Muhlemann, J. K. | Search bioRxiv

bioRxiv2024

Ethylene Receptor Gain- and Loss-of-function Mutants Reveal an ETR1-dependent Transcriptional Network in Roots

In Arabidopsis, a family of five receptors mediates ethylene responses in roots, with Ethylene Response 1 (ETR1) controlling increases in root hair proliferation and decreases in lateral root formation. To define the ETR1-dependent gene regulatory network (GRN) controlling root development, we profiled the root transcriptome from Col-0 and the etr1-3 gain-of-function and etr1-7 loss-of-function mutants in the presence and absence of ethylene or the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). We identified 4,522 differentially expressed (DE) transcripts in Col-0 roots with altered abundance in response to ethylene and/or ACC treatment, with larger magnitude changes induced by ethylene. These included 553 DE transcripts that were ETR1 dependent, defined by a lack of response to treatment with ethylene and/or ACC in ethylene-insensitive etr1-3 and constitutively altered in etr1-7 in the presence and absence of treatment relative to time-0 Col-0. Within these ETR1-dependent transcripts were ethylene biosynthesis genes and transcription factors. ACC OXIDASE 2 (ACO2) and ACO3 convert ACC to ethylene and were ETR1-dependent, and ACO-promoter-driven reporter fusions were ACC regulated in root tissues in appropriate locations to control root development, with ACO5 localized to root hairs. Abundance of ETR1-dependent transcripts that were predicted to encode transcription factors and ACOs were examined in Col-0 and an ein3eil1 mutant with and without ACC treatment, suggesting the ETR1 and EIN3/EIL1 canonical ethylene signaling pathway regulated some, but not all, of these transcriptional responses. Together, these findings reveal features of an ETR1-dependent GRN that controls both ethylene synthesis and root growth and development. One sentence summaryTranscriptional responses in etr1 LOF and GOF mutants reveal an ethylene-mediated ETR1- and EIN3 dependent gene regulatory network that modulates ethylene signaling and synthesis and root development.

plant biology↗

bioRxiv2022

Partitioned Local Depth analysis of time course transcriptomic data reveals elaborate community structure

Transcriptome studies that provide temporal information are valuable for identifying groups of similarly-behaving transcripts, giving insight into overarching gene regulatory networks. Nevertheless, inferring transcriptional networks from time series data is challenging, in part because it is difficult to holistically consider both local relationships and global structure of these complex and overlapping transcriptional responses. To address this need, we employed the Partitioned Local Depth (PaLD) method to examine four time series transcriptomic datasets generated using the model plant Arabidopsis thaliana. Here, we provide a self-contained description of the method and demonstrate how it can be used to make predictions about gene regulatory networks based on time series data. The analysis provides a global network representation of the data from which graph partitioning methods and neighborhood analysis can reveal smaller, more well-defined groups of like-responding transcripts. These groups of transcripts that change in response to hormone treatment (e.g., auxin or ethylene) or high salinity were demonstrated to be enriched in common biological function and/or binding of transcription factors that were not identified with prior analyses of this data using other clustering and inference methodologies. These results reveal the ability of PaLD to generate predictions about gene regulatory networks using time series transcriptomic data, which can be of value to the systems biology community.

systems biology↗