E-GEOD-37338 - Genome-wide non-polyadenylated transcription in differentiating mouse embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

Released on 17 April 2013, last updated on 25 April 2013
Mus musculus
Samples (2)
Protocols (3)
The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention in recent years, but reports have so far been confined to the polyadenylated fraction of RNA, while the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family, which is mainly comprised of fundamental components of the RNA translational machinery, the RNA splicing machinery, and RNA-RNA or RNA-DNA interacting complexes, has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in murine ESCs and ESC-derived Neural Progenitor Cells (NPCs) using a combination of whole genome tiling arrays and Next Generation Sequencing technologies. This strategy allowed for the transcriptional characterization of already well-defined NPA RNA subclasses in this unique biological context as well as the identification of many new members of these functional ncRNA classes. In addition, we describe a group of novel, conserved RNAs (snacRNAs: small, non-polyadenylated conserved), some of which are differentially expressed between ESC and NPCs, providing the first evidence of a novel group of potentially functional ncRNAs involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal snRNAs, which are non-polyadenylated, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that non-polyadenylated RNA, both known and novel, play important roles in embryonic stem cells. We extracted total RNA from undifferentiated ESCs and 7 day NPCs. Total RNA was divided into poly(A+) and poly(A-) enriched fractions using a modified version of Oligotex extraction (Qiagen). Briefly, after the hybridization of the total RNA to oligo(dT) beads, supernatants were saved rather than discarded and then subjected to isopropanol-ethanol extraction to obtain the Poly(A-) fraction. This submission represents RNA-Seq component of study.
Experiment type
RNA-seq of coding RNA 
Ilana Livyatan <ilana.forst-livya@mail.huji.ac.il>, Eran Meshorer, Malka Nissim-Rafinia, Radha Duttagupta, Thomas R Gingeras
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-37338.idf.txt
Sample and data relationshipE-GEOD-37338.sdrf.txt
Processed data (2)E-GEOD-37338.processed.1.zip, E-GEOD-37338.processed.2.zip