ArticleNature genetics2024
Widespread position-dependent transcriptional regulatory sequences in plants.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Upstream, downstream: nemo learns where plant regulatory sequences act.Plant physiology · 2026Article
- Molecular integration of seasonal temperature signals in flowering time control.Nature reviews. Genetics · 2026Review
- Systemic and Local Regulation of Root Growth by Vascular Trehalose 6-Phosphate is Correlated With Re-allocation of Primary Metabolites Between Shoots and Roots.Plant, cell & environment · 2026Article
- Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.Molecular systems biology · 2026Article
- A functional atlas of transposon-encoded products and their integration into host networks.Nature communications · 2026Article
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Comparative genomics and transcriptomics on salt tolerance ofBreeding science · 2026Article
- Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression.Nature biotechnology · 2026Article
- Protocol for chromatin immunoprecipitation using isolated antheridia of Marchantia polymorpha.STAR protocols · 2026Article
- Article
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- Multiplexed profiling of transcriptional regulators in plant cells.Nature biotechnology · 2025Article
- Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7.Plant physiology · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- Small DNA elements can act as both insulators and silencers in plants.The Plant cell · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Much of what we know about eukaryotic transcription stems from animals and yeast; however, plants evolved separately for over a billion years, leaving ample time for divergence in transcriptional regulation. Here we set out to elucidate fundamental properties of cis-regulatory sequences in plants. Using massively parallel reporter assays across four plant species, we demonstrate the central role of sequences downstream of the transcription start site (TSS) in transcriptional regulation. Unlike animal enhancers that are position independent, plant regulatory elements depend on their position, as altering their location relative to the TSS significantly affects transcription. We highlight the importance of the region downstream of the TSS in regulating transcription by identifying a DNA motif that is conserved across vascular plants and is sufficient to enhance gene expression in a dose-dependent manner. The identification of a large number of position-dependent enhancers points to fundamental differences in gene regulation between plants and animals.
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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 OpenQuestion graph.