Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

Abstract

Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy-many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.

Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues

“…We also confirmed and quantified functional enrichments reported in previous studies of local regulation of gene expression in humans. We observed a large enrichment in coding regions (11.413; SE ¼ 0.87; p < 10 À12 ), which confirmed previous findings 9,14 (Table S1) and is consistent with a recent study reporting that exonic regions are often involved in transcription factor binding 45 47,48 We also observed significant enrichments at DHSs, enhancers, and TFBSs, consistent with previous studies (Table S1). We analyzed additional RNA sequencing (RNA-seq) (GTEx) and gene expression array (MuTHER) datasets spanning a total of 15 tissues (Table 1; see Material and Methods).…”

Production of Proinflammatory Cytokines by Monocytes in Liver-Transplanted Recipients with De Novo Autoimmune Hepatitis Is Enhanced and Induces TH1-like Regulatory T Cells

“…There are several possible explanations for this. Protein expression is determined at many levels including (1) RNA expression, (2) translation efficiency and (3) protein stability (48). Indeed protein levels have been shown to often correlate poorly with RNA expression (49).…”

A common class of transcripts with 5′-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification

“…Finally, we examined the relationship between 5IMP score and translation efficiency, as measured by the steady-state number of ribosomes per mRNA molecule. To this end, we used a large set of ribosome profiling and RNA-seq experiments from human lymphoblastoid cell lines (Cenik et al 2015). From this, we calculated the average number of ribosomes on each transcript and identified transcripts with high or low ribosome occupancy (respectively defined by occupancy at least one standard deviation above or below the mean; see Materials and Methods).…”

“…Translation efficiency was calculated as previously described (Cenik et al 2015). Median translation efficiency across the different cell types was used for each transcript.…”