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Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells (part 2)

ABSTRACT: Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken a strand-specific RNA sequencing of multiple cellular RNA fractions (>18Gb) to uncover the transcriptional complexity of human ES cells. We have shown that human ES cells display a high degree of transcriptional diversity, with more than half? of active genes generating RNAs that differ from conventional gene models. We found evidence that more than >1000 genes express long 5’ and/or extended 3’ UTRs, which was confirmed by “virtual northern” analysis. Exhaustive sequencing the membrane-polysome and cytosolic/untranslated fractions of hESC was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. Finally, the impact of this newly defined transcriptional complexity on known gene-centric network models such as the Plurinet and the cell surface signalling machinery in human ES cells revealed a significant expansion of protein coding components at play, many of which alternative actions based on altered domain content.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25842 | GEO | 2011/07/01

SECONDARY ACCESSION(S): PRJNA135759

REPOSITORIES: GEO

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Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells (part 2)

Project description:Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken a strand-specific RNA sequencing of multiple cellular RNA fractions (>18Gb) to uncover the transcriptional complexity of human ES cells. We have shown that human ES cells display a high degree of transcriptional diversity, with more than half? of active genes generating RNAs that differ from conventional gene models. We found evidence that more than >1000 genes express long 5’ and/or extended 3’ UTRs, which was confirmed by “virtual northern” analysis. Exhaustive sequencing the membrane-polysome and cytosolic/untranslated fractions of hESC was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. Finally, the impact of this newly defined transcriptional complexity on known gene-centric network models such as the Plurinet and the cell surface signalling machinery in human ES cells revealed a significant expansion of protein coding components at play, many of which alternative actions based on altered domain content. Human ES cells fractionated for mRNA, cytosolic polysome, membrane polysome

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