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Mus musculus

ABSTRACT: Genome-wide EBF1 occupancy in pro-B cells

PROVIDER: PRJNA315009 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3222625_1.fastq.gz	Fastqsanger.gz
	SRR3222625_2.fastq.gz	Fastqsanger.gz
	SRR3222626_1.fastq.gz	Fastqsanger.gz
	SRR3222626_2.fastq.gz	Fastqsanger.gz
	SRR3222627_1.fastq.gz	Fastqsanger.gz

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Mus musculus

Project description:Genome-wide occupancy of EBF1-wt & EBF1-H240A

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Interaction of CNOT3 with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis

Project description:EBF1 interacts with CNOT3 and histidine 240 of EBF1 is a critical residue for this interaction. We studied H240 dependent EBF1 occupancy and gene expression regulation by genome-wide ChIP and microarray analysis. We also performed RNASeq analysis in pro-B cells to study the role of Cnot3 in early B cells development. This SuperSeries is composed of the SubSeries listed below.

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Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferative expansion and survival of B cells [EBF1]

Project description:Transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into differentiation stage-specific functions of Ebf1, we conditionally inactivated Ebf1. We found that Ebf1 is required for proliferation, survival and signaling of pro-B cells and peripheral B cell subsets. The proliferation defect of Ebf1-deficient pro-B cells, including the impaired expression of IL-7Ra and several cell cycle regulators, is overcome by transformation with v-Abl. The survival defect of transformed Ebf1fl/fl pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-xL. In mature B cells, Ebf1 deficiency interferes with the BAFF-R and BCR-dependent Akt signaling pathways, as well as with germinal center formation and class switch recombination. Genome-wide analyses of Ebf1 binding and Ebf1-mediated gene expression in mature B cells and comparison with reported data sets in pro-B cells provide insight into the basis for lineage- and stage-specific functions of Ebf1. EBF1 binding in splenic B cells in mice

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Genome-wide occupancy of EBF1-wt & EBF1-H240A

Project description:To study the function of EBF1-H240 residue, genome-wide EBF1 ChIP was performed in A-MuLV transformed pro-B (Ebf1fl/fl;RERTCre) cells transduced with Ebf1wt and Ebf1H240A expressing vectors.

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Mus musculus

Project description:Gene expression analysis after reconstitution of Ebf1-deficient pre-pro-B cells with Ebf1

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Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferative expansion and survival of B cells [H3K4me2 and H3K4me3]

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Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferative expansion and survival of B cells [EBF1]

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Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.

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