Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors.

Neuroscience Bulletin
Kuan TianYan Zhou

Abstract

Long non-coding RNAs (lncRNAs) regulate transcription to control development and homeostasis in a variety of tissues and organs. However, their roles in the development of the cerebral cortex have not been well elucidated. Here, a bioinformatics pipeline was applied to delineate the dynamic expression and potential cis-regulating effects of mouse lncRNAs using transcriptome data from 8 embryonic time points and sub-regions of the developing cerebral cortex. We further characterized a sense lncRNA, SenZfp536, which is transcribed downstream of and partially overlaps with the protein-coding gene Zfp536. Both SenZfp536 and Zfp536 were predominantly expressed in the proliferative zone of the developing cortex. Zfp536 was cis-regulated by SenZfp536, which facilitates looping between the promoter of Zfp536 and the genomic region that transcribes SenZfp536. Surprisingly, knocking down or activating the expression of SenZfp536 increased or compromised the proliferation of cortical neural progenitor cells (NPCs), respectively. Finally, overexpressing Zfp536 in cortical NPCs reversed the enhanced proliferation of cortical NPCs caused by SenZfp536 knockdown. The study deepens our understanding of how lncRNAs regulate the propagation of co...Continue Reading

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Datasets Mentioned

BETA
GSE55600

Methods Mentioned

BETA
dissection
RNA-seq
Assay
electrophoresis
in vitro transcription
X-ray
PCR
acetylation
HiC-Seq
ChIP-seq

Software Mentioned

R package ‘ pheatmap ’
ShinyGO
WGCNA
CPC2 ( Coding Potential Calculator )
R package
CPAT ( Coding - Potential Assessment Tool )
GREAT
StringTie
WGCNA ( Weighted Gene Co - Expression Network Analysis )
L2L

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