title: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.
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 strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (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 of the membrane-polysome and cytosolic/untranslated fractions of hESCs 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. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains.
authors: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Queensland 4072, Australia.
authors: Gabriel
authors: G
authors: Kolle
authors: Jill L
authors: JL
authors: Shepherd
authors: Brooke
authors: B
authors: Gardiner
authors: Karin S
authors: KS
authors: Kassahn
authors: Nicole
authors: N
authors: Cloonan
authors: David L A
authors: DL
authors: Wood
authors: Ehsan
authors: E
authors: Nourbakhsh
authors: Darrin F
authors: DF
authors: Taylor
authors: Shivangi
authors: S
authors: Wani
authors: Hun S
authors: HS
authors: Chy
authors: Qi
authors: Q
authors: Zhou
authors: Kevin
authors: K
authors: McKernan
authors: Scott
authors: S
authors: Kuersten
authors: Andrew L
authors: AL
authors: Laslett
authors: Sean M
authors: SM
authors: Grimmond
mesh_terms: D020413:3' Untranslated Regions / Q000502:physiology*; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D008957:Models, Genetic; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome / Q000502:physiology*
chemical_list: D020413:3' Untranslated Regions