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A simple but robust approach for isolating chromatin associated RNAs in Arabidopsis thaliana

ABSTRACT: A simple but robust approach for isolating chromatin associated RNAs in Arabidopsis thaliana

PROVIDER: PRJNA881599 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21616068_1.fastq.gz	Fastqsanger.gz
	SRR21616068_2.fastq.gz	Fastqsanger.gz
	SRR21616069_1.fastq.gz	Fastqsanger.gz
	SRR21616069_2.fastq.gz	Fastqsanger.gz
	SRR21616070_1.fastq.gz	Fastqsanger.gz

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A simple but robust approach for isolating chromatin associated RNAs in Arabidopsis thaliana

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Project description: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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