SRA

MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established. We describe here a new map of the transcriptional regulatory circuitry of ES cells that incorporates both protein-coding and miRNA genes, and which is based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types. We find that the key ES cell transcription factors are associated with promoters for most miRNAs that are preferentially expressed in ES cells and with promoters for a set of silent miRNA genes. This silent set of miRNA genes is co-occupied by Polycomb Group proteins in ES cells and expressed in a tissue-specific fashion in differentiated cells. These data reveal how key ES cell transcription factors promote the miRNA expression program that contributes to self-renewal and cellular differentiation, and integrate miRNAs and their targets into an expanded model of the regulatory circuitry controlling ES cell identity. Keywords: ChIP-seq analysis of ES cell transcriptional regulators and chromatin modifications. Cell-type comparison of short RNA transcritome. Analysis of changes in short RNA transcritome upon Oct4 ablation. Overall design: ChIP-seq in murine embryonic stem cells for Oct4, Sox2 (2 runs), Nanog (2 runs), Tcf3 (2 runs), Suz12 (2 runs), H3K4me3 (4 runs), H3k79me2 (2 runs), H3k36me3 (2 runs) and whole cell extract input DNA (WCE, 2 runs). Short transcript sequencing from murine embryonic stem cells (mES, v6.5), mouse embryonic fibroblasts (MEF), murine neural precursor cells (NPC), and ZHBT-c4 cells (from Austin Smith) untreated (0h), with 12 hours of doxycyclin treatment (12h), and with 24 hours of doxycyclin treatment (24h).