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

In the transcription process, Pol II produces the nascent RNA which associates with chromatin. To acquire co-transcriptional RNA is easy to understand the RNA transcription status. We use a simple and effective way to separate the intact cell nucleus and wash the nucleoplasm, then acquire the chromatin component. With the help of Illumina RNA sequencing, we analyze the nascent RNA extracted from chromatin component in whole genome. We demonstrate the method descripted in this paper can be suitable for analyze co-transcriptional splicing ratio effectively. Interestingly, we find the first intron globally has lower co-transcriptional splicing efficiency. In brief, our method can be used for analyze the nascent RNA in elongating process and the fully transcribed RNA with poly-A tail but not yet released from chromatin. Overall design: We describe a step-by-step protocol for isolating chromatin-bound RNAs from the pool of cellular RNAs in Arabidopsis thaliana. With this protocal we also can separate the elongating RNAs and full-length polyA RNAs from the chromatin-bound RNAs.