic expression associated with a recombination hotspot in Zea mays. The Plant Journal, DOI: 10.1111/tpj.12537.
Gene expression is a complex process, requiring precise spatial and temporal regulation of transcription factor activity; however, modifications of individual cis- and trans-acting modules can be molded by natural selection to create a sizeable number of novel phenotypes. Results from decades of research indicate that developmental and phenotypic divergence among eukaryotic organisms is driven primarily by variation in levels of gene expression that are dictated by mutations either in structural or regulatory regions of genes. The relative contributions and interplay of cis- and trans-acting regulatory factors to this evolutionary process, however, remain poorly understood. Analysis of 8 genes in the Bz1-Sh1 interval of maize indicates significant allele-specific expression biases in at least one tissue for all genes, ranging from 1.3-fold to 36-fold. All detected effects were cis-regulatory in nature, although genetic background may also influence the level of expression bias and tissue specificity for some allelic combinations. Most allelic pairs exhibited the same direction and approximate intensity of bias across all four tissues; however, a subset of allelic pairs show alternating dominance across different tissue types or variation in the degree of bias in different tissues. In addition, the genes showing the most striking levels of allelic bias co-localize with a previously described recombination hotspot in this region, suggesting a naturally occurring genetic mechanism for creating regulatory variability for a subset of plant genes that may ultimately lead to evolutionary diversification.
Helitron Scanner uncovers a large overlooked cache of Helitron transposons in many genomes.
Xiong, W, He L, Lai J, Dooner HK, Du C. 2014. Helitron Scanner uncovers a large overlooked cache of Helitron transposons in many genomes. Proc. Natl. Acad. Sci. USA. DOI 10.1073/pnas.1410068111
Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner’s predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5’ and 3’ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by polymerase chain reaction (PCR) assays or by in-silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.
TED, an autonomous and rare maize transposon of the mutator superfamily with a high gametophytic excision frequency.
Li, Y, Harris L, Dooner HK. 2013. TED, an autonomous and rare maize transposon of the mutator superfamily with a high gametophytic excision frequency. The Plant cell. 25(9):3251-65.
Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.
InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data.
Xiong, W, He L, Li Y, Dooner HK, Du C. 2013. InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. BMC genomics. 14:679.
The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of samples. These regions can be amplified by PCR and sequenced by next-generation methods using a multidimensional pooling strategy. However, there is at present no available generalized tool for the computational analysis of target-enriched NGS data from multidimensional pools.
Gene tagging with engineered Ds elements in maize.
Li, Y., Segal, G., Wang, Q., Dooner HK. 2013. Gene tagging with engineered Ds elements in maize. Methods in Molecular Biology: Plant Transposable Elements. :83-99.
Transposons and gene creation.
Dooner, HK, Weil CF. 2013. Transposons and gene creation. Molecular Genetics and Epigenetics of Plant Transposons. :143-167.
Hugo K. Dooner, Distinguished Professor Emeritus of the Waksman Institute of Microbiology and Plant Biology Department at Rutgers. He was elected to the National Academy of Sciences in 2007 for his studies on the contribution of transposable elements and recombination to the genetic diversity of maize. He discovered extreme haplotype variation among inbred maize lines and developed heterologous transposon tagging to isolate genes of agricultural importance. His lab studies transposon architecture and interactions to elucidate gene function and to create a more efficient resource for reverse genetics. Dr. Dooner is known primarily for his research into the genetics of maize (corn) that has demonstrated the adaptability of its genome and its propensity for reorganizing the mobile DNA elements that carry the genes.
Former Research Faculty
- Yubin Li
Former Research Associates
- Qinghua Wang
- Mithu Chatterjee
Former Lab Researchers
- Limei Du (He)
- Harrison Wang