The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

BMC Genomics

Research Article

Sergey Nikolaev¹  Stylianos Antonarakis²  Pascale Gubler-Jaquier³  Francois-Xavier Dieudonné³  Haleh Yasrebi³  Beatrice Conne⁴  Joseph Curran⁵  Patrick B. F. O’Connor⁶  Pavel V. Baranov⁶ 

[1] Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland;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;Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland;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;Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland;The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland;School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland;

关键词: Translatome;    Transcriptome;    Proteome;    5′ mRNA heterogeneity;    5′ transcript leader;    Translation;    Cancer;   

DOI  :  10.1186/s12864-015-2179-8

 received in 2015-06-19, accepted in 2015-10-31,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsIn 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).ConclusionsThe 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.

【 授权许可】

CC BY   
© Dieudonné et al. 2015