Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.
mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Roshan
R
Mascarenhas
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America; Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America.
Maciej
M
Pietrzak
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Ryan M
RM
Smith
Department of Biomedical Informatics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Amy
A
Webb
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Danxin
D
Wang
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Audrey C
AC
Papp
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Julia K
JK
Pinsonneault
Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America; Department of Mathematics and Computer Science, University of Lodz, Lodz, Poland; Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, United States of America.
Michal
M
Seweryn
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America; Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America; Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, United States of America.
Grzegorz
G
Rempala
Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America; Department of Medical Genetics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.
Wolfgang
W
Sadee
D018435:ATP Binding Cassette Transporter, Subfamily B / Q000235:genetics; D000483:Alleles; D000818:Animals; D001191:Arylamine N-Acetyltransferase / Q000235:genetics; D016466:CHO Cells; D002460:Cell Line; D003412:Cricetulus; D006367:HeLa Cells; D006801:Humans; D007527:Isoenzymes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011132:Polyribosomes / Q000235:genetics*; D014176:Protein Biosynthesis; D059368:RNA Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D017450:Receptors, Opioid, mu / Q000235:genetics; D059467:Transcriptome
C513055:ABCB1 protein, human; D018435:ATP Binding Cassette Transporter, Subfamily B; D007527:Isoenzymes; C485764:OPRM1 protein, human; D059368:RNA Isoforms; D012333:RNA, Messenger; D022661:RNA, Untranslated; D017450:Receptors, Opioid, mu; D001191:Arylamine N-Acetyltransferase; C089384:N-acetyltransferase 1