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Transgenic mice with an R342X mutation in Phf6 have reduced protein levels and behavior deficits yet few prominent features of Börjeson-Forssman-Lehmann Syndrome (BFLS).

ABSTRACT: Transgenic mice with an R342X mutation in Phf6 have reduced protein levels and behavior deficits yet few prominent features of Börjeson-Forssman-Lehmann Syndrome (BFLS).

PROVIDER: PRJNA657849 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12469145_1.fastq.gz	Fastqsanger.gz
	SRR12469145_2.fastq.gz	Fastqsanger.gz
	SRR12469146_1.fastq.gz	Fastqsanger.gz
	SRR12469146_2.fastq.gz	Fastqsanger.gz
	SRR12469147_1.fastq.gz	Fastqsanger.gz

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Transgenic mice with an R342X mutation in Phf6 have reduced protein levels and behavior deficits yet few prominent features of Börjeson-Forssman-Lehmann Syndrome (BFLS).

Project description:The PHF6 mutation, R342X, is a recurrent cause of Börjeson-Forssman-Lehmann Syndrome (BFLS), a neurodevelopmental disorder (MIM#301900). We generated transgenic mice with the identical substitution using CRISPR technology. We show that the R342X mutation causes a reduction in PHF6 protein levels, in both mice and humans, from nonsense mediated decay and nonsense-associated alternative splicing. MRI studies indicated that R342X mice had a reduced brain volume on a mixed genetic background but developed hydrocephaly and a high incidence of postnatal death on a C57BL/6 background. Cortical development proceeded normally while hippocampus and hypothalamus relative brain volumes were reduced. Behavior testing demonstrated deficits in associative learning, spatial memory and an anxiolytic phenotype, although other BFLS clinical features were not observed in the R342X mice. We performed RNA-seq analysis on the cerebral cortices of neonatal R342X mice with the purpose of finding a relationship between gene expression profiles, the behavioral phenotype and the cortical morphology.

2022-11-28 | GSE156404 | GEO

PHF6 OCCUPANCYIN HUMAN T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA

Project description:Here we identify the genome-wide occupancy of PHF6 in T-ALL cells. Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total PHF6 (Bethyl A301-451A). This represents the ChIP-seq portion of this dataset.

2014-04-01 | E-GEOD-45864 | biostudies-arrayexpress

RNA sequencing of isogenic Phf6 wild type and Phf6 knockout mouse T-ALL cells

Project description:Loss-of-function mutations Phf6 occur frequently in both adult and pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL). Although Phf6 is widely expressed, little is known about its proposed function as epigenetic regulator and tumor suppressor. To address the role of Phf6 in the leukemia development, here we analyze by RNAseq the gene expression profiles of isogenic Phf6 wild type and Phf6 knockout leukemia cells transformed by overexpression of an oncogenic mutant form of the NOTCH1 receptor.

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PHF6 knockdown in rat cortical neurons

Project description:E18 embryonic rat cortical neurons cultured in vitro are infected with lentivirus expressing control or PHF6shRNA-2, and harvested 5 days after infection pLL3.7 lentivirus expressing control or PHF6shRNA-2 was generated in 293T cells and concentrated using ultracentrifuge. In vitro cultured cortical neurons were infected and RNA was harvested 5 days after infection. PHF6 knockdown was validated by QPCR before sample was processed for microarray analysis.

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Transcriptomic changes in PHF6 knockout THP1 human AML cell line on rescue with PHF6 wildtype (with and without PHIP) or rescue with PHF6R274Q mutant

Project description:PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand the effect of loss and clinical mutation of PHF6 on the transcriptome of myeloid cells, we generated multiple wildtype and PHF6 knockout clones, as well as clones expressing the most common clinical mutant of the protein-PHF6R274Q. We observed that both single and double knockouts and mutation of PHF6 shifted the cells towards stemness and away from differentiation. Additionally we identified PHIP as a possible functional partner for PHF6. To investigate their common biological function, we generated multiple single knockout clones of PHIP as well as double knockout clones of PHIP and PHF6, and observed that, similar to single knockout of PHF6, PHIP knockout and double knockout also shifted cells towards stemness and away from differentiation. Collectively, our experiments show that PHF6 and PHIP, separately identified as being mutated in AML, exert similar downstream effects on the AML transcriptome.

2024-11-15 | GSE281624 | GEO

Changes in H3K27 acetylation in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype clones

Project description:PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand how PHF6 and its functional partner PHIP interact with each other on chromatin, we performed ChIP-Seq for PHF6 (in the presence and absence of PHIP), for PHF6R274Q mutant, and for PHIP. We observd that PHF6 and PHIP peaks overlap on chromatin, and PHF6 requires PHIP for its chromatin occupancy. ATAC-Seq and H3K27ac ChIP-Seq showed that PHF6 and PHIP occupy open and active regions of the genome.

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Chromatin accessibility changes caused by PHF6 knockout in THP1 human AML cell line

Project description:PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand how PHF6 and its functional partner PHIP interact with each other on chromatin, we performed ChIP-Seq for PHF6 (in the presence and absence of PHIP), and for PHIP. We observd that PHF6 and PHIP peaks overlap on chromatin, and PHF6 requires PHIP for its chromatin occupancy. ATAC-Seq and H3K27ac ChIP-Seq showed that PHF6 and PHIP occupy open and active regions of the genome.

2024-11-15 | GSE281626 | GEO

Gene expression in Phf6-deleted and Phf6-intact foetal mouse cortical neurons and foetal mouse cortex assessed by RNA-seq

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