Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
Chris Coté
Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
Yihan Wan
School of Life Sciences, Westlake University, Hangzhou, China
Sareh Bayatpour
Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
Heather L Drexler
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
Katherine A Alexander
Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
Fei Chen
Broad Institute of MIT and Harvard, Cambridge, United States
Asmamaw T Wassie
Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, United States
Rohan Patel
Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
Kenneth Pham
Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, United States
Edward S Boyden
Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of Technology, Cambridge, United States
Shelly Berger
Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
Jennifer Phillips-Cremins
Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
Department of Bioengineering, University of Pennsylvania, Philadelphia, United States; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
