Global transcriptional activity in pluripotent embryonic stem cells.. Mus musculus

The molecular mechanisms underlying pluripotency and lineage specification from embryonic (ES) cells are largely unclear. Differentiation pathways may be determined by the targeted activation of lineage specific genes or by selective silencing of genome regions during differentiation. Here we show that large fractions of the ES cell genome are transcriptionally active and undergo global silencing as cells differentiate. Normally silent repeat regions are active in ES cells and tissue-specific genes are sporadically expressed at low levels. Whole genome tiling arrays demonstrate widespread transcription in both coding and non-coding regions in pluripotent ES cells whereas the transcriptional landscape becomes more discrete as differentiation proceeds. The transcriptional hyperactivity in ES cells is accompanied by disproportionate expression of chromatin-remodeling and the general transcription machinery, but not histone modifying activities. Interference with several chromatin remodeling activities in ES cells affects their proliferation and differentiation behavior. We propose that global transcriptional activity is a hallmark of pluripotent ES cells that contributes to their plasticity and that lineage specification is strongly driven by reduction of the actively transcribed portion of the genome. Keywords: mouse embryonic stem cell, time course profiling, tiling array, transcriptome Overall design: A total of 4 samples from a differentiation time course of mouse embryonic stem cell(i.e 00hr ES state, 12 hr EB state, 24 hr EB state and 168hr NPC state) were analyzed. Three independent biological replicas were generatedfor each of these samples and hybridized to the Mouse Tiling 1.0R array containing the entire mouse non-repetitive genome in 16 chips at 30bp resolution as measured from the central position of adjacent 25-mer oligonucleotides. Taken together hybridization data from 192 chips were collected to generate whole genome transcriptome information for this study.