ArticleGenetics2015
Nascent transcription affected by RNA polymerase IV in Zea mays.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 80 citations in OpenAlex.
- Genome level identification of transcription start sites by nanoCAGE sequence in soybean.Scientific data · 2025Article
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Plant enhancers exhibit both cooperative and additive interactions among their functional elements.The Plant cell · 2024Article
- Genome organization and botanical diversity.The Plant cell · 2024Review
- Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.PLoS genetics · 2024Article
- Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.G3 (Bethesda, Md.) · 2024Article
- Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation.Current opinion in genetics & development · 2024Review
- Comparative analysis of nascent RNA sequencing methods and their applications in studies of cotranscriptional splicing dynamics.The Plant cell · 2023Article
- Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.bioRxiv : the preprint server for biology · 2023Article
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.Plant methods · 2022Article
- Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat.Genome biology · 2022Article
- The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis.Current biology : CB · 2021Article
- Dynamics of DNA Methylation and Its Functions in Plant Growth and Development.Frontiers in plant science · 2021Review
- Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf.Frontiers in plant science · 2021Article
- Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function.PLoS genetics · 2020Article
- Characterization ofThe Plant cell · 2020Article
- Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize.G3 (Bethesda, Md.) · 2020Article
- Metabolic Labeling of RNAs Uncovers Hidden Features and Dynamics of the Arabidopsis Transcriptome.The Plant cell · 2020Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3'-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.
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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.