RT Journal
A1 Kolle, Gabriel
A1 Shepherd, Jill L.
A1 Gardiner, Brooke
A1 Kassahn, Karin S.
A1 Cloonan, Nicole
A1 Wood, David L.A.
A1 Nourbakhsh, Ehsan
A1 Taylor, Darrin F.
A1 Wani, Shivangi
A1 Chy, Hun S.
A1 Zhou, Qi
A1 McKernan, Kevin
A1 Kuersten, Scott
A1 Laslett, Andrew L.
A1 Grimmond, Sean M.
T1 Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
JF Genome Research 
JO Genome Research 
YR 2011 
FD December 01 
VO 21 
IS 12 
SP 2014 
OP 2025 
DO 10.1101/gr.119321.110 
UL http://genome.cshlp.org/content/21/12/2014.abstract 
AB 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.