Transcriptomics,Multiomics

Dataset Information

4

Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [microRNA expression]


ABSTRACT: Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In this study, we investigated the processes implicated in the maturation of primary neuronal cultures based on RNA expression profiling. Correlation between neuron specific gene ontologies of mRNA and non-coding RNAs identified direct regulation of axonogenesis and dendritogenesis. Temporally regulated mRNA and their associated long non-coding RNAs were significantly overrepresented in proliferation and differentiation associated signalling, cell adhesion molecules and neurotrophin signalling pathways during neuronal maturation. Long non-coding RNAs associated with Axin2, Cntn1, Ncam1, Negr1, Ntrk2, Nrxn1 and Sh2b3 displayed an inverse expression profile to their mRNA whereas long non-coding RNA -mRNA pairs for Kit, Prkcb and Ralgds displayed similar expression profiles. These genes were also predicted targets of the altered miRNAs, miR-124, -128, -129-5p, -203, -218, -290-5p, -326, -329, -377 and -495. These microRNAs particularly regulate the cell adhesion molecules, Cntn1, Ncam1, Negr1 and Nrxn1 that determine axonogenesis and dendritogenesis, supporting the observed co-regulation of these biological processes by non-coding RNAs. Verification of expression of these long non-coding RNA-mRNA pairs in an in vitro model of ischemic-reperfusion injury showed an inverse expression profile, thus confirming their role(s) in maintenance of the neuronal structure and function. This neuronal transcriptome (mRNAs, lncRNAs, miRNAs) is in turn orchestrated by C/EBPα/β transcription factors and CTCF, thereby governing intricate control of neuronal development. microRNA expression profiling of maturing primary cortical neurons from E15 mouse embryos. Maturing neurons were harvested on Days 2, 4, 6 and 8.

OTHER RELATED OMICS DATASETS IN: PRJNA192570PRJNA192569PRJNA192266

ORGANISM(S): Mus musculus  

SUBMITTER: A Armugam   S Sepramaniam  Kandiah Jeyaseelan  P Kaur  K Jeyaseelan 

PROVIDER: E-GEOD-44832 | ArrayExpress | 2014-10-24

SECONDARY ACCESSION(S): GSE44832PRJNA192569

REPOSITORIES: GEO, ArrayExpress

Dataset's files

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E-GEOD-44832.idf.txt Idf
E-GEOD-44832.processed.1.zip Processed
E-GEOD-44832.raw.1.zip Raw
E-GEOD-44832.sdrf.txt Txt
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Publications

Expression profiling of RNA transcripts during neuronal maturation and ischemic injury.

Kaur Prameet P   Karolina Dwi Setyowati DS   Sepramaniam Sugunavathi S   Armugam Arunmozhiarasi A   Jeyaseelan Kandiah K  

PloS one 20140725 7


Neuronal development is a pro-survival process that involves neurite growth, synaptogenesis, synaptic and neuronal pruning. During development, these processes can be controlled by temporal gene expression that is orchestrated by both long non-coding RNAs and microRNAs. To examine the interplay between these different components of the transcriptome during neuronal differentiation, we carried out mRNA, long non-coding RNA and microRNA expression profiling on maturing primary neurons. Subsequent  ...[more]

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