Bio


Michael earned his PhD in the lab of Ueli Grossniklaus at the University of Zurich studying the epigenetic phenomenon of genomic imprinting during Arabidopsis seed development. During his PhD, Michael acquired a solid background in plant genetics, epigenetics and molecular biology. Since 2014, he is a SNSF- and LSRF-sponsored postdoctoral fellow in the lab of Dominique Bergmann at Stanford University. At Stanford, he studies how developmental innovations affect form and function of grass stomata, which are tiny pores through which plants “breathe” and exchange gases with the environment. He is applying developmental genetics and cell biology approaches in the wheat relative and grass model Brachypodium distachyon.

Honors & Awards


  • LSRF Postdoctoral fellowship, Life Science Research Foundation and Gordon and Betty Moore Foundation (2015-2018)
  • Early.Postdoc Mobility Fellowship, Swiss National Science Foundation (2014-2015)

Professional Education


  • Doctor of Philosophy, Universitat Zurich (2013)
  • Master of Science, Universitat Zurich (2007)
  • Bachelor of Science, Universitat Zurich (2005)

Stanford Advisors


Community and International Work


  • Organizer of weekly Round Table Seminar at Carnegie Institute for Science

    Ongoing Project

    No

    Opportunities for Student Involvement

    No

  • Co-Organizer of Stanford’s Biology Department Postdoc Symposium

    Ongoing Project

    No

    Opportunities for Student Involvement

    No

All Publications


  • Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity. Proceedings of the National Academy of Sciences of the United States of America Raissig, M. T., Abrash, E., Bettadapur, A., Vogel, J. P., Bergmann, D. C. 2016; 113 (29): 8326-8331

    Abstract

    Stomata, epidermal valves facilitating plant-atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix-loop-helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot's developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity.

    View details for DOI 10.1073/pnas.1606728113

    View details for PubMedID 27382177

  • Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2 PLOS GENETICS Raissig, M. T., Bemer, M., Baroux, C., Grossniklaus, U. 2013; 9 (12)

    Abstract

    Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner and is regulated by the differential epigenetic marking of the parental alleles. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a tissue nourishing the developing embryo that does not contribute to the next generation. In Arabidopsis, the genes MEDEA (MEA) and PHERES1 (PHE1), which are imprinted in the endosperm, are also expressed in the embryo; whether their embryonic expression is regulated by imprinting or not, however, remains controversial. In contrast, the maternally expressed in embryo 1 (mee1) gene of maize is clearly imprinted in the embryo. We identified several imprinted candidate genes in an allele-specific transcriptome of hybrid Arabidopsis embryos and confirmed parent-of-origin-dependent, monoallelic expression for eleven maternally expressed genes (MEGs) and one paternally expressed gene (PEG) in the embryo, using allele-specific expression analyses and reporter gene assays. Genetic studies indicate that the Polycomb Repressive Complex 2 (PRC2) but not the DNA METHYLTRANSFERASE1 (MET1) is involved in regulating imprinted expression in the embryo. In the seedling, all embryonic MEGs and the PEG are expressed from both parents, suggesting that the imprint is erased during late embryogenesis or early vegetative development. Our finding that several genes are regulated by genomic imprinting in the Arabidopsis embryo clearly demonstrates that this epigenetic phenomenon is not a unique feature of the endosperm in both monocots and dicots.

    View details for DOI 10.1371/journal.pgen.1003862

    View details for Web of Science ID 000330533300001

    View details for PubMedID 24339783

  • Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus GENES & DEVELOPMENT Woehrmann, H. J., Gagliardini, V., Raissig, M. T., Wehrle, W., Arand, J., Schmidt, A., Tierling, S., Page, D. R., Schoeb, H., Walter, J., Grossniklaus, U. 2012; 26 (16): 1837-1850

    Abstract

    Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus.

    View details for DOI 10.1101/gad.195123.112

    View details for Web of Science ID 000307884700007

    View details for PubMedID 22855791

  • SNP-Ratio Mapping (SRM): Identifying Lethal Alleles and Mutations in Complex Genetic Backgrounds by Next-Generation Sequencing GENETICS Lindner, H., Raissig, M. T., Sailer, C., Shimosato-Asano, H., Bruggmann, R., Grossniklaus, U. 2012; 191 (4): 1381-U476

    Abstract

    We present a generally applicable method allowing rapid identification of causal alleles in mutagenized genomes by next-generation sequencing. Currently used approaches rely on recovering homozygotes or extensive backcrossing. In contrast, SNP-ratio mapping allows rapid cloning of lethal and/or poorly transmitted mutations and second-site modifiers, which are often in complex genetic/transgenic backgrounds.

    View details for DOI 10.1534/genetics.112.141341

    View details for Web of Science ID 000309000500026

    View details for PubMedID 22649081

  • Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis CELL Autran, D., Baroux, C., Raissig, M. T., Lenormand, T., Wittig, M., Grob, S., Steimer, A., Barann, M., Klostermeier, U. C., Leblanc, O., Vielle-Calzada, J., Rosenstiel, P., Grimanelli, D., Grossniklaus, U. 2011; 145 (5): 707-719

    Abstract

    Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis, we combined deep-sequencing-based RNA profiling and genetic analyses. At the 2-4 cell stage there is a strong, genome-wide dominance of maternal transcripts, although transcripts are contributed by both parental genomes. At the globular stage the relative paternal contribution is higher, largely due to a gradual activation of the paternal genome. We identified two antagonistic maternal pathways that control these parental contributions. Paternal alleles are initially downregulated by the chromatin siRNA pathway, linked to DNA and histone methylation, whereas transcriptional activation requires maternal activity of the histone chaperone complex CAF1. Our results define maternal epigenetic pathways controlling the parental contributions in plant embryos, which are distinct from those regulating genomic imprinting.

    View details for DOI 10.1016/j.cell.2011.04.014

    View details for Web of Science ID 000291018600011

    View details for PubMedID 21620136

  • Regulation and Flexibility of Genomic Imprinting during Seed Development PLANT CELL Raissig, M. T., Baroux, C., Grossniklaus, U. 2011; 23 (1): 16-26

    Abstract

    Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner. It is achieved by the differential epigenetic marking of parental alleles. Over the past decade, studies in the model systems Arabidopsis thaliana and maize (Zea mays) have shown a strong correlation between silent or active states with epigenetic marks, such as DNA methylation and histone modifications, but the nature of the primary imprint has not been clearly established for all imprinted genes. Phenotypes and expression patterns of imprinted genes have fueled the perception that genomic imprinting is specific to the endosperm, a seed tissue that does not contribute to the next generation. However, several lines of evidence suggest a potential role for imprinting in the embryo, raising questions as to how imprints are erased and reset from one generation to the next. Imprinting regulation in flowering plants shows striking similarities, but also some important differences, compared with the mechanisms of imprinting described in mammals. For example, some imprinted genes are involved in seed growth and viability in plants, which is similar in mammals, where imprinted gene regulation is essential for embryonic development. However, it seems to be more flexible in plants, as imprinting requirements can be bypassed to allow the development of clonal offspring in apomicts.

    View details for DOI 10.1105/tpc.110.081018

    View details for Web of Science ID 000287860300005

    View details for PubMedID 21278124