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Genome-wide maps of histone H3K9 acetylation in the mouse strains C57BL/6J, MSM/Ms, and their F1 hybrids

ABSTRACT: Genome-wide maps of histone H3K9 acetylation in the mouse strains C57BL/6J, MSM/Ms, and their F1 hybrids

PROVIDER: PRJNA657437 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12459186_1.fastq.gz	Fastqsanger.gz
	SRR12459186_2.fastq.gz	Fastqsanger.gz
	SRR12459187_1.fastq.gz	Fastqsanger.gz
	SRR12459187_2.fastq.gz	Fastqsanger.gz
	SRR12459188_1.fastq.gz	Fastqsanger.gz

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Gene expression in livers and thymi of uninjected or MegaFasL-injected C57BL/6 and MSM/Ms mice

Project description:Here we examine the expression of genes in unstimulated or following intraperitoneal injection with MegaFasL in MSM/Ms and C57BL/6 mouse livers and thymi This dataset is from two groups of 2 mice (1 MSM/Ms [MSM] and 1 C57BL/6 [B6] mouse) - either untreated (#1-#4) or injected intraperitoneally with 1.5ug of MegaFasL (#5-#8). Each group has four (4) samples - one liver (L) and one thymus (T) sample from each mouse. The liver and thymi were harvested from the same mouse. Unstimulated samples: 1_S1 = B6 T, 2_S=MSM T, 3_S3=B6 L, 4_S4=MSM L; MegaFasL-injected samples: 5_S1=B6 T, 6_S2=MSM T, 7_S3=B6 L, 8_S4=MSM L.

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Gene expression analysis of mouse F1 hybrids to study cis regulatory variations

Project description:To analyze the difference in gene expression between alleles of F1 hybrids of mouse C57BL6/J (B6) and MSM/Ms (MSM) strains, we sequenced these F1 hybrids of reciprocal crosses. While most genes did show allelic bias, a small number of genes showed either B6- or MSM-biaed expression in both crosses. These allelic differences were associated with the allelic differences in histone acetylation in promoter regions determined by another experiments.

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Genome-wide maps of histone H3K9 acetylation in the mouse strains C57BL/6J, MSM/Ms, and their F1 hybrids

Project description:More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of B1 and B2 SINE families within Mus musculus. Using a novel RNA sequencing method developed here, we detected the expression of SINEs in testes at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs contained transcripts from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses revealed that polymorphic B2 insertions served as a chromatin boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, a total of > 100 polymorphic B2 insertions were bound by CTCF, a well-known chromatin boundary protein. These results suggest that the currently active B2 copies are mobile chromatin boundary elements that can modulate gene expression level, and are likely involved in epigenomic and phenotypic diversification of the mouse species.

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Expression data from liver of male mouse at 10-week-old

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