Célia Baroux1*, Daphné Autran2 Michael T. Raissig1, Daniel Grimanelli2 and Ueli Grossniklaus1 – Biography
1Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Switzerland
2Institut de Recherche pour le Développement, UMR232; CNRS, ERL5300; Université de Montpellier II, France
In plants and animals, embryo development becomes ultimately controlled by zygotic genes, but the timing of zygotic genome activation (ZGA) varies greatly between organisms[1,2]. We recently showed that the transcriptome of young Arabidopsis embryos is dominated by maternal transcripts with a progressive ZGA under the maternal control of epigenetic pathways . In contrast, another study reported that both parental genomes contribute equally to the transcriptome of young embryos, suggesting that ZGA occurs immediately after fertilization. How to explain such dramatic differences? We propose that the discrepancies between these two studies likely reflect genuine biological differences between the two experiments, paving the road towards exciting discoveries on ZGA mechanisms in plants.
In animals, early stages of embryo development are associated with extensive epigenetic reprogramming to coordinate zygotic genome activation (ZGA) . ZGA is typically delayed, although to a varying extent depending on the species, with a gradual loss of the maternal dominance and increase of zygotic influence [1,2]. In flowering plants, maternal effects on seed development have been recognized, yet are difficult to investigate because of the intricate relationships between the embryo, the embryo-nourishing endosperm, and the maternal seed coat . To understand the interaction of parental genomes following fertilization, allele-specific assays were used to distinguish paternal and maternal contributions for selected loci or at the genome-wide level in dissected embryos (reviewed in ), with surprisingly different results. Yet, the diversity of species (Arabidopsis, maize, tobacco) and developmental stages analyzed made it difficult to draw general conclusions. In fact, the observed differences may reflect yet undiscovered biological factors controlling ZGA in flowering plants.
We have previously shown that the transcriptome of Arabidopsis embryos derived from crosses between the accessions Landsberg erecta (Ler) and Columbia (Col) is largely dominated by maternal reads (88%) at early stages (2-4 cells). Despite this maternal dominance, 66% of the genes have transcripts from both parental alleles, consistent with the fact that many embryo lethal mutations with preglobular developmental phenotypes are zygotically recessive . Transcriptome analyses at the globular stage, in conjunction with expression analyses of seven reporter gene loci, confirmed a gradual increase of paternal transcripts during embryogenesis, reflecting progressive ZGA. We also demonstrated that paternal loci are epigenetically regulated by two antagonistic maternal pathways: a siRNA-based mechanism involving genes of the RNA-dependent DNA methylation (RdDM) pathway restricts expression of paternal alleles, while their activation relies on a nucleosome-remodeling pathway. As a result, kyp/KYP embryos derived from mothers lacking the activity of the histone methyltransferase KRYPTONITE (KYP), show both a higher proportion of paternal reads (34% vs 12% in the wild type) and a gene distribution that is skewed towards higher paternal contributions (based on a statistical best-fit model).In contrast, a recent study using Arabidopsis embryos derived from crosses between the accessions Cape Verde Island (Cvi) and Col, showed a transcriptome with an equal contribution of paternal and maternal transcripts. To explain this discrepancy, the authors suggested that transcripts derived from the maternal seed coat might have contaminated our embryo samples. However, this hypothesis does not explain the following observations: First, our genetic results on the regulation of parental contributions obtained in profiling studiesand by reporter gene analyses; second, other studies analyzing expression of specific loci or reporter genes (reviewed in ); and third, the observation that 1003 embryo-expressed genes, which were not detected in a seed coat transcriptome, are covered by 84% maternal reads (Raissig, Baroux, Lenormand, Wittig, Rosenstiel, Grossniklaus, unpublished). So are there possible biological explanations that have not been explored? We believe that there are several exciting hypotheses worth investigating before closing the debate on ZGA, for the benefit of the scientific endeavor.
In fact, the two experiments do not only differ in the way the embryos were isolated (discussed elsewhere) but in at least two other respects (Figure 1): First, different hybrid combinations, Ler x Col  and Cvi x Col  were used. Cvi is being known for its singular epigenetic configuration involving atypical DNA methylation and transposon insertion patterns as well as structural heterochromatin phenotypes reminiscent of a dominant-negative effect on RdDM control . In this respect, the results reported by Nodine and Bartel would be clearly consistent with our former conclusion that embryos maternally deficient in RdDM components show a precocious bi-allelic expression of many genes. Alternatively, the diverging genetic relatedness of Cvi with Col and Ler may influence parental contributions in hybrid embryos, consistent with our proposition that the maternal control of paternal expression is expected to become weaker with increasing genetic distance . Second, while we profiled mRNAs irrespective of their polyadenylation status, the other study specifically analyzed polyadenylated mRNAs. In animals, cytoplasmic poly(A)-elongation is prevalent as a mechanism for the regulation of maternal mRNAs during early development . Although data with respect to polyadenylation of plant mRNAs is scarce, it is possible that different mRNAs subpopulations were studied in the two experiments. Given that alternative polyadenylation during development is highly dynamic in plants, that Arabidopsis has a cytoplasmic polyadenylase, and that maternal mRNAs populations with short poly(A)-tails have been reported in maize and rice [9,10, 11] this seems a plausible scenario. Polyadenylated mRNA might represent a distinctive fraction of the embryonic pool of mRNA possibly under-representing maternally provided transcripts. Given these possible biological differences, future investigations on the mechanisms and natural variation in plant zygotic genome activation promise to shed new light onto this essential phase of the plant life cycle, which has consequences for many basic and applied aspects of plant biology.
Figure 1. Different readouts of parental contributions to the embryo transcriptome may reflect genuine biological differences. The parental contribution to the Arabidopsis embryo transcriptome were determined by RNA-Seq (pie charts; white: maternal sequence reads, grey: paternal sequence reads). Differences in the biological materials used in the two studies may explain the different readouts. First, different maternal genotypes were used, with either wild-type Ler (a)  or Cvi (c) , the latter showing a well-characterized difference in heterochromatin formation (nuclei insets), largely due to a dominant effect conveyed by the HDA6 locus, affecting chromatin organization and gene silencing .Second, different mRNA populations were sampled with respect to their polyadenylation status (black line with head: mRNA with a long poly(A) tail; black line without head: mRNA with no or a short poly(A) tail). Interestingly, the higher paternal contribution in Cvi/Col embryos (c) is partially mimicked in Ler/Col embryos maternally deficient in the histone H3K9-methyltransferase KYP (b),a component of the siRNA pathway regulating parental contributions 
Image sources (upper panel): seedlings  nuclei insets [7, 13] .
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- Autran D, Baroux C, Raissig MT, Lenormand T, Wittig M, Grob S, Steimer A, Barann M, Klostermeier UC, Leblanc O, et al.: Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 2011, 145:707-719.
- Nodine MD, Bartel DP: Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 2012.
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- Raissig MT, Gagliardini V, Jaenisch J, Grossniklaus U, Baroux C: Efficient and rapid isolation of early-stage embryos from Arabidopsis thaliana seeds. Journal of Vizualised Experiments 2012, in press.
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- Grimanelli D, Perotti E, Ramirez J, Leblanc O: Timing of the maternal-to-zygotic transition during early seed development in maize. Plant Cell 2005, 17:1061-1072.
- Shen Y, Venu RC, Nobuta K, Wu X, Notibala V, Demirci C, Meyers BC, Wang GL, Ji G, Li QQ: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res 2011, 21:1478-1486.
- Luo, M., Taylor, J. M., Spriggs, A., Zhang, H., Wu, X., Russell, S., Singh, M. and Koltunow, A. (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm, PLoS Genet 7(6): e1002125.
- Norman Jaimie M. Van, Benfey Philip N.. Arabidopsis thaliana as a model organism in systems biology. WIREs Syst Biol Med 2009, 1: 372-379.
- Fischer, A.; Hofmann, I.; Naumann, K.; Reuter, G. (2006) Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis. Journal of Plant Physiology, 163, Issue 3, February 2006, Pages 358-368
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