Dataset Information

A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.

ABSTRACT:

Background

Chromatin-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.

Result

Here, 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.

Conclusion

This optimized chromatin-bound RNAs purification method is simple and robust and can be used to study transcription and its-coupled RNA processing in plants.

SUBMITTER: Zhang Q

PROVIDER: S-EPMC9743689 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Publications

A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.

Zhang Qiqi Q Zhao Fengli F Wu Zhe Z Zhu Danling D

Plant methods 20221212 1

<h4>Background</h4>Chromatin-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.<h4>Result</h4>Here, we describe our updated method and the associated step-by-step protocol for chromatin-bound RNAs isolation in A. thaliana. ...[more]

PMID: 36510301

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Dataset Information

A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.

Background

Result

Conclusion

Publications

A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis.

Similar Datasets

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