Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in
            <i>Arabidopsis</i>

Kim, Hyo Jung; Park, Ji-Hwan; Kim, Jingil; Kim, Jung Ju; Hong, Sunghyun; Kim, Jeong-Sik; Kim, Jin Hee; Woo, Hye Ryun; Hyeon, Changbong; Lim, Pyung Ok; Nam, Hong Gil; Hwang, Daehee

doi:10.1073/pnas.1721523115

Cited by 111 publications

(137 citation statements)

References 49 publications

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“…Transcriptome analysis of the double mutant confirmed upregulation of many SA-pathway genes (Figure 8D-E), which likely explains the enhanced resistance against (hemi)-biotrophic pathogens. In support of our findings, a recent study of a NAC TF network during developmental leaf senescence by (Kim et al, 2018) also linked ANAC090 to SA signalling. In that study, they identified ANAC090 as a negative regulator of SA-mediated leaf senescence and they showed that loss of ANAC090 led to increased SA levels and accelerated leaf senescence.…”

Section: Discussionsupporting

confidence: 91%

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

Hickman

Mendes

Verk

et al. 2019

Preprint

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The phytohormone salicylic acid (SA) is a central regulator of plant immunity.Antagonistic and synergistic actions between SA and other defense-associated hormones like jasmonic acid (JA) play key roles in determining the outcome of the plant immune response. To obtain a deeper understanding of SA-mediated transcriptional reprogramming and SA/JA crosstalk, we generated a high-resolution time series of gene expression from Arabidopsis leaves treated with SA alone and a combination of SA and methyl JA (MeJA), sampled at 14 time points over a 16-h period. We found that approximately one-third of the Arabidopsis genome was differentially expressed in response to SA, and temporal changes in gene expression could be partitioned into 45 distinct clusters of process-specific coregulated genes, linked to specific cis-regulatory elements and binding of transcription factors (TFs).Integration of our expression data with information on TF-DNA binding allowed us to generate a dynamic gene regulatory network model of the SA response, recovering known regulators and identifying novel ones. We found that 12% of SA-responsive genes and 69% of the MeJA-responsive genes exhibited antagonistic or synergistic expression levels in the combination treatment. Multi-condition co-clustering of the single-and combined-hormone expression profiles predicted underlying regulatory mechanisms in signal integration. Finally, we identified the TFs ANAC061 and ANAC090 as negative regulators of SA pathway genes and defense against biotrophic pathogens. Collectively, our data provide an unprecedented level of detail about transcriptional changes during the SA response and SA/JA crosstalk, serving as a valuable resource for systems-level network studies and functional plant defense studies.

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Section: Discussionsupporting

confidence: 91%

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

Hickman

Mendes

Verk

et al. 2019

Preprint

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“…2; Supplemental Table S4), suggesting it too may play a role in regulating senescence in wheat. ANAC082 and ANAC090 form part of a NAC regulatory module that governs the shift from positive to negative regulation among NACs at a pre-senescence stage in Arabidopsis (Kim et al, 2018). However, ANAC082 and ANAC090 were not differentially expressed in Arabidopsis, and the majority of their wheat orthologs were also not differentially expressed during senescence (the third member of the regulatory module ANAC017 did not have a wheat ortholog).…”

Section: Conservation Of Senescence-related Genes Between Wheat Ricementioning

confidence: 98%

Identification of Transcription Factors Regulating Senescence in Wheat through Gene Regulatory Network Modelling

et al. 2019

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Senescence is a tightly regulated developmental program coordinated by transcription factors. Identifying these transcription factors in crops will provide opportunities to tailor the senescence process to different environmental conditions and regulate the balance between yield and grain nutrient content. Here, we use ten time points of gene expression data along with gene network modeling to identify transcription factors regulating senescence in polyploid wheat (Triticum aestivum). We observe two main phases of transcriptional changes during senescence: early down-regulation of housekeeping functions and metabolic processes followed by up-regulation of transport and hormone-related genes. These two phases are largely conserved with Arabidopsis (Arabidopsis thaliana), although the individual genes underlying these changes are often not orthologous. We have identified transcription factor families associated with these early and later waves of differential expression. Using gene regulatory network modeling, we identified candidate transcription factors that may control senescence. Using independent, publicly available datasets, we found that the most highly ranked candidate genes in the network were enriched for senescencerelated functions compared with all genes in the network. We validated the function of one of these candidate transcription factors in senescence using wheat chemically induced mutants. This study lays the groundwork to understand the transcription factors that regulate senescence in polyploid wheat and exemplifies the integration of time-series data with publicly available expression atlases and networks to identify candidate regulatory genes.

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“…The purified EV protein preparation (9 µg) was desalted with SDS-PAGE loaded onto the stacking gel followed by staining and destaining. The in-gel trypsin digestion was carried out obtained by randomly permuting the WT/KO labels for all proteins, as previously described 128 .…”

Section: Comparative Proteomicsmentioning

confidence: 99%

A reference map of the human protein interactome

Luck

Kim

Lambourne

et al. 2019

Preprint

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Global insights into cellular organization and function require comprehensive understanding of interactome networks. Similar to how a reference genome sequence revolutionized human genetics, a reference map of the human interactome network is critical to fully understand genotype-phenotype relationships. Here we present the first human "all-by-all" binary reference interactome map, or "HuRI". With ~53,000 highquality protein-protein interactions (PPIs), HuRI is approximately four times larger than the information curated from small-scale studies available in the literature. Integrating HuRI with genome, transcriptome and proteome data enables the study of cellular function within essentially any physiological or pathological cellular context. We demonstrate the use of HuRI in identifying specific subcellular roles of PPIs and protein function modulation via splicing during brain development. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI thus represents an unprecedented, systematic reference linking genomic variation to phenotypic outcomes.

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Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in Arabidopsis

Cited by 111 publications

References 49 publications

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

Identification of Transcription Factors Regulating Senescence in Wheat through Gene Regulatory Network Modelling

A reference map of the human protein interactome

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