ArticleProceedings of the National Academy of Sciences of the United States of America2015
Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 77 citations in OpenAlex.
- Decoding the Temporal Accumulation Pattern of Anthocyanins From Dynamic Expression of Purple aleurone1 Gene in Blue- and Red-kernel Maize Breeding Lines.Applied biochemistry and biotechnology · 2026Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Evolutionary Divergence, Predicted Interaction Interface, and Regulatory Specialization of MTB as a Non-Catalytic Scaffold in the Plant m6A Writer Complex.Current issues in molecular biology · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Web-Based Discovery of Regulatory Motifs in Non-model Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Neutral transcriptome rewiring promotes quantitative disease resistance evolvability at the species level.The Plant cell · 2025Article
- Evolutionary dynamics and functional diversification of BBX transcription factors in CFrontiers in plant science · 2025Article
- Powdery mildew effectors AVRMolecular plant pathology · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues.Plant biotechnology journal · 2023Article
- A spatiotemporal transcriptomic network dynamically modulates stalk development in maize.Plant biotechnology journal · 2022Article
- Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Plant-DTI: Extending the landscape of TF protein and DNA interaction in plants by a machine learning-based approach.Frontiers in plant science · 2022Article
- Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana.Nature communications · 2021Article
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.Plant physiology · 2021Article
- Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor.PLoS computational biology · 2021Article
- Genome-wide analysis of spatiotemporal expression patterns during rice leaf development.BMC genomics · 2021Article
- Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis.Plant biotechnology journal · 2021Article
- A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR.The Plant journal : for cell and molecular biology · 2021Article
Corrections and comments
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Authors and funding
16 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.
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