Selective translational usage of TSS and core promoters revealed by translatome sequencing

Abstract

Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. Electronic supplementary material The online version of this article (10.1186/s12864-019-5650-0) contains supplementary material, which is available to authorized users.

Implications of differential transcription start site selection on chronic myeloid leukemia and prostate cancer cell protein expression

“…However, although previous studies have reported the translational impact of transcripts isoforms derived from multiple closely situated promoters, 19 , 25 , 26 , 27 , 28 , 29 minor TSSs (alternative TSS selection within the same cluster) have been considered as nonadaptive and the product of molecular errors. 30 …”

“…This highlights a potential relevance in gene expression regulation. After all, a differential TSS selection will change the overall length of the mRNA 5' UTR, likely altering the presence of regulatory elements such as upstream open reading frames (uORF); upstream start codons (uAUG); RNA secondary structures; and internal ribosomal entries sites 19-24 . However, although previous studies have reported the translational impact of transcripts isoforms derived from multiple closely situated promoters 19,[25][26][27][28][29] , minor TSSs (alternative TSS selection within the same cluster) have been considered as nonadaptive and the product of molecular errors 30 .…”

Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells

“…Particularly, CAGE was originally used to construct a precise map of transcription start sites (TSSs) and elucidate the "promoteromes" of mammalian cells and tissues. In one analysis involving the tagging of m7G caps on mRNAs, nearly 25% of mammalian m7G caps were not located at already known TSS (14,15). Whole-transcriptome network analyses via technologies such as CAGE might enable a much more comprehensive understanding of the divergence of promoteromes in the precursors of malignancies such as pancreatic cancer (16).…”