title: Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation.
abstract: The presence of multiple variants for many mRNAs is a major contributor to protein diversity. The processing of these variants is tightly controlled in a cell-type specific manner and has a significant impact on gene expression control. Here we investigate the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC derived Neural Precursor Cells (NPCs) using polysome profiling coupled to RNA sequencing. We show that there are a significant number of detectable mRNA variants in ESCs and NPCs and that many of them show variant specific translation rates. This is correlated with differences in the UTRs of the variants with the 5'UTR playing a predominant role. We suggest that mRNA variants that contain alternate UTRs are under different post-transcriptional controls. This is likely due to the presence or absence of miRNA and protein binding sites that regulate translation rate. This highlights the importance of addressing translation rate when using mRNA levels as a read out of protein abundance. Additional analysis shows that many annotated non-coding mRNAs are present on the polysome fractions in ESCs and NPCs. We believe that the use of polysome fractionation coupled to RNA sequencing is a useful method for analysis of the translation state of many different RNAs in the cell.
authors.affiliation: Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore.
authors.forename: Queenie Wing-Lei
authors.initials: QW
authors.lastname: Wong
authors.affiliation: Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore.
authors.forename: Candida
authors.initials: C
authors.lastname: Vaz
authors.affiliation: Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore.
authors.forename: Qian Yi
authors.initials: QY
authors.lastname: Lee
authors.affiliation: Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore.
authors.forename: Tian Yun
authors.initials: TY
authors.lastname: Zhao
authors.affiliation: Life Technologies, 10 Biopolis Road, 138670, Singapore, Singapore.
authors.forename: Raymond
authors.initials: R
authors.lastname: Luo
authors.affiliation: Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia.
authors.forename: Stuart K
authors.initials: SK
authors.lastname: Archer
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Science, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra), Australian Capital Territory, Australia.|Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales, Australia.
authors.forename: Thomas
authors.initials: T
authors.lastname: Preiss
authors.affiliation: Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore.|Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore.
authors.forename: Vivek
authors.initials: V
authors.lastname: Tanavde
authors.affiliation: Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore.|School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore.
authors.forename: Leah A
authors.initials: LA
authors.lastname: Vardy
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D002454:Cell Differentiation; D002478:Cells, Cultured; D053595:Embryonic Stem Cells / Q000166:cytology / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental; D007335:Insulin-Like Growth Factor II / Q000235:genetics; D051379:Mice; D058953:Neural Stem Cells / Q000502:physiology; D011132:Polyribosomes / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; C513121:IGF2 protein, mouse; D012333:RNA, Messenger; D012261:Ribonucleoproteins; C498284:Rnps1 protein, mouse; D007335:Insulin-Like Growth Factor II