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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements

ABSTRACT: Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements

PROVIDER: PRJNA887727 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21834805.fastq.gz	Fastqsanger.gz
	SRR21834806.fastq.gz	Fastqsanger.gz
	SRR21834807.fastq.gz	Fastqsanger.gz
	SRR21834808.fastq.gz	Fastqsanger.gz
	SRR21834809.fastq.gz	Fastqsanger.gz

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements

Project description:Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s Disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq + snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell-type specific transposase accessible regions that are enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements [ChIP-seq]

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements [ChIP-seq]

Project description:Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements [ChIP-seq]

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements [Multi-omics]

Project description:Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s Disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq + snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell-type specific transposase accessible regions that are enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respe ctively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements [Multi-omics]

Project description:Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements [Multi-omics]

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Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific <i>cis</i>-regulatory elements.

Project description:Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglia links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

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Non adherent macrophage of mafb null and WT

Project description:MafB is a member of the large Maf family of transcription factors that share similar basic region/leucine zipper DNA binding motifs and N-terminal activation domains.Although it is well known that MafB is specifically expressed in macrophages, characterization of the null mutant phenotype in these tissues has not been previously reported. To investigate suspected MafB functions macrophages, we generated mafB/green fluorescent protein (GFP) knock-in null mutant mice. MafB deficiency was found to dramatically suppress F4/80 expression in nonadherent macrophages. To investigate detail function of MafB in nonadherent macrophages, we performed microarray analysis. Macrophages were derived from day 14.5 fetal livers of mafB- /- and WT mice. Suspensions of single fetal liver cells were prepared by mechanical disruption . A total of 106 cells in suspension were centrifuged at 1,200 rpm for 5 min, and the cell pellet was resuspended in Dulbeccoâs modified Eagleâs medium supplemented with 10% fetal calf serum (heat inactivated), streptomycin and penicillin (100 units/ml), and macrophage colony-stimulating factor (M-CSF) (10 ng/ml) and then seeded either onto a nonadhesive dishes coated with hydrophilic polymers (Hydrocell; Cell Seed, Tokyo). The culture medium was not changed throughout the experiment. M-CSF (final concentration, 10 ng/ml) was added every day from day 4 onwards. One, 2, 4, and 6 days after seeding, the cells were harvested and analyzed by flow cytometry. After 6 day culture, macrophages of Mafb-/- and WT were use microarray analysis .

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