ArticlePlant methods2022
A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.
Article in Plant methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- HASTY-dependent miRNA cell-to-cell movement is required for systemic pathogen resistance in Arabidopsis.Plant communications · 2026Article
- 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
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants.Nature communications · 2025Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundChromatin-bound RNAs are the primary product of transcription that undergo on-chromatin processing such as capping, splicing, and polyadenylation. These processing steps then determine the fate of RNAs. Albeit its vital importance, a simple and robust method for isolating different fractions of chromatin-bound RNAs is missing in plants.
resultHere, we describe our updated method and the associated step-by-step protocol for chromatin-bound RNAs isolation in A. thaliana. The chromatin-bound RNAs isolation is based on the 1 M UREA wash that removes the majority of non-chromatin-associated proteins from the nucleus, as previously developed in mammalian cells. On-demand, the isolated chromatin-bound RNAs can be either used directly for gene-specific analysis or subject to further rRNA removal and also the optional polyadenylated RNA removal, followed by high-throughput sequencing. Detailed protocols for these procedures are also provided. Comparison of sequencing results of chromatin-bound RNAs with and without polyadenylated RNA removal revealed that a small fraction of CB-RNAs is polyadenylated but not yet fully spliced, representing RNA-processing intermediate on-chromatin.
conclusionThis optimized chromatin-bound RNAs purification method is simple and robust and can be used to study transcription and its-coupled RNA processing in plants.
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