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Functional roles of the chromatin remodeler SMARCA5(SNF2H) in mouse and bovine preimplantation embryos

ABSTRACT: Functional roles of the chromatin remodeler SMARCA5(SNF2H) in mouse and bovine preimplantation embryos

PROVIDER: PRJNA720824 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14195106_1.fastq.gz	Fastqsanger.gz
	SRR14195106_2.fastq.gz	Fastqsanger.gz
	SRR14195107_1.fastq.gz	Fastqsanger.gz
	SRR14195107_2.fastq.gz	Fastqsanger.gz
	SRR14195108_1.fastq.gz	Fastqsanger.gz

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Functional roles of the chromatin remodeler SMARCA5(SNF2H) in mouse and bovine preimplantation embryos

Project description:Upon fertilization, extensive chromatin reprogramming occurs during preimplantation development. Growing evidence reveals species-dependent regulations of this process in mammals. ATP-dependent chromatin remodeling factor SMARCA5 (also known as SNF2H) is required for peri-implantation development in mice. However, the specific functional role of SMARCA5 in preimplantation development and if it is conserved among species remain unclear. Herein, comparative analysis of public RNA-seq datasets reveals that SMARCA5 is universally expressed during oocyte maturation and preimplantation development in mice, cattle, humans and pigs with species-specific patterns. Immunostaining analysis further describes the temporal and spatial changes of SMARCA5 in both mouse and bovine models. siRNA-mediated SMARCA5 depletion reduces the developmental capability and compromises the specification and differentiation of inner cell mass in mouse preimplantation embryos. Indeed, OCT4 is not restricted into the inner cell mass and the formation of epiblast and primitive endoderm disturbed with reduced NANOG and SOX17 in SMARCA5-deficient blastocysts. RNA-seq analysis shows SMARCA5 depletion causes limited effects on the transcriptomics at the morula stage, however, dysregulates 402 genes, including genes involved in transcription regulation and cell proliferation at the blastocyst stage in mice. By comparison, SMARCA5 depletion does not affect the development through the blastocyst stage but significantly compromises the blastocyst quality in cattle. Primitive endoderm formation is greatly disrupted with reduced GATA6 in bovine blastocysts. Overall, our studies demonstrate the importance of SMARCA5 in fostering the preimplantation development in mice and cattle while there are species-specific effects.

2021-05-31 | GSE171760 | GEO

Human SMARCA5 interactome in transgenic SMARCA5 mouse model

Project description:We hypothesize that the ISWI ATPase Smarca5 plays a role in hematopoietic stem cell development via its interaction partners, and to study the role, we used a mouse model with transgenic expression of SMARCA5 coupled with mass spectrometry analysis. The study uses transgenic SMARCA5 mouse model with conditional hypomorphic allele (lower expression on protein level compared to controls) incorporated into Rosa26 locus, transgenic allele uses endogenous Rosa26 promoter. The transgenic human SMARCA5 protein has a FLAG tag at its C-terminus, which allows specific immunoprecipitation and also differentiation from the endogenous protein (human and mouse SMARCA5 are almost identical at the protein level). To ensure the highest possible expression of the transgenic allele, we used a model that also had one endogenous Smarca5 allele deleted. Various organs (thymus, spleen, brain, kidney, liver, testes, muscle, fetal liver) were isolated from transgenic mice, lysed and then immunoprecipitated using anti-FLAG antibody. The immunoprecipitates were then analyzed using mass spectrometry to determine SMARCA5 interactomes in various tissues. Transgenic human SMARCA5 was confirmed to form all the expected complexes and capable of replacing the functions of the mouse protein. For details, see the publication of Turkova et al. 2024 in Communications Biology.

2024-06-22 | PXD049034 | Pride

Chromatin remodeling in bovine oocytes and preimplantation embryos

Project description:Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.

2023-02-16 | GSE193640 | GEO

Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler

Project description:SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.

2023-08-03 | GSE197979 | GEO

The chromatin remodeler Snf2h is essential for oocyte meiotic cell cycle progression

Project description:Oocytes are indispensable for mammalian life. Thus, it is important to understand how mature oocytes are generated. As a critical stage of oocytes development, meiosis has been extensively studied, yet how chromatin remodeling contributes to this process is largely unknown. Here, we demonstrate that the ATP-dependent chromatin remodeling factor Snf2h (also known as Smarca5) plays a critical role in regulating meiotic cell cycle progression. Females with oocyte-specific depletion of Snf2h are infertile and oocytes lacking Snf2h fail to undergo meiotic resumption. Mechanistically, depletion of Snf2h results in dysregulation of meiosis-related genes, which causes failure of maturation-promoting factor (MPF) activation. ATAC-seq analysis in oocytes revealed that Snf2h regulates transcription of a key meiotic gene, Prkar2b, by increasing its promoter chromatin accessibility. Our studies thus not only demonstrate the importance of Snf2h in oocyte meiotic resumption, but also reveal the mechanism underlying how a chromatin remodeling factor can regulate oocyte meiosis.

2020-01-19 | GSE134279 | GEO

Effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos

Project description:Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing. A total of eight Holstein dairy cows were used in this study. Preimplantation embryos recovered from each cow were pooled in order to generate two replicates per cow assayed. Each pool consisted of 2-4 expanded blastocysts with excellent quality. Overall, a total of 16 embryo pools underwent RNA extraction, amplification, and subsequent sequencing.

2013-06-21 | E-GEOD-48147 | biostudies-arrayexpress

Effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos

2013-06-21 | GSE48147 | GEO

The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h

Project description:Domain level interactions between the ISWI remodeler SNF2h and reconstituted mononucleosomes were probed by EDC crosslinking under different biochemical conditions: ADP, ADP-BeFx, ADP-BeFx with LANA peptide added (which binds at the acidic patch). A semi quantitative approach was used to monitor domain-domain interactions enriched during the remodeling cycle.

2018-03-07 | MSV000082136 | MassIVE

Chromatin remodeling in bovine oocytes and preimplantation embryos

Project description:Chromatin remodeling in bovine oocytes and preimplantation embryos

| PRJNA797029 | ENA

KSN01_Proteome_CellLine: Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H

Project description:Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H

2020-12-15 | PXD010107 | JPOST Repository

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