Dr. Hugo K. Dooner

Dr. Hugo K. Dooner is a Distinguished Professor in the Plant Biology Department at Rutgers and a Principal Investigator in the Waksman Institute.  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.

Research Summary
His lab performs studies on genome structure, homologous meiotic recombination, and functional genomics in maize.  They have observed that rather than adhering to a rigid plan, the genomes of many organisms, like maize and humans, comprise mobile, gene-coding DNA elements. 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.

Research in the Dooner Lab Focuses on Three Main Areas:

1. 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.

2. 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.

3. 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.

Recent Publications

Xiong, W, He L, Lai J, Dooner HK, Du C.  2014.  HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes.. Proc. Natl. Acad. Sci. USA. DOI 10.1073/pnas.1410068111 AbstractWebsite
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.
He, L., Dooner HK.  2009.  Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc. Natl. Acad. Sci. U.S.A.. 106:8410–8416. Abstract
We have asked here how the remarkable variation in maize haplotype structure affects recombination. We compared recombination across a genetic interval of 9S in 2 highly dissimilar heterozygotes that shared 1 parent. The genetic interval in the common haplotype is approximately 100 kb long and contains 6 genes interspersed with gene-fragment-bearing Helitrons and retrotransposons that, together, comprise 70% of its length. In one heterozygote, most intergenic insertions are homozygous, although polymorphic, enabling us to determine whether any recombination junctions fall within them. In the other, most intergenic insertions are hemizygous and, thus, incapable of homologous recombination. Our analysis of the frequency and distribution of recombination in the interval revealed that: (i) Most junctions were circumscribed to the gene space, where they showed a highly nonuniform distribution. In both heterozygotes, more than half of the junctions fell in the stc1 gene, making it a clear recombination hotspot in the region. However, the genetic size of stc1 was 2-fold lower when flanked by a hemizygous 25-kb retrotransposon cluster. (ii) No junctions fell in the hypro1 gene in either heterozygote, making it a genic recombination coldspot. (iii) No recombination occurred within the gene fragments borne on Helitrons nor within retrotransposons, so neither insertion class contributes to the interval's genetic length. (iv) Unexpectedly, several junctions fell in an intergenic region not shared by all 3 haplotypes. (v) In general, the ability of a sequence to recombine correlated inversely with its methylation status. Our results show that haplotypic structural variability strongly affects the frequency and distribution of recombination events in maize.
Li, Y., Dooner HK.  2009.  Excision of Helitron transposons in maize. Genetics. 182:399–402. Abstract
Helitrons are novel transposons discovered by bioinformatic analysis of eukaryotic genome sequences. They are believed to move by rolling circle (RC) replication because their predicted transposases are homologous to those of bacterial RC transposons. We report here evidence of somatic Helitron excision in maize, an unexpected finding suggesting that Helitrons can exhibit an excisive mode of transposition.
Du, C., Fefelova, N., Caronna, J., He, L., Dooner HK.  2009.  The polychromatic Helitron landscape of the maize genome. Proc. Natl. Acad. Sci. U.S.A.. 106:19916–19921. Abstract
150 copies of a transposon-like sequence, termed Heltir, that has terminal inverted repeats resembling Helitron 3' termini. Nonautonomous Helitrons make up at least 2% of the maize genome and most of those tested show +/- polymorphisms among modern inbred lines.