Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations

Frontiers in Cellular Neuroscience
Beena M KadakkuzhaSathyanarayanan V Puthanveettil

Abstract

Despite the importance of the long non-coding RNAs (lncRNAs) in regulating biological functions, the expression profiles of lncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC), the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2759 lncRNAs and 17,859 mRNAs in the hippocampus and 2561 lncRNAs and 17,464 mRNAs expressed in the PFC. The lncRNAs identified correspond to ~14% of the transcriptome of the hippocampus and PFC and ~70% of the lncRNAs annotated in the mouse genome (NCBIM37) and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that a few of the tested lncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic lncRNA expression signatures. These results reveal an unexpected complexity of the lncRNA expression in the mouse brain.

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Datasets Mentioned

BETA
GM14290
GM9968
GM2115
GM13644
GM11549
GM12371

Methods Mentioned

BETA
RNAseq
laser capture microdissection
RNA-Seq
PCR
RNA seq
in vitro transcription
dissection

Software Mentioned

Qiagen
Ingenuity Pathway Analysis (
HTSeq
Tophat2
Tophat
Cufflinks
Ingenuity Pathway Analysis
R Bioconductor
IPA
DESeq

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