POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5'ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). In particular, we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5'P-RNA at polyadenylation sites. Furthermore, POINT-nano reveals that splicing occurs either immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing. Overall design: POINT technology was employed over HeLa and HCT116 cells in order to reveal the RNA processing at the nascent level. Thus, POINT-nano, POINT-seq and PONT-5 samples were generated either untreated or with PlaB/DMSO in order to evaluate the splicing kinetics. Also, POINT technology was performed under XRN2 and CPSF73 KDs to study 3'end processing.