ArticleThe Plant cell2013
SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.
Article in The Plant cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed, 146 citations in OpenAlex.
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- The PtrC2H2.2-6-PtrCYP86A7/A8 Module Regulates Poplar Drought Tolerance Through Mediating Cutin and Wax Biosynthesis Pathways.Plant biotechnology journal · 2026Article
- Integrated morpho-physiological and transcriptomic dissection of waterlogging tolerance inFrontiers in plant science · 2026Article
- The role of PagC3H3 in lignin biosynthesis and insect resistance in Populus alba × Populus glandulosa.Plant cell reports · 2025Article
- The auxin-PLETHORA 5 module regulates wood fibre development in Populus tomentosa.Nature plants · 2025Article
- Epigenetic regulation of lignin biosynthesis in wood formation.The New phytologist · 2025Article
- Identification of the RNA m5C methyltransferase genes inForestry research · 2025Article
- Genome-wide identification and gene expression networks of LBD transcription factors in Populus trichocarpa.BMC genomics · 2024Article
- Transcriptome analysis of the transition from primary to secondary growth of vertical stem in Eucalyptus grandis.BMC plant biology · 2024Article
- Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation.Horticulture research · 2024Article
- Molecular mechanism of salinity and waterlogging tolerance in mangroveFrontiers in plant science · 2024Article
- Expression Quantitative Trait Locus of Wood Formation-Related Genes inInternational journal of molecular sciences · 2023Article
- Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML.Plant molecular biology · 2023Article
- TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization.NAR genomics and bioinformatics · 2023Article
- Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize.The Plant cell · 2023Article
- Article
- Single-cell transcriptomics unveils xylem cell development and evolution.Genome biology · 2023Article
- Transcriptional regulatory cascade ofFrontiers in plant science · 2023Article
- Biomass formation and sugar release efficiency ofPlant direct · 2022Article
- QTL mapping of drought-related traits in the hybrids of Populus deltoides 'Danhong'×Populus simonii 'Tongliao1'.BMC plant biology · 2022Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.
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