Expression of mRNA transcripts encoding membrane transporters detected with whole transcriptome sequencing of human brain and liver

Abstract

Background: Membrane transporters control the influx and efflux of endogenous and xenobiotic substrates, including nutrients and drugs, across cellular membranes.

Objective: Whole transcriptome sequencing enables simultaneous analysis of overall and allele-specific mRNA expression, and the detection of multiple RNA isoforms.

Methods: Here we characterize variation in RNA transcripts emanating from gene loci encoding transporters based on RNAseq data from 10 human brains (including cocaine overdose and normal brain tissues) and 12 normal livers.

Results: mRNA expression was detected in 65% of transporter genes in either tissue, with many genes generating multiple mRNA transcripts. Single-nucleotide polymorphisms within transporters with previous evidence for pharmacogenomics impact were detected. We also identified noncoding RNAs in the vicinity of transporter genes with potential regulatory functions.

Conclusion: The results obtained with RNAseq provide detailed information on transporter mRNA expression at the molecular level, affording new avenues for the study of membrane transport, with relevance to drug efficacy and toxicity.

Fig. 1

Read alignments across SLC38A2, using the Integrative Genomic Viewer. Read alignments for four liver samples are shown. Although peaks locate over the annotated exonic regions, peaks also occur consistently within the intronic regions. The range of the histogram is between 0 and 1000 reads for each sample. The height of the peak indicates the number of reads covering a base location. Exon locations are indicated as gray boxes along the line at the bottom of the figure.

Fig. 2

Correlation of expression estimated by RNAseq and RT-PCR. Plot of the log₁₀ transform of the average measurement of expression by RT-PCR and RNAseq is shown. Brain and liver are plotted separately. Comparing each tissue separately yielded a correlation of r=0.94 for each.

Fig. 3

(a) Transcripts assembled by Cufflinks for SLC22A1. Transcripts assembled by Cufflinks for SLC22A1, limited to unique transcripts highlighting the major differences such as extended 3′-UTR or missing exons are shown, (b) Sizes of PCR products detected from SLC22A1. Shown are the peaks detected from fluorescent PCR of sequences from SLC22A1. Peaks with heights greater than 800 were detected at 1 04, 207, 221, and 321, corresponding to transcripts including or excluding of exons 9 and 10, consistent with the transcript predicted from RNAseq (Fig. 3a). UTR, untranslated region.