ArticleNature communications2020
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Cis- and trans-action of the cold-induced lncRNAs, SVALKA and SVALNA, regulate CBF1 and CBF3 in Arabidopsis.EMBO reports · 2025Article
- Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy.Nature communications · 2025Article
- The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis.Plant physiology · 2024Article
- Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.Molecular cell · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response.Horticulture research · 2023Article
- Comparative analysis of nascent RNA sequencing methods and their applications in studies of cotranscriptional splicing dynamics.The Plant cell · 2023Article
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis.The EMBO journal · 2023Article
- RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis.The Plant cell · 2023Article
- Cotranscriptional RNA processing and modification in plants.The Plant cell · 2023Review
- Plant terminators: the unsung heroes of gene expression.Journal of experimental botany · 2023Review
- A ribose world: current status and future challenges of plant RNA biology.Journal of experimental botany · 2023Article
- Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis.Nature communications · 2022Article
- Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (International journal of molecular sciences · 2022Article
- The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis.Nucleic acids research · 2022Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.
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