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Translatome of A549, H1299 and HBE cells

ABSTRACT: We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes

ORGANISM(S): Homo sapiens

PROVIDER: GSE42006 | GEO | 2013/03/05

SECONDARY ACCESSION(S): PRJNA178748

REPOSITORIES: GEO

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Translatome of A549, H1299 and HBE cells

Project description:We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes Total RNA and ribosome-bound RNA were extracted from A549, H1299 and HBE cells, and the polyA+ mRNA was sequenced using Illumina GAIIx and HiSeq-2000. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

2013-03-05 | E-GEOD-42006 | biostudies-arrayexpress

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Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

Project description:As a well-known phenomenon, total mRNAs poorly correlate to proteins in their abundances as reported. Recent findings calculated with bivariate models suggested even poorer such correlation, whereas focusing on the translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) subset. In this study, we analysed the relative abundances of mRNAs, RNC-mRNAs and proteins on genome-wide scale, comparing human lung cancer A549 and H1299 cells with normal human bronchial epithelial (HBE) cells, respectively. As discovered, a strong correlation between RNC-mRNAs and proteins in their relative abundances could be established through a multivariate linear model by integrating the mRNA length as a key factor. The R2 reached 0.94 and 0.97 in A549 versus HBE and H1299 versus HBE comparisons, respectively. This correlation highlighted that the mRNA length significantly contributes to the translational modulation, especially to the translational initiation, favoured by its correlation with the mRNA translation ratio (TR) as observed. We found TR is highly phenotype specific, which was substantiated by both pathway analysis and biased TRs of the splice variants of BDP1 gene, which is a key transcription factor of transfer RNAs. These findings revealed, for the first time, the intrinsic and genome-wide translation modulations at translatomic level in human cells at steady-state, which are tightly correlated to the protein abundance and functionally relevant to cellular phenotypes.

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Project description:We performed ribosome profiling to assess the translation elongation on translating RNA in HBE, A549, and H1299. We detected the new proteins in the cells.

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Project description:We evaluated the profile of lncRNA and mRNA expression in control and 50Î¼g/ml DEP treated HBE cells using the Arraystar Human LncRNA Array v3.0 array,7th generation. Our findings implicates that dysregulation of mitochondria invovled mRNAs may play important role in cytotoxicity of DEP. Examination of lncRNA and mRNA expression in control or DEP-treated HBE cells

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