Dynamic profiling of the protein life cycle in response to pathogens

Abstract

Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

“…Comparison with previously generated full-length libraries generated by the same laboratory, using the same protocol at two different times (Garber et al 2012;Jovanovic et al 2015), showed that the difference between end-sequence and full-length libraries was similar to the difference between full-length libraries from biological replicates made by different people at different times (Supplemental Fig. S2).…”

“…Alternative promoter and polyadenylation usage are two key mechanisms by which expression can be controlled transcriptionally or post-transcriptionally (Elkon et al 2013;de Klerk and 't Hoen 2015). Although the response of mBMDCs to LPS has been extensively characterized (Amit et al 2009;Garber et al 2012;Rabani et al 2014;Jovanovic et al 2015), the exact contribution of these two mechanisms to the transcriptional response to LPS is largely unknown.…”

“…RNA was isolated after the LPS-stimulation time course. This is a well-studied transcriptional response model for which there is a wealth of expression data available (Garber et al 2012;Rabani et al 2014;Jovanovic et al 2015). It is therefore an optimal experimental system to evaluate computational approaches for gene expression analysis of end-sequence data.…”

“…Technical replicates shown in Figure 2, and Supplemental Figures S1-S3 represent libraries made from different wells after LPS stimulation. Full-length libraries were downloaded from the Gene Expression Omnibus under accession number GSE59793 (Jovanovic et al 2015) and GSE36104 (Garber et al 2012), remapped, and requantified using RSEM (v 1.2.7) (Li and Dewey 2011) to obtain expected counts.…”

Transcriptional Signatures, Imaging, and Coronary Artery Disease Diagnosis

“…In addition, extracellular RNAs, especially microRNAs, as well as long non-coding RNAs may also be of diagnostic utility [9,10]. Finally, recent analysis of the relative global importance of transcriptional and translational regulation of protein expression has suggested that the former has been underestimated in prior work and that transcriptional regulation accounts for a large majority of variation in the expressed genome, reinforcing the importance of examining RNA levels [11][12][13].…”