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Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE58112 | GEO | 2014/12/01

SECONDARY ACCESSION(S): PRJNA251348

REPOSITORIES: GEO

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Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells [Array]

Project description:To identify which genes were regulated by mRNA helicase activity, the effect of eIF4A1 knockdown on the MCF7 cell transcriptome and translatome was determined. eIF4A1-dependent mRNAs were highly enriched for several classes of genes with oncogenic potential, which leads to a model whereby dysregulation of mRNA unwinding contribues to the malignant phenotype in breast cancer cells via preferential translation of a subset of genes.

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Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells [RNA-Seq]

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Genome-wide DNA-methylation and transcriptome change due to lncRNA H19 knockdown in myotubes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis.

Project description:One gene could be transcribed to different RNA isoforms, and then produce various forms of protein sequences. This mechanism largely diversifies the cellular pool and allows natural selection to select from a wider range of substrates. In the cancer field, the isoform switches between tumor and normal tissues, such as the alternative splicing, stop codon read-through, or protein domestication, are significantly ignored by the traditional differential expression analyses. The intention of this work is to fill this gap. We collected public transcriptome and translatome data from ten patients with liver cancer, and performed genome-wide comparison on the stop codon read-through and protein domestication events. Both events diversify the proteome during long-term evolution. Surprisingly, we found that the tumor tissues globally have higher occurrence of stop codon read-through events as well as protein domestication events (translation signals of non-coding repetitive elements). These read-through and domestication events show limited overlapping across the ten patients, indicating the randomness of their occurrence and their deleterious nature. These tumor-specific events might have been purged by natural selection if they are not collected timely. Our work manifests the role of protein extension and domestication in liver cancer oncogenesis, adding new aspects to the cancer field.

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A genome-wide transcriptome and translatome analysis of <i>Arabidopsis</i> transposons identifies a unique and conserved genome expression strategy for <i>Ty1/Copia</i> retroelements.

Project description:Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similar to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant genomes, and how such features impact their biology. Genome-wide transcript profiling revealed a unique and widely conserved alternative splicing event coupled to premature termination that allows for the synthesis of a short subgenomic RNA solely dedicated to production of the GAG structural protein and that preferentially associates with polysomes for efficient translation. Mutations engineered in a transgenic version of the Arabidopsis EVD Ty1/Copia element further show how alternative splicing is crucial for the appropriate coordination of full-length and subgenomic RNA transcription. We propose that this hitherto undescribed genome expression strategy, conserved among plant Ty1/Copia elements, enables an excess of structural versus catalytic components, mandatory for mobilization.

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Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue

Project description:This SuperSeries is composed of the SubSeries listed below.

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RNMT regulates the CD4 T cell transcriptome and translatome

Project description:This SuperSeries is composed of the SubSeries listed below.

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Transcriptome and translatome co-evolution in mammals.

Project description:Gene-expression programs define shared and species-specific phenotypes, but their evolution remains largely uncharacterized beyond the transcriptome layer1. Here we report an analysis of the co-evolution of translatomes and transcriptomes using ribosome-profiling and matched RNA-sequencing data for three organs (brain, liver and testis) in five mammals (human, macaque, mouse, opossum and platypus) and a bird (chicken). Our within-species analyses reveal that translational regulation is widespread in the different organs, in particular across the spermatogenic cell types of the testis. The between-species divergence in gene expression is around 20% lower at the translatome layer than at the transcriptome layer owing to extensive buffering between the expression layers, which especially preserved old, essential and housekeeping genes. Translational upregulation specifically counterbalanced global dosage reductions during the evolution of sex chromosomes and the effects of meiotic sex-chromosome inactivation during spermatogenesis. Despite the overall prevalence of buffering, some genes evolved faster at the translatome layer-potentially indicating adaptive changes in expression; testis tissue shows the highest fraction of such genes. Further analyses incorporating mass spectrometry proteomics data establish that the co-evolution of transcriptomes and translatomes is reflected at the proteome layer. Together, our work uncovers co-evolutionary patterns and associated selective forces across the expression layers, and provides a resource for understanding their interplay in mammalian organs.

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