Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo

Alexander D. Ramos, Aaron Diaz, Abhinav Nellore, Ryan N. Delgado, Ki Youb Park, Gabriel Gonzales-Roybal, Michael C. Oldham, Jun S. Song, Daniel A. Lim

Research output: Contribution to journalArticle

150 Scopus citations

Abstract

Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease.

Original languageEnglish (US)
Pages (from-to)616-628
Number of pages13
JournalCell Stem Cell
Volume12
Issue number5
DOIs
StatePublished - May 2 2013

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ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Cell Biology

Cite this

Ramos, A. D., Diaz, A., Nellore, A., Delgado, R. N., Park, K. Y., Gonzales-Roybal, G., Oldham, M. C., Song, J. S., & Lim, D. A. (2013). Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell, 12(5), 616-628. https://doi.org/10.1016/j.stem.2013.03.003