ArticleJournal of experimental botany2016
Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation.
Article in Journal of experimental botany, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 22 citations in OpenAlex.
- A dominant role of transcriptional regulation during the evolution of CNature communications · 2025Article
- C4 Phosphoenolpyruvate Carboxylase: Evolution and transcriptional regulation.Genetics and molecular biology · 2024Article
- Effects ofPlants (Basel, Switzerland) · 2023Article
- CScience advances · 2023Article
- De novo transcriptome assemblies of CBMC genomics · 2023Article
- Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.BMC genomics · 2020Article
- Beyond the darkness: recent lessons from etiolation and de-etiolation studies.Journal of experimental botany · 2020Review
- Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in CFrontiers in plant science · 2020Article
- What Matters for CFrontiers in plant science · 2020Article
- Genetic determinants controlling maize rubisco activase gene expression and a comparison with rice counterparts.BMC plant biology · 2019Article
- The genetics of convergent evolution: insights from plant photosynthesis.Nature reviews. Genetics · 2019Review
Corrections and comments
- Erratum issuedCorrigendum.2017
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.
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