ArticleFrontiers in genetics2020
Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 28 citations in OpenAlex.
- Enhancer-based gene therapy: a new path for precision medicine.Hereditas · 2026Review
- High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance.Scientific data · 2026Article
- High-throughput evaluation of cardiac-specific promoters for adeno-associated virus mediated cardiac gene therapy.Gene therapy · 2026Article
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Miniature inverted repeat transposable elements in the genome of sugar beet and their impact on gene expression.Scientific reports · 2025Article
- Liver-specific enhancers evolved from independent episodes of MITE domestication in Xenopus tropicalis.Mobile DNA · 2025Article
- Plant MITEs: miniature transposable elements with major impacts.Mobile DNA · 2025Review
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot.Journal of applied genetics · 2025Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.Nucleic acids research · 2024Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.Genome biology · 2023Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- A comprehensive map of preferentially located motifs reveals distinct proximalFrontiers in plant science · 2022Article
- Article
- Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
9 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancers are key players in the spatio-temporal coordination of gene expression during numerous crucial processes, including tissue differentiation across development. Characterizing the transcription factors (TFs) and genes they connect, and the molecular functions underpinned is important to better characterize developmental processes. In plants, the recent molecular characterization of enhancers revealed their capacity to activate the expression of several target genes. Nevertheless, identifying these target genes at a genome-wide level is challenging, particularly for large-genome species, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to plant regulatory networks remains poorly understood. Here, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage (V2-IST) and husks (bracts) at flowering. Using systems biology, we integrate genomic, epigenomic, and transcriptomic data to model the regulatory relationships between TFs and their potential target genes, and identify regulatory modules specific to husk and V2-IST. We show that leaves at the V2-IST stage are characterized by the response to hormones and macromolecules biogenesis and assembly, which are regulated by the BBR/BPC and AP2/ERF TF families, respectively. In contrast, husks are characterized by cell wall modification and response to abiotic stresses, which are, respectively, orchestrated by the C2C2/DOF and AP2/EREB families. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon
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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.