Plant Development and Hypoxia Unit

Ongoing

Previous studies have revealed that regulatory networks conserved across species in response to flooding include a characteristic response to low oxygen availability. This research area aims to characterise regulatory mechanisms involving conserved transcription factors (TFs), focusing on their role in cellular reprogramming for lateral root development and nodule formation during legume–rhizobium interactions. Evidence suggests that most cis-regulatory elements are located in accessible chromatin regions found in different cell populations. To analyse regulatory changes mediated by these TFs, we use ATAC-seq in cells involved in lateral root and nodule development. Conserved TFs that are candidates for a role in cellular reprogramming are being further evaluated using chromatin immunoprecipitation. This new information will be integrated with previously described metabolic and signalling pathways to better understand the key biological processes that determine plant root plasticity.

This research area also remains shared with Root Biology.

Ongoing

Gene regulation in roots during flooding has conserved features across angiosperms. Although legume species vary in their susceptibility to flooding, both soil waterlogging and complete submergence have severe negative effects on most forage and grain legumes. During flooding, the low solubility and diffusion of gases in water cause oxygen deficiency (hypoxia), which inhibits respiration, and carbon dioxide deficiency, which reduces photosynthesis, resulting in an energy crisis. At the same time, the gaseous hormone ethylene produced by plants accumulates in plant cells. This accumulation acts as a signal that mediates the regulation of ethylene response transcription factors (ERFs) at the transcriptional, translational and post-translational levels, enabling multiple adaptations, including the activation of anaerobic metabolism and hormonal adjustments. These responses help plants tolerate short periods of flooding. Subsequently, high oxygen levels after flooding, dehydration and the reactivation of respiration and photosynthesis also cause severe damage to plants that have experienced an energy crisis. Understanding the role of conserved regulators of plant responses to flooding stress is a priority for developing and maintaining sustainable agriculture. This research area therefore aims to evaluate the role of conserved TFs in flooding stress tolerance and understand their function. This knowledge may enable changes to the activation of response pathways before stress occurs, promoting protection against subsequent flooding.

Study of gene expression regulation during the formation of lateral roots and nitrogen-fixing nodules.

We analyze the transcriptional and translational reprogramming of root cells, together with changes in the stability of long and small non-coding RNAs. We focus on the dynamics of DNA methylation, histone modifications and epitranscriptomic marks, especially m6A methylation.

We combine genetic and biochemical approaches with massively parallel sequencing technologies to understand how these signals regulate chromatin accessibility, RNA stability and translatability during organogenesis. The knowledge obtained can contribute to improving crop productivity.

Participants: María Eugenia Zanetti, Flavio Blanco, Mauricio Reynoso, Soledad Traubenik, Cristina Kirolinko, Milagros Ferrari, Jesica Rivero, Marianela Cueva, Milagros Yacullo and Camila Coronel.

Analysis of the regulatory circuits that coordinate infection and nodule formation in specific root cell types.

During the legume–rhizobium interaction, root cells execute coordinated genetic programs of infection and organogenesis. We study epidermal and cortical cell responses at the transcriptional, post-transcriptional and translational levels, including chromatin remodeling, DNA methylation, RNA dynamics and translational status.

We apply INTACT, ATAC-seq, bisulfite sequencing, RNA-seq, small RNA-seq and TRAP to identify regulatory events associated with symbiotic efficiency and to characterize genes involved in the strain-specific response. These results can guide breeding programs that optimize plant–rhizobium compatibility and reduce the use of nitrogen fertilizers.

Participants: Flavio Blanco, María Eugenia Zanetti, Mauricio Reynoso, Claudio Rivero, Carla Roda, Jennifer Artunián, Andrés Eylenstein, Lourdes Nassarov and Marina Cretton.