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Related Experiment Video

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Single-cell analysis of long non-coding RNAs in the developing human neocortex.

Siyuan John Liu1,2,3, Tomasz J Nowakowski2,4,3, Alex A Pollen2,4,3

  • 1Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.

Genome Biology
|April 16, 2016
PubMed
Summary

Long non-coding RNAs (lncRNAs) are abundant in individual human brain cells, not just in bulk tissue. This cell-specific expression is key to understanding brain development and distinguishing neural cell types.

Keywords:
CRISPRiDeveloping brainSingle-cell RNA-seqlncRNA

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Area of Science:

  • Neuroscience
  • Molecular Biology
  • Genetics

Background:

  • Long non-coding RNAs (lncRNAs) regulate crucial molecular and cellular processes in brain development and disease.
  • LncRNA expression is known to be cell type- and tissue-specific, yet their role in the developing human brain remains largely unexplored.
  • It is unclear if lncRNAs are highly expressed in specific cell subsets within tissues, despite low expression in bulk samples.

Purpose of the Study:

  • To deeply profile lncRNA expression in the developing human neocortex.
  • To investigate the cell type-specific expression patterns of lncRNAs using single-cell transcriptomics.
  • To determine the functional role of specific lncRNAs in neural cell development.

Main Methods:

  • Strand-specific RNA sequencing (RNA-seq) of polyadenylated and total RNA from human neocortex across developmental stages.
  • Single-cell transcriptomic analysis of hundreds of neocortex cells.
  • CRISPR interference (CRISPRi) mediated knockdown of the lncRNA LOC646329.

Main Results:

  • Deep profiling revealed that while lncRNAs show low expression in bulk tissues, many are abundantly expressed in individual cells.
  • Single-cell transcriptomics demonstrated cell type-specific expression patterns for numerous lncRNAs.
  • The lncRNA LOC646329 was found to be enriched in radial glia cells and its knockdown regulated cell proliferation.

Conclusions:

  • lncRNAs exhibit discrete and abundant expression within individual neural cells.
  • This cell-specific expression has significant implications for understanding lncRNA biological function.
  • lncRNAs can serve as valuable markers for distinguishing different neural cell types.