title: SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.
abstract: 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.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Jesse M
authors.initials: JM
authors.lastname: Gray
authors.affiliation: Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: David A
authors.initials: DA
authors.lastname: Harmin
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Boswell
authors.affiliation: Genomic Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
authors.forename: Nicole
authors.initials: N
authors.lastname: Cloonan
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Mullen
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Ling
authors.affiliation: 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.
authors.forename: Nimrod
authors.initials: N
authors.lastname: Miller
authors.affiliation: Epicentre, Madison, Wisconsin, United States of America.
authors.forename: Scott
authors.initials: S
authors.lastname: Kuersten
authors.affiliation: 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.
authors.forename: Yong-Chao
authors.initials: YC
authors.lastname: Ma
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Steven A
authors.initials: SA
authors.lastname: McCarroll
authors.affiliation: Institute for Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Springer
mesh_terms: D017398:Alternative Splicing; D044946:Biflavonoids / Q000494:pharmacology; D006367:HeLa Cells / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns; D008962:Models, Theoretical; D009010:Monte Carlo Method; D012313:RNA / Q000235:genetics; D012322:RNA Precursors; D012326:RNA Splicing; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D014158:Transcription, Genetic
chemical_list: D044946:Biflavonoids; D012322:RNA Precursors; D012333:RNA, Messenger; C452984:isoginkgetin; D012313:RNA