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PLoS One. 2014 Feb 26;9(2):e89673. doi: 10.1371/journal.pone.0089673. eCollection 2014.

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.

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Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America.
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
Genomic Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
Departments of Pediatrics, Neurology, and Physiology, Northwestern University Feinberg School of Medicine and Lurie Children's Hospital of Chicago Research Center, Chicago, Illinois, United States of America.
Epicentre, Madison, Wisconsin, United States of America.
Institute for Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.


mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA. SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA. We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors. SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.

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