Tzfadia, O. | bioRxiv Science

bioRxiv2017

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

To provide means for novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. Here, we build on a reliable Arabidopsis (Arabidopsis thaliana L.) immune signalling model, extending it with the information from diverse publically available resources. The resulting prior knowledge network (20,012 nodes, 70,091 connections) was then translated to potato (Solanum tuberosum L.) and superimposed with an ensemble network inferred from potato time-resolved transcriptomics data. We used different network modelling approaches to generate specific hypotheses of potato immune signalling mechanisms. An interesting finding was the identification of a string of molecular events, illuminating the ethylene pathway modulation of the salicylic acid pathway through NPR1 gene expression. Functional validations confirmed this modulation, thus confirming the potential of our integrative network modelling approach for unravelling molecular mechanisms in complex systems.\n\nOne-sentence summaryAnalysis of integrated prior knowledge and ensemble networks highlights a novel connection between ethylene and salicylic acid signalling modules in potato.

systems biology↗

bioRxiv2017

T-DNA integration is rapid and influenced by the chromatin state of the host genome.

Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of integration showed that selected events reported on previously were associated with extremely low methylation and nucleosome occupancy. Conversely, non-selected events from this study showed chromatin marks, such as high nucleosome occupancy and high H3K27me3 that correspond to 3D-interacting heterochromatin islands embedded within euchromatin. Such structures might play a role in capturing and silencing invading T-DNA.

plant biology↗