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.
Bibliographical noteFunding Information:
We thank S. Schwartz for assistance in analyzing splicing signals, J. Bochicchio for project management and the Broad Sequencing Platform for all sequencing work. I.A. was supported by the Human Frontiers Science Program. Work was supported by the Howard Hughes Medical Institute, a National Institutes of Health PIONEER DP1-00003958-01 award, a Burroughs Wellcome Fund Career Award at the Scientific Interface and the Merkin Foundation for Stem Cell Research at the Broad Institute (A.R.) by a US-Israel Bi-national Science Foundation award (N.F. and A.R.) and the EU FP7 “MODEL-IN” consortium grant (N.F.) .