ArticlePlant physiology2016
A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 86 citations in OpenAlex.
- Article
- Identification of Accessible Transcription Factor Binding Sites During the Seed-to-Seedling Transition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Establishment and maintenance of NRT2.1 inter-individual variability in plants.PLoS genetics · 2025Article
- Defying Death: A Multi-Omics Approach to Understanding Desiccation Tolerance and Senescence inPlants (Basel, Switzerland) · 2025Article
- Dt1 interacts with HB40 to affect lateral root primordium development by regulating CDC48 in soybean.Plant biotechnology journal · 2025Article
- Polycomb repressive complex 2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence.The Plant cell · 2025Article
- Developmental phylotranscriptomics in grapevine suggests an ancestral role of somatic embryogenesis.Communications biology · 2025Article
- Article
- A spatially resolved multiomic single-cell atlas of soybean development.bioRxiv : the preprint server for biology · 2024Article
- The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures.The Plant cell · 2024Article
- Exploring the diversity of galls onPlant direct · 2024Article
- Developmental pleiotropy of SDP1 from seedling to mature stages in B. napus.Plant molecular biology · 2024Article
- Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors.Scientific reports · 2024Article
- Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.Nature communications · 2024Article
- SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination.Journal of experimental botany · 2023Article
- Brassinosteroid gene regulatory networks at cellular resolution in theScience (New York, N.Y.) · 2023Article
- Identification and functional validation of super-enhancers inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Seed-to-Seedling Transition inPlants (Basel, Switzerland) · 2022Article
- Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height.BMC plant biology · 2022Article
- The evolutionarily conserved kinase SnRK1 orchestrates resource mobilization during Arabidopsis seedling establishment.The Plant cell · 2022Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis (Arabidopsis thaliana). Using the transcriptome signature from these developmental stages, we obtained a coexpression gene network that highlights interactions between known regulators of the seed-to-seedling transition and predicts the functions of uncharacterized genes in seedling establishment. The coexpressed gene data sets together with the transcriptional module indicate biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knockout mutants for athb13 showed increased primary root length as compared with wild-type (Columbia-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time that cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for a vigorous seedling, such as root growth. This study demonstrates that a gene coexpression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.