ArticleGenome biology2023
A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Integrative machine learning and gene regulatory network analysis identifies novel genes for leafy head formation in Brassica rapa and B. oleracea.Molecular horticulture · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dissecting spatial patterning and signaling with directional diffusion in spatial multi-omics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A sweet corn metabolic regulatory network spanning the entire life cycle.Molecular horticulture · 2026Article
- A Multidimensional Approach to Cereal Caryopsis Development: Insights into Adlay (Plants (Basel, Switzerland) · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum.Nature communications · 2025Article
- Integrated 16 S rRNA and transcriptome analysis reveal molecular and microbial mechanisms of cold-tolerant germination in hulless barley.BMC genomics · 2025Article
- Identification of key candidate genes regulating hundred-grain weight in the maize inbred line Ye107 from Southern China.Plant cell reports · 2025Article
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- GWAS combined with transcriptomics revealed key regulatory genes for inflorescence traits and fruit set rate in Litchi (Litchi chinensis Sonn.).BMC genomics · 2025Article
- Big data and artificial intelligence-aided crop breeding: Progress and prospects.Journal of integrative plant biology · 2025Review
- A dynamic regulome of shoot-apical-meristem-related homeobox transcription factors modulates plant architecture in maize.Genome biology · 2024Article
- Dynamic Viscoelastic Behavior of Maize Kernel: Application of Frequency-Temperature Superposition.Foods (Basel, Switzerland) · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- A Comprehensive Identification and Expression Analysis of the WUSCHEL Homeobox-Containing Protein Family Reveals Their Special Role in Development and Abiotic Stress Response inInternational journal of molecular sciences · 2023Article
- The Genome-Wide Identification, Characterization, and Expression Analysis of the Strictosidine Synthase-like Family in Maize (International journal of molecular sciences · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMaize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omics GRN connecting the translatome and transcriptome is lacking, hampering our understanding and exploration of the maize regulatome.
resultsWe collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, we construct a multi-omics GRN integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, we reconcile some known regulatory networks. We identify a novel transcription factor, ZmGRF6, which is associated with growth. Furthermore, we characterize a function related to drought response for the classic transcription factor ZmMYB31.
conclusionsOur findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.
Indexed as
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.