Axel A. Elling

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

This work examines the molecular basis of heterosis by comprehensively describing the epigenetic modifications and transcriptional output, including both mRNA and small RNAs, of two rice subspecies and their reciprocal hybrids. The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.Epigenetic modifications and small RNAs play an important role in gene regulation. Here, we discuss results of our Solexa/Illumina 1G sequencing-based survey of DNA methylation, activating and repressive histone modifications, small RNAs and mRNA in the maize genome. We analyze tissue-specific epigenetic patterns, discuss antagonistic relationships between repressive epigenetic marks and highlight synergistic relationships between activating histone modifications. We discuss our observation that small RNAs show a tissue-specific distribution in maize. Whereas 24-nucleotide long small interfering RNAs (siRNAs) accumulated preferentially in shoots, 21-nucleotide long micro RNAs (miRNAs) were the most abundant group in roots, which follows the transcript level of mop1. Furthermore, we discuss the possibility that a novel class of 22-nucleotide siRNAs might originate from long double-stranded RNAs in an RNA-dependent RNA polymerase (RdRP)-independent manner. This supports the intriguing possibility that maize possesses at least two distinct pathways to generate siRNAs, one of which relies on RdRP and a second one that might be RdRP-independent.

Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis

Although landscapes of several histone marks are now available for Arabidopsis thaliana and Oryza sativa, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here, we analyzed the effects of light on four histone modifications (acetylation and trimethylation of lysines 9 and 27 on histone H3: H3K9ac, H3K9me3, H3K27ac, and H3K27me3, respectively). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are nontransposable element gene-specific. By contrast, we found that H3K9me3 and H3K27me3 target nontransposable element genes, but also intergenic regions and transposable elements. Specific light conditions affected the number of modified regions as well as the overall correlation strength between the presence of specific modifications and transcription. Furthermore, we observed that acetylation marks not only ELONGATED HYPOCOTYL5 and HY5-HOMOLOG upon deetiolation, but also their downstream targets. We found that the activation of photosynthetic genes correlates with dynamic acetylation changes in response to light, while H3K27ac and H3K27me3 potentially contribute to light regulation of the gibberellin metabolism. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plants changing light environment and strengthens the concept that histone modifications represent an additional layer of control for light-regulated genes involved in photomorphogenesis.

Nematode effector proteins: an emerging paradigm of parasitism

Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda.

The Epigenome and Plant Development

The epigenomic regulation of chromatin structure and genome stability is essential for the interpretation of genetic information and ultimately the determination of phenotype. High-resolution maps of plant epigenomes have been obtained through a combination of chromatin technologies and genomic tiling microarrays and through high-throughput sequencing-based approaches. The transcriptomic activity of a plant at a certain stage of development is controlled by genome-wide combinatorial interactions of epigenetic modifications. Tissue- or environment-specific epigenomes are established during plant development. Epigenomic reprogramming triggered by the activation and movement of small RNAs is important for plant gametogenesis. Genome-wide loss of DNA methylation in the endosperm and the accompanying endosperm-specific gene expression during seed development provide a genomic insight into epigenetic regulation of gene imprinting in plants. Global changes of histone modifications during plant responses to different light environments play an important regulatory role in a sophisticated light-regulated transcriptional network. Epigenomic natural variation that developed during evolution is important for phenotypic diversity and can potentially contribute to the molecular mechanisms of complex biological phenomena such as heterosis in plants.

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression.

Lysine residue 9 of histone H3 can either be acetylated or mono-, di-, or tri-methylated. These epigenetic states have a diverse impact on regulating gene transcriptional activity and chromatin organization. H3K9ac is invariably correlated with transcriptional activation, whereas H3K9me2 has been reported to be mainly located in constitutive heterochromatin in Arabidopsis. Here, we present epigenetic landscapes for histone H3 lysine 9 acetylation (H3K9ac) and dimethylation (H3K9me2) in Arabidopsis seedlings. The results show that H3K9ac targeted 5,206 non-transposable element (non-TE) genes and 321 transposable elements (TEs), whereas H3K9me2 targeted 2,281 TEs and 1,112 non-TE genes. H3K9ac was biased towards the 5′ end of genes and peaked at the ATG position, while H3K9me2 tended to span the entire gene body. H3K9ac correlated with high gene expression, while H3K9me2 correlated with low expression. Analyses of H3K9ac and H3K9me2 with the available datasets of H3K27me3 and DNA methylation revealed a correlation between the occurrence of multiple epigenetic modifications and gene expression. Genes with H3K9ac alone were actively transcribed, while genes that were also modified by either H3K27me3 or DNA methylation showed a lower expression level, suggesting that a combination of repressive marks weakened the positive regulatory effect of H3K9ac. Furthermore, we observed a significant increase of the H3K9ac modification level of selected target genes in hda19 (histone deacetylase 19) mutant seedlings, which indicated that HDA19 plays an important role in regulating the level of H3K9ac and thereby influencing the transcriptional activity in young seedlings.

Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions

Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.

GmEREBP1 Is a Transcription Factor Activating Defense Genes in Soybean and Arabidopsis

Ethylene-responsive element-binding proteins (EREBPs) are plant-specific transcription factors, many of which have been linked to plant defense responses. Conserved EREBP domains bind to the GCC box, a promoter element found in pathogenesis-related (PR) genes. We previously identified an EREBP gene from soybean (GmEREBP1) whose transcript abundance decreased in soybean cyst-nematode-infected roots of a susceptible cultivar, whereas it increased in abundance in infected roots of a resistant cultivar. Here, we report further characterization of this gene. Transient expression analyses showed that GmEREBP1 is localized to the plant nucleus and functions as a transcriptional activator in soybean leaves. Transgenic soybean plants expressing GmEREBP1 activated the expression of the ethylene (ET)-responsive gene PR2 and the ET- and jasmonic acid (JA)-responsive gene PR3, and the salicylic acid (SA)-responsive gene PR1 but not the SA-responsive PR5. Similarly, transgenic Arabidopsis plants expressing GmEREBP1 showed elevated mRNA abundance of the ET-regulated gene PR3 and the ET- and JA-regulated defense-related gene PDF1.2 but not the ET-regulated GST2, and the SA-regulated gene PR1 but not the SA-regulated PR2 and PR5. Transgenic soybean and Arabidopsis plants inoculated with cyst nematodes did not display a significantly altered susceptibility to nematode infection. These results collectively show that GmEREBP1 functions as a transacting inducer of defense gene expression in both soybean and Arabidopsis and mediates the expression of both ET- and JA- and SA-regulated defense-related genes in these plant species.

Sequence mining and transcript profiling to explore cyst nematode parasitism

BackgroundCyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants.ResultsWe present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean Genome Array GeneChip, which contains probeset sequences for 6,860 genes derived from preparasitic and parasitic H. glycines life stages. Targeting the identification of additional H. glycines parasitism-associated genes, we isolated 633 genes encoding secretory proteins using algorithms to predict secretory signal peptides. Furthermore, because some of the known H. glycines parasitism proteins have strongest similarity to proteins of plants and microbes, we searched for predicted protein sequences that showed their highest similarities to plant or microbial proteins and identified 156 H. glycines genes, some of which also contained a signal peptide. Analyses of the expression profiles of these genes allowed the formulation of hypotheses about potential roles in parasitism. This is the first study combining sequence analyses of a substantial EST dataset with microarray expression data of all major life stages (except adult males) for the identification and characterization of putative parasitism-associated proteins in any parasitic nematode.ConclusionWe have established an expression atlas for all known H. glycines parasitism genes. Furthermore, in an effort to identify additional H. glycines genes with putative functions in parasitism, we have reduced the currently known 6,860 H. glycines genes to a pool of 788 most promising candidate genes (including known parasitism genes) and documented their expression profiles. Using our approach to pre-select genes likely involved in parasitism now allows detailed functional analyses in a manner not feasible for larger numbers of genes. The generation of the candidate pool described here is an important enabling advance because it will significantly facilitate the unraveling of fascinating plant-animal interactions and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the exploration of true parasitism genes verified from the gene pool delineated here will identify weaknesses in the nematode life cycle that can be exploited by novel anti-nematode efforts.

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

BackgroundThe soybean cyst nematode Heterodera glycines is the most important parasite in soybean production worldwide. A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date.ResultsWe report an extensive genomic analysis of H. glycines, beginning with the generation of 20,100 expressed sequence tags (ESTs). In-depth analysis of these ESTs plus approximately 1,900 previously published sequences predicted 6,860 unique H. glycines genes and allowed a classification by function using InterProScan. Expression profiling of all 6,860 genes throughout the H. glycines life cycle was undertaken using the Affymetrix Soybean Genome Array GeneChip. Our data sets and results represent a comprehensive resource for molecular studies of H. glycines. Demonstrating the power of this resource, we were able to address whether arrested development in the Caenorhabditis elegans dauer larva and the H. glycines infective second-stage juvenile (J2) exhibits shared gene expression profiles. We determined that the gene expression profiles associated with the C. elegans dauer pathway are not uniformly conserved in H. glycines and that the expression profiles of genes for metabolic enzymes of C. elegans dauer larvae and H. glycines infective J2 are dissimilar.ConclusionOur results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species.