The maturing of the human embryonic stem cell transcriptome profile

doi:10.1016/j.tibtech.2004.10.001

Trends in Biotechnology

Volume 22, Issue 12, December 2004, Pages 609-612

https://doi.org/10.1016/j.tibtech.2004.10.001 Get rights and content

Several recent reports used microarray, serial analysis of gene expression (SAGE), and expressed sequence tags (EST) strategies to characterize the human embryonic stem cell transcriptome and those of their differentiated derivatives. All three approaches yielded valuable data and highlight the fact that a large percentage of genes remain uncharacterized in these cells representative of early human development.

Section snippets

Microarrays

Microarrays are the most accessible transcriptome profiling method available because they allow the expression analysis of thousands of genes relatively quickly and inexpensively. Worth mentioning is the likely over-estimation of gene content on the vast majority of current microarrays due to incomplete annotation of the human genome and redundancy in the Unigene database (http://www.ncbi.nlm.nih.gov/UniGene/; there are currently 106 000 human Unigene clusters for an estimated 30 000 genes).

Short sequence tag detection

Methods generating short tag sequences (10–20 bp) with frequencies representative of gene expression are useful because they are not dependent on prior expression information. A caveat is the possible mapping ambiguities resulting from such short sequences. Serial analysis of gene expression (SAGE) was employed by Richards et al. [13] to generate a combined total of 145 015 SAGE tags from undifferentiated ES03 and ES04 hESC lines containing 11 404 distinct tags with counts of 2 or greater.

Generation of expressed sequence tags

The lack of hESC expressed sequence information led Brandenberger et al. to choose the EST approach to expression profiling [6]. The ability to generate de novo sequence – with lengths that would provide unambiguous mapping to the human genome – were clear advantages. Tens of thousands of high quality ESTs from four different hESC-derived RNA populations were generated from the WA01, WA07, and WA09 lines (Table 1). Undifferentiated hESC grown feeder-free (GRN_ES) were compared with three

The known genes: insights into hESC biology

Despite the level of novelty in the hESC transcriptome, all these hESC expression profiling studies provide extremely useful information on known molecular pathways. For instance a view of the hESC transcriptome can explain the previously determined lack of responsiveness of these cells to leukemia inhibitory factor (LIF) as the microarray, SAGE, and EST studies 6, 8, 13 all reveal the absence or at least very minimal expression of the two receptors (LIFR and IL6ST/gp130) responsible for

Concluding remarks

From the transcriptome studies completed to date it is clear that hESCs and their differentiating derivatives contain a large number of transcripts that remain uncharacterized be it ESTs, genes encoding hypothetical proteins or genes whose transcripts have yet to be identified. This highlights the need to continue the sequencing (and the corresponding annotation) of transcripts from hESC-derived cell-types both to extend current ESTs into full-length transcripts and to continue to identify

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Trends in Biotechnology

Research FocusThe maturing of the human embryonic stem cell transcriptome profile

Section snippets

Microarrays

Short sequence tag detection

Generation of expressed sequence tags

The known genes: insights into hESC biology

Concluding remarks

Trends Biotechnol.

Dev. Biol.

Blood

Dev. Biol.

Dev. Biol.

Embryonic stem cell lines derived from human blastocysts

Science

Transcriptome Analysis of Mouse Stem Cells and Early Embryos

PLoS Biol.

BMP4 initiates human embryonic stem cell differentiation to trophoblast

Nat. Biotechnol.

Research Focus
The maturing of the human embryonic stem cell transcriptome profile