Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

Kolle, Gabriel, Shepherd, Jill L., Gardiner, Brooke, Kassahn, Karin S., Cloonan, Nicole, Wood, David L. A., Nourbakhsh, Ehsan, Taylor, Darrin F., Wani, Shivangi, Chy, Hun S., Zhou, Qi, McKernan, Kevin, Kuersten, Scott, Laslett, Andrew L. and Grimmond, Sean M. (2011) Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells. Genome Research, 21 12: 2014-2025. doi:10.1101/gr.119321.110


Author Kolle, Gabriel
Shepherd, Jill L.
Gardiner, Brooke
Kassahn, Karin S.
Cloonan, Nicole
Wood, David L. A.
Nourbakhsh, Ehsan
Taylor, Darrin F.
Wani, Shivangi
Chy, Hun S.
Zhou, Qi
McKernan, Kevin
Kuersten, Scott
Laslett, Andrew L.
Grimmond, Sean M.
Title Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2011-12
Sub-type Article (original research)
DOI 10.1101/gr.119321.110
Open Access Status DOI
Volume 21
Issue 12
Start page 2014
End page 2025
Total pages 12
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Collection year 2012
Language eng
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.
Keyword Eukaryotic Transcriptome
Differentiation
Identification
Elements
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Institute for Molecular Bioscience - Publications
 
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