Vu Hoang Nguyen

Plants have an impressive repertoire to react to stress conditions that limit regular growth. Elevated temperatures beyond the optimal range cause rapid and specific transcriptional responses, resulting in developmental alterations and plasticity. Heat stress also causes chromatin decondensation and activation of some transposable elements (TEs), endangering genomic integrity. This is especially risky for stem cells in the shoot apical meristem (SAM) that potentially contribute to the next generation. We examined how the heat stress response in SAM stem cells of Arabidopsis (Arabidopsis thaliana) is different from that in other tissues and whether the elements of epigenetic TE control active in the meristem are involved in specific heat protection of stem cells. Using fluorescence-activated nuclear sorting to isolate and characterize SAM stem cells after exposure to conditions that activate a heat-responsive TE, we found that SAM stem cells maintain their developmental program and suppress the heat-response pathways dominating in surrounding somatic cells. Furthermore, mutants defective in DNA methylation recovered less efficiently from heat stress and persistently activated heat response factors and heat-responsive TEs. Heat stress also induced epimutations at the level of DNA methylation, especially in the CHG sequence context. Regions with modified DNA methylation patterns remained altered for at least 3 wk beyond the stress. These findings urge for disentangling cell type-specific responses under different stress types, especially for stem cells as bridges to the next generation.

In sexually propagating organisms, genetic, and epigenetic mutations are evolutionarily relevant only if they occur in the germline and are hence transmitted to the next generation. In contrast to most animals, plants are considered to lack an early segregating germline, implying that somatic cells can contribute genetic information to progeny. Here we demonstrate that 2 ARGONAUTE proteins, AGO5 and AGO9, mark cells associated with sexual reproduction in Arabidopsis (Arabidopsis thaliana) throughout development. Both AGOs are loaded with dynamically changing small RNA populations derived from highly methylated, pericentromeric, long transposons. Sequencing of single stem cell nuclei revealed that many of these transposons are co-expressed within an AGO5/9 expression domain in the shoot apical meristem (SAM). Co-occurrence of transposon expression and specific ARGONAUTE (AGO) expression in the SAM is reminiscent of germline features in animals and supports the existence of an early segregating germline in plants. Our results open the path to investigating transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.

Summary: Post-embryonic plant development must be coordinated in response to and with environmental feedback. Development of above-ground organs is orchestrated from stem cells in the center of the shoot apical meristem (SAM). Heat can pose significant stress to plants and induces a rapid heat response, developmental alterations, chromatin decondensation, and activation of transposable elements (TEs). However, most plant heat-stress studies are conducted with whole plants, not resolving cell-type-specific responses. Heat stress consequences in stem cells are of particular significance, as they can potentially influence the next generation. Here we use fluorescent-activated nuclear sorting to isolate and characterize stem cells after heat exposure and after a recovery period in wild type and mutants defective in TE defense and chromatin compaction. Our results indicate that stem cells can suppress the heat response pathways that dominate surrounding somatic cells and maintain their developmental program. Furthermore, mutants defective in DNA methylation recover less efficiently from heat stress and persistently activate heat response factors and heat-inducible TEs. Heat stress also induces epimutations at the level of DNA methylation, and we find hundreds of DNA methylation changes three weeks after stress. Our results underline the importance of disentangling cell type-specific environmental responses for understanding plant development.

Significance: While DNA methylation in plants occurs at CG, CHG, and CHH sequence contexts, their comparative roles in genome regulation remain elusive. Here, we utilized Physcomitrella patens as a plant model suitable to study this question. By profiling transcriptomes in a series of context-specific methylation mutants, we found redundancy between asymmetric (CHH) methylation and symmetric methylation in silencing transposons, and that CHH methylation regulates the expression of CG/CHG-depleted transposons. Specific elimination of CG methylation had a significantly smaller effect on transcription than elimination of non-CG methylation. Additionally, we found CHG methylation as a stronger silencer than CG methylation. These results disentangle the transcriptional roles of the individual methylation contexts and elucidate the crucial role of non-CG methylation in genome regulation.

The Vibrio cholerae O1 (VCO1) El Tor biotype appeared during the seventh cholera pandemic starting in 1961, and new variants of this biotype have been identified since the early 1990s. This pandemic has affected Vietnam, and a large outbreak was reported in southern Vietnam in 2010. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem-repeat analyses (MLVA) were used to screen 34 VCO1 isolates from the southern Vietnam 2010 outbreak (23 patients, five contact persons, and six environmental isolates) to determine if it was genetically distinct from 18 isolates from outbreaks in southern Vietnam from 1999 to 2004, and two isolates from northern Vietnam (2008). Twenty-seven MLVA types and seven PFGE patterns were identified. Both analyses showed that the 2008 and 2010 isolates were distinctly clustered and separated from the 1999–2004 isolates.