EPIHYBRIDS: The role of small RNAs in genomic imprinting and hybrid barriers

In this project an array of small RNAs that guide epigenetic modification are hypothesized to play an important role in imprinted gene expression, resulting in diverging imprinting patterns, and/or affecting other seed developmental regulatory cascades, ultimately leading to post-zygotic species barriers in hybrid seeds.

Simplified model for canonical and non-canonical RdDM. In canonical PolIV-RdDM, single stranded RNA transcribed by PolIV is made into dsRNA by RDR2 and diced to 24nt siRNA by DCL3 and then bound by AGO4. During Pol V-mediated transcription, the AGO4-bound siRNA is believed to base-pair with the nascent Pol V transcript and recruit DRM2 to catalyse de novo methylation at the homologous genomic sites. In non-canonical RDR6-RdDM, PolI transcripts are turned into dsRNA by RDR6 and further diced by DCL2 or DCL4 to generate 21-22nt dsRNA. Upon association with AGO1 the complex is guided by base pairing to PolV transcripts and induce de novo DNA methylation by DRM2 similar to canonical RdDM. Modiefied from  Bond and Baulcombe, 2015; Matzke and Mosher, 2014; Wierzbicki et al., 2012.

About the project

Fertilization in plants generates the seed, a structure with two fertilization products, the embryo, carrying the genetic makeup of the next generation, and the endosperm, a nourishing tissue. In analogy to the mammalian placenta, the endosperm is a site for the epigenetic phenomenon genomic imprinting; parent-of-origin dependent expression of genes due to epigenetic regulatory marks established in the male and female germ line. Genomic imprinting is a highly captivating example of gene regulation. The underlying epigenetic mechanisms must be able to distinguish two identical alleles and reside in the same nucleus. Imprinted expression results from differences in epigenetic marks, and the major mechanisms include maintenance DNA methylation and post-translational modifications of histones on the parental alleles. However, by far all imprinted genes can be explained by these mechanisms, and a novel type of DNA methylation guided by small, single stranded RNA emerge as a mechanistic alternative. A related and insufficiently investigated role of small RNAs is speciation. When different species interact in fertilization, hybrid seeds are generated, that usually abort due to post-zygotic barriers, traditionally explained by mis-regulation of imprinted genes. In the proposed research, small RNAs that guide epigenetic modification are hypothesized to play significant roles in imprinted gene regulation and further to act through imprinted genes or affecting other seed regulatory cascades to erect post-zygotic species barriers.  To test these hypotheses we propose to use a combination of genetic dissection, transcriptomics and epigenomics.  We will identify imprinted genes regulated by small RNA in the genus Arabidopsis, and further test the hypothesis that imprinted genes are evolutionary conserved between related species. Finally, we propose to experimentally demonstrate that small RNAs are involved in the establishment of post-zygotic hybrid barriers and thus speciation.

Project kickoff: June 2018


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Published Dec. 3, 2017 11:20 PM - Last modified Dec. 3, 2017 11:40 PM