ArticleProceedings of the National Academy of Sciences of the United States of America2016
Nascent RNA sequencing reveals distinct features in plant transcription.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers, 1 of them a synthesis that pooled it.
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Who cites it
101 citing papers in PubMed, 1 synthesis or guideline pooled it, 180 citations in OpenAlex.
- Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.International journal of molecular sciences · 2022Pooled it
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- RNA Interference Silences Genes at Post-Transcriptional Level Without Impacting Nascent RNA in Soybean Hairy Roots.Plants (Basel, Switzerland) · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- 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
- Plant long noncoding RNAs: why do we not know more?Biological research · 2025Review
- ZmSSRP1 facilitates the progression of RNA polymerase II and is essential for kernel development in maize.The Plant cell · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Characterization of DNA methylation reader proteins inGenome research · 2024Article
- Efficient small fragment sequencing of human, cattle, and bison miRNA, small RNA, or csRNA-seq libraries using AVITI.BMC genomics · 2024Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Transcriptome analysis and characteristics of drought resistance related genes in four varieties of foxtail millet [Heliyon · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo.Development (Cambridge, England) · 2024Article
- Plant enhancers exhibit both cooperative and additive interactions among their functional elements.The Plant cell · 2024Article
- Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steady-state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.
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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.