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ABSTRACT: Genome sequencing of the African striped mouse (Rhabdomys pumilio)

PROVIDER: PRJNA858857 | ENA |

REPOSITORIES: ENA

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			Action	DRS
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	SRR20229577_1.fastq.gz	Fastqsanger.gz
	SRR20229577_2.fastq.gz	Fastqsanger.gz

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RNA sequencing of suprachiasmatic nuclues, retina, liver and lung collected at day and night from African Four Striped Mice (Rhabdomys pumilio) housed under dim vs bright daytime light

Project description:Circadian clocks are essential for generating and coordinating rhythms in animals’ physiology, behaviour, and metabolism. These activities are regulated by intracellular molecular clocks that operate with a ~24 hour periodicity. The African striped mouse, Rhabdomys pumilio, is notable for undergoing temporal niche switching from ancestrally nocturnal to diurnal, although the molecular components of its’ circadian organization remain unknown. We undertook transcriptome profiling of daily rhythms in the suprachiasmatic nucleus (SCN) and in the liver, lung and retina of Rhabdomys stably housed under a stable 12h:12h light:dark cycle with bright (n=10) or dim (n=10) daytime light intensity. Tissues were collected at two time points: two hours after lights on (Zeitgeber Time (ZT2)) coinciding with high behavioural activity, or two hours after lights off (ZT14) during the animal’s resting/sleep period, and RNA-sequencing performed.

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Project description:Rhabdomys pumilio overview

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RNA sequencing of suprachiasmatic nuclues, retina, liver and lung collected at day and night from African Four Striped Mice (Rhabdomys pumilio) housed under dim vs bright daytime light

Project description:RNA sequencing of suprachiasmatic nuclues, retina, liver and lung collected at day and night from African Four Striped Mice (Rhabdomys pumilio) housed under dim vs bright daytime light

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Project description:Environmental and evolutionary drivers of species distributions and range limits : the case of the African four striped mouse (Rhabdomys sp.)

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Project description:Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO response elements (PREs) in target mRNAs. NORAD is a noncoding RNA that negatively regulates PUMILIO activity. The goal of this study was to determine the gene expression changes that result from knockout of NORAD or overexpression of PUMILIO and to test whether NORAD knockout causes PUMILIO hyperactivity. Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Sample Preparation kit (Illumina) and sequenced using the 100 bp paired-end protocol on an Illumina HiSeq 2000. For comparing NORAD+/+ and NORAD-/- HCT116 cells, 3 biological replicates per genotype were sequenced. For PUM overexpression experiments, 3 replicates of GFP-expressing HCT116 cells (negative control) and 2 independent PUM1- or PUM2-overexpressing clones (2 replicates each) were sequenced. Results: Gene expression profiles show that PUMILIO target genes are downregulated in both NORAD knockout cells and PUMILIO overexpressing cells. Conclusions: These data indicate that NORAD sequesters PUMILIO, preventing excessive repression of PUMILIO target genes that are important for maintaining genomic stability.

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