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Substantial and robust changes in microRNA transcriptome support postnatal development of the hypothalamus in rat.

Scientific reports | 2016

MicroRNAs (miRNAs) modulate gene expression in male germ cells and somatic tissues of mammals on a genome-wide scale. Hundreds of miRNAs are encoded by mammalian genomes, a large fraction of which is expressed in brain. Here we have investigated the complexity and dynamics of miRNA transcriptomes that associate with neuronal network maturation of hypothalamic arcuate nucleus and median eminence (ARC/ME) in rat by analysing more than 300 miRNAs from 3-7 biological replicates at 5 postnatal time-points. The network connecting ARC/ME to other hypothalamic and extra-hypothalamic regions maturates in an environment-dependent manner. We therefore analyzed miRNA transcriptomes of progeny of dams fed either a balanced or unbalanced diet during gestation and lactation. More than 30% of the miRNAs displayed significative changes of expression between stages P8 and P14, and P21 and P28; half of the changes were greater than 3-fold. Among those miRNAs were well-known and dozens of still poorly documented miRNAs. Progeny of dams fed an unbanced diet displayed a severe growth retardation phenotype, lower levels of plasma leptin but almost identical miRNA transcriptomes. Together these data demonstrate that two substantial and robust changes in miRNA transcriptome of ARC/ME occur at a period crucial for neuronal network functional organization.

Pubmed ID: 27118433 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


miRanalyzer (tool)

RRID:SCR_000163

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.

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miRBase (tool)

RRID:SCR_003152

Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.

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FastQC (tool)

RRID:SCR_014583

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

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miRDeep (tool)

RRID:SCR_010829

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

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