ArticleThe Plant cell2014
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Genome-wide mapping of DCP2-dependent 5' cap footprints inNAR genomics and bioinformatics · 2026Article
- Genome level identification of transcription start sites by nanoCAGE sequence in soybean.Scientific data · 2025Article
- Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning.Genome biology · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- A foundational large language model for edible plant genomes.Communications biology · 2024Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- FAM222A, Part of the BET-Regulated Basal Endothelial Transcriptome, Is a Novel Determinant of Endothelial Biology and Angiogenesis-Brief Report.Arteriosclerosis, thrombosis, and vascular biology · 2024Article
- Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat.Nature communications · 2023Article
- In Silico Verification of Predicted Potential Promoter Sequences in the Rice (Plants (Basel, Switzerland) · 2023Article
- Review
- Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Review
- A native promoter-gene fusion created by CRISPR/Cas9-mediated genomic deletion offers a transgene-free method to drive oil accumulation in leaves.FEBS letters · 2022Article
- BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.The Plant journal : for cell and molecular biology · 2022Article
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.Genome biology · 2022Article
- CAGE reveals expanded transcriptional dynamics and protein-coding capacity in the PTI response.The Plant cell · 2022Article
- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants.Nature plants · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
7 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5' ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into "TSS tag clusters" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad "TATA-less" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.
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