Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution. Transcriptome-wide interrogation of the functional intronome by spliceosome profiling. The spliceosome: design principles of a dynamic RNP machine. Ordered and dynamic assembly of single spliceosomes. Coupling mRNA processing with transcription in time and space. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Splicing of nascent RNA coincides with intron exit from RNA polymerase II. Nascent RNA analyses: tracking transcription and its regulation. Regulation of alternative splicing through coupling with transcription and chromatin structure. Introduction to cotranscriptional RNA splicing. The majority of the intron retention events in Arabidopsis are at pts introns, suggesting that chromatin-tethered post-transcriptional splicing is a major contributor to the widespread intron retention that is observed in plants, and could be a mechanism to produce fully spliced functional mRNAs for rapid response. Analysis of around 6,500 public RNA-sequencing libraries found that the splicing of pts introns requires the function of splicing-related proteins such as PRMT5 and SKIP, and is also influenced by various environmental signals.

These introns are nearly absent in the cytoplasm and are resistant to nonsense-mediated decay, suggesting that they are post-transcriptionally spliced before the transcripts are released into the cytoplasm we therefore termed these introns post-transcriptionally spliced introns (pts introns). Many of the full-length chromatin-bound RNA molecules are polyadenylated, yet still contain unspliced introns at specific positions.

We found that more than half of the introns remain unspliced after Pol-II transcribes 1 kb past the 3′ splice site, which is much slower than the rate of splicing reported in yeast 4, 5. Here, we developed a Nanopore-based method to profile chromatin-bound RNA that enables the simultaneous detection of splicing status, Pol-II position and polyadenylation at the genome-wide scale in Arabidopsis. In eukaryotes, genes are transcribed by RNA polymerase-II (Pol-II) and introns are removed by the spliceosome largely cotranscriptionally 1, 2, 3 analysis using long-read sequencing revealed that splicing occurs immediately after Pol-II passes introns in yeast 4, 5.

How to use filezilla for transcription