Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

Shin, Jaehoon, Berg, Daniel A, Zhu, Yunhua, Shin, Joseph Y, Song, Juan, Bonaguidi, Michael A, Enikolopov, Grigori, Nauen, David W, Christian, Kimberly M, Ming, Guo-li, Song, Hongjun (August 2015) Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. Cell Stem Cell, 17 (3). pp. 360-372. ISSN 1934-5909

URL: http://www.ncbi.nlm.nih.gov/pubmed/26299571
DOI: 10.1016/j.stem.2015.07.013

Abstract

Somatic stem cells contribute to tissue ontogenesis, homeostasis, and regeneration through sequential processes. Systematic molecular analysis of stem cell behavior is challenging because classic approaches cannot resolve cellular heterogeneity or capture developmental dynamics. Here we provide a comprehensive resource of single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny. We further developed Waterfall, a bioinformatic pipeline, to statistically quantify singe-cell gene expression along a de novo reconstructed continuous developmental trajectory. Our study reveals molecular signatures of adult qNSCs, characterized by active niche signaling integration and low protein translation capacity. Our analyses further delineate molecular cascades underlying qNSC activation and neurogenesis initiation, exemplified by decreased extrinsic signaling capacity, primed translational machinery, and regulatory switches in transcription factors, metabolism, and energy sources. Our study reveals the molecular continuum underlying adult neurogenesis and illustrates how Waterfall can be used for single-cell omics analyses of various continuous biological processes.

Item Type: Paper
Subjects: organism description > animal > developmental stage > adult
organs, tissues, organelles, cell types and functions > cell types and functions > cell functions > neurogenesis
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > Enikopolov lab
Depositing User: Matt Covey
Date: 20 August 2015
Date Deposited: 24 Aug 2015 18:45
Last Modified: 01 Dec 2015 15:49
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31696

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