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

doi:10.1016/j.stem.2013.03.003

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 journal › Article › peer-review

201 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 language	English (US)
Pages (from-to)	616-628
Number of pages	13
Journal	Cell Stem Cell
Volume	12
Issue number	5
DOIs	https://doi.org/10.1016/j.stem.2013.03.003
State	Published - May 2 2013
Externally published	Yes

ASJC Scopus subject areas

Molecular Medicine
Genetics
Cell Biology

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10.1016/j.stem.2013.03.003

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

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.",

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

note = "Funding Information: This project was supported by NIH DP2-OD006505-01, VA 1I01 BX000252-01, and the Sontag Foundation to D.A.L., NIH R01CA163336 and the Sontag Foundation to J.S.S., the UCSF Program for Breakthrough Biomedical Research, which is funded in part by the Sandler Foundation, to M.C.O., NIH GMS K12-GM081266 to G.G.-R., a training grant from the California Institute for Regenerative Medicine (CIRM) to A.D.R., MSTP training grant 2T32GM007618-34 to A.D.R. and R.N.D, and facilities and resources provided by the San Francisco Veterans Affairs Medical Center. ",

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doi = "10.1016/j.stem.2013.03.003",

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AU - Ramos, Alexander D.

AU - Diaz, Aaron

AU - Nellore, Abhinav

AU - Delgado, Ryan N.

AU - Park, Ki Youb

AU - Gonzales-Roybal, Gabriel

AU - Oldham, Michael C.

AU - Song, Jun S.

AU - Lim, Daniel A.

N1 - Funding Information: This project was supported by NIH DP2-OD006505-01, VA 1I01 BX000252-01, and the Sontag Foundation to D.A.L., NIH R01CA163336 and the Sontag Foundation to J.S.S., the UCSF Program for Breakthrough Biomedical Research, which is funded in part by the Sandler Foundation, to M.C.O., NIH GMS K12-GM081266 to G.G.-R., a training grant from the California Institute for Regenerative Medicine (CIRM) to A.D.R., MSTP training grant 2T32GM007618-34 to A.D.R. and R.N.D, and facilities and resources provided by the San Francisco Veterans Affairs Medical Center.

PY - 2013/5/2

Y1 - 2013/5/2

N2 - 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.

AB - 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.

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

Abstract

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