Transcriptome Profiling of Human and Murine ESCs Identifies Divergent Paths Required to Maintain the Stem Cell State

Abstract

Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

“…Previous studies have reported tissue-specific TAF variants and alterations in TAF expression (reviewed in D'Alessio et al, 2009; Müller et al, 2010), but the composition of hESC TAFs is unprecedented and is likely highly specific, if not unique, to hESCs. For example, we find that mouse ESCs, which bear both similarities and differences to hESCs (Ginis et al, 2004; Wei et al, 2005; Schnerch et al, 2010), express all TFIID TAFs analyzed (Figure 9), consistent with the results of a recent study that focused on the role of TAF3 in mouse ESCs (Liu et al, 2011).

10.7554/eLife.00068.024Figure 9.TAF expression in mouse ESCs.Immunoblot analysis monitoring TAF levels in PGK12.1 mouse ESCs and, as a control, HeLa cells.

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Assessing Self-Renewal and Differentiation in Human Embryonic Stem Cell Lines

“…hESCs are also similar in their ability to proliferate and differentiate into cell types of the three germ layers in vitro and in vivo [9 -16]. Properties of hESCs have also been compared using microarray, expressed sequence tag (EST) scan, serial analysis of gene expression (SAGE), and massively parallel signature sequencing (MPSS) [4,[17][18][19][20][21][22][23][24][25][26][27]. These studies suggest that it is likely that markers shared by hESC lines, but absent in other cell populations, exist.…”

Cell cycle dependent phosphorylation and subnuclear organization of the histone gene regulator p220NPAT in human embryonic stem cells

“…The unique proliferative properties of human ES cells may be related to a naïve transcriptome which is dedicated to self-propagation through mitotic cell division and sustenance of a pluripotent uncommitted state (Thomson et al, 1998;Amit et al, 2000;Pera et al, 2000;Bhattacharya et al, 2004;Brandenberger et al, 2004;Miura et al, 2004;Rao et al, 2004;Boyer et al, 2005;Wei et al, 2005). Defining the molecular basis of pluripotency and the capability of human ES cells for self renewal is critical for the rational design of biomedical applications of human ES cells as a cellular source for tissue replacement (Carpenter et al, 2003;Sato et al, 2003;Heins et al, 2004;Stojkovic et al, 2004;Zwaka and Thomson, 2005).…”