title: Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.
abstract: Cellular RNA levels are determined by the interplay of RNA production, processing and degradation. However, because most studies of RNA regulation do not distinguish the separate contributions of these processes, little is known about how they are temporally integrated. Here we combine metabolic labeling of RNA at high temporal resolution with advanced RNA quantification and computational modeling to estimate RNA transcription and degradation rates during the response of mouse dendritic cells to lipopolysaccharide. We find that changes in transcription rates determine the majority of temporal changes in RNA levels, but that changes in degradation rates are important for shaping sharp 'peaked' responses. We used sequencing of the newly transcribed RNA population to estimate temporally constant RNA processing and degradation rates genome wide. Degradation rates vary significantly between genes and contribute to the observed differences in the dynamic response. Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Michal
authors.initials: M
authors.lastname: Rabani
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.forename: Manuel
authors.initials: M
authors.lastname: Garber
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D019921:Biotinylation / Q000379:methods; D002478:Cells, Cultured; D019295:Computational Biology; D003713:Dendritic Cells / Q000378:metabolism; D015536:Down-Regulation; D005260:Female; D056726:Genetic Association Studies; D008070:Lipopolysaccharides / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D008958:Models, Molecular; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D015854:Up-Regulation
chemical_list: D008070:Lipopolysaccharides; D012333:RNA, Messenger; D014157:Transcription Factors; D012313:RNA; D012319:RNA Polymerase II