Regulating RNA Polymerase Pausing and Elongation in Embryonic Stem Cell Transcription

Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome’s primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide, nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally-engaged RNA polymerases in mouse embryonic stem cells (ESCs) and embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ~40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II’s entry into elongation. Furthermore, “bivalent” ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb Group Complexes PRC 1 and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5’ proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation. Overall design: Mapping engaged RNA polymerase density in two cell types by sequencing run-on transcripts. SUPPLEMENTARY FILES: All fastq files have sanger-fastq format q values. Alignments were generated with eland and the mm9 mouse genome assembly. Reads aligning to regions annotated as similar to rRNA by RepeatMasker were then removed. Wiggle files are in units of RPKM (reads per kilobase per million aligned reads) and are broken up by cell type and chromosome to aid in uploading to UCSC. Each file furthermore contains two tracks - one for each strand. As in the published paper, plus strand RPKM densities are in red with positive values and minus strand RPKM densities are in blue with negative values.

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Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT