ArticleNucleic acids research2020
Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 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
- Article
- RNA Interference Silences Genes at Post-Transcriptional Level Without Impacting Nascent RNA in Soybean Hairy Roots.Plants (Basel, Switzerland) · 2026Article
- The Rice Cis-Natural Antisense Transcript NAT1850 of Pri-miR1850 Negatively Regulates Cold Tolerance by Repressing NPR3.Plant biotechnology journal · 2026Article
- Epigenetic regulation under light and temperature fluctuations: chromatin remodeling and transcriptional memory in plants.Plant cell reports · 2026Review
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Co-transcriptional splicing changes combine with reduced productive transcription initiation for cold-induced repression of FLC.Nucleic acids research · 2026Article
- Article
- Cis- and trans-action of the cold-induced lncRNAs, SVALKA and SVALNA, regulate CBF1 and CBF3 in Arabidopsis.EMBO reports · 2025Article
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response.Nature structural & molecular biology · 2025Article
- The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis.Plant physiology · 2024Article
- Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.The Plant cell · 2024Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- A CPF-like phosphatase module links transcription termination to chromatin silencing.Molecular cell · 2024Article
- ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels.Plant biotechnology journal · 2024Article
- The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide.Plant physiology · 2024Article
- A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.Nature communications · 2024Article
- Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.Nature communications · 2024Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.
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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.