title: The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype.
abstract: BACKGROUND
  The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell's protein composition. Since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. However, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mRNA population (the translatome). This is particularly pertinent for genes using multiple transcriptional start sites (TSS) generating mRNAs with heterogeneous 5' transcript leaders (5'TL). Furthermore, the relative abundance of the TSS gene variants is frequently cell-type specific. Indeed, promoter switches have been reported in pathologies such as cancer. The consequences of this 5'TL heterogeneity within the transcriptome for the translatome remain unresolved. This is not a moot point because the 5'TL plays a key role in regulating mRNA recruitment onto polysomes.
  
  
  RESULTS
  In this article, we have characterised both the transcriptome and translatome of the MCF7 (tumoural) and MCF10A (non-tumoural) cell lines. We identified ~550 genes exhibiting differential translation efficiency (TE). In itself, this is maybe not surprising. However, by focusing on genes exhibiting TSS heterogeneity we observed distinct differential promoter usage patterns in both the transcriptome and translatome. Only a minor fraction of these genes belonged to those exhibiting differential TE. Nonetheless, reporter assays demonstrated that the TSS variants impacted on the translational readout both quantitatively (the overall amount of protein expressed) and qualitatively (the nature of the proteins expressed).
  
  
  CONCLUSIONS
  The results point to considerable and distinct cell-specific 5'TL heterogeneity within both the transcriptome and translatome of the two cell lines analysed. This observation is in-line with the ribosome filter hypothesis which posits that the ribosomal machine can selectively filter information from within the transcriptome. As such it cautions against the simple extrapolation transcriptome → proteome. Furthermore, polysomal occupancy of specific gene 5'TL variants may also serve as novel disease biomarkers.
authors.affiliation: Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Francois-Xavier
authors.initials: FX
authors.lastname: Dieudonné
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Patrick B F
authors.initials: PB
authors.lastname: O'Connor
authors.affiliation: Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Pascale
authors.initials: P
authors.lastname: Gubler-Jaquier
authors.affiliation: Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Haleh
authors.initials: H
authors.lastname: Yasrebi
authors.affiliation: Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.|Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Beatrice
authors.initials: B
authors.lastname: Conne
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Sergey
authors.initials: S
authors.lastname: Nikolaev
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.|The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
authors.forename: Stylianos
authors.initials: S
authors.lastname: Antonarakis
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.affiliation: Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland. Joseph.Curran@unige.ch.|The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. Joseph.Curran@unige.ch.
authors.forename: Joseph
authors.initials: J
authors.lastname: Curran
mesh_terms: D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D005786:Gene Expression Regulation; D006801:Humans; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D011132:Polyribosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D012315:RNA Caps; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D012315:RNA Caps; D012333:RNA, Messenger