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YY1-dependent transcriptional regulation manifests at the morula stage

ABSTRACT: YY1-dependent transcriptional regulation manifests at the morula stage

PROVIDER: PRJNA1057211 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27352910_1.fastq.gz	Fastqsanger.gz
	SRR27352910_2.fastq.gz	Fastqsanger.gz
	SRR27352911_1.fastq.gz	Fastqsanger.gz
	SRR27352911_2.fastq.gz	Fastqsanger.gz
	SRR27352912_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

YY1-dependent transcriptional regulation manifests at the morula stage

Project description:YY1 plays multifaceted roles in various cell types. We recently reported that YY1 regulates nucleosome organization in early mouse embryos (Sakamoto et al. Genes Dev 2023). However, despite the impaired nucleosome organization in the absence of YY1, the transcriptome was minimally affected in eight-cell embryos. We then hypothesized that YY1 might prepare a chromatin environment to regulate gene expression at later stages. To test this possibility, we performed a transcriptome analysis at the morula stage. We found that a substantial number of genes are aberrantly expressed in the absence of YY1. Furthermore, our analysis revealed that YY1 is required for the transcription of retrotransposons in early embryos.

2023-12-26 | GSE252053 | GEO

ChIP-seq profile in in vitro produced mouse morula stage embryos treated with siRNA targeting Pcgf5

Project description:We obtained H3K27me3 profiles in mouse morula stage embryos (72 h post-insemination (hpi)) which had been in vitro treated with siRNA targeting Pcgf5 from one-cell stage (3 hpi).

2024-11-07 | GSE280946 | GEO

Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development

Project description:Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Downregulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting that the chromatin assembly pathway might be linked to fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements, through identifying YY1-binding sites in 8-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the 8-cell and morula stages and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.

2023-07-16 | GSE220074 | GEO

Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage

Project description:Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage

| PRJNA376831 | ENA

Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1

Project description:YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These changes may alter its DNA binding ability and hence its transcriptional activity. In addition to its oligomeric state, the interaction of YY1 with proteins such as FOXP2 can impact its role in transcription. The aim of this work is to study the structure and dynamics of YY1 binding to DNA and to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. Size exclusion chromatography, fluorescence anisotropy and electrophoretic mobility shift assays were used to study YY1 oligomerisation and interaction with FOXP2. To better understand potential structural changes to YY1 upon DNA binding, hydrogen deuterium exchange mass spectrometry was used. The results indicate that YY1 consists of specific structured regions, while most of the sequence remains disordered. Furthermore, the oligomeric nature of the protein is dependent on ionic strength. DNA affects oligomerisation and the protein undergoes changes in structure and dynamics upon DNA binding. YY1 and FOXP2 were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore, likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 forms with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development.

2024-01-26 | PXD038431 | Pride

STING-Dependent Signaling Manifests IL-10 Controlled Inflammatory Colitis

Project description:STING-Dependent Signaling Manifests IL-10 Controlled Inflammatory Colitis

| PRJNA421445 | ENA

Nr5a2 is dispensable for ZGA but essential for morula development [RNA-seq]

Project description:Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. While the TFs specifying the blastocyst’s lineages are well characterised, those playing earlier roles are ill-defined. Using mouse models of the TF Nr5a2, we show that Nr5a2-/- embryos arrest at the early morula stage and exhibit overt phenotypical problems such as altered lineage specification, frequent mitotic failure and substantial chromosome segregation defects. Transcriptomic profiling shows that Nr5a2 is a master regulator required for appropriate expression of thousands of genes at the 8-cells stage, including lineage-specifying TFs and genes involved in mitosis, telomere maintenance and DNA repair. We conclude that Nr5a2 coordinates proliferation, genome stability and lineage specification to ensure proper morula development.

2024-07-12 | GSE223673 | GEO

YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle

Project description:Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion. Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer-promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer-promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1's architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.

2024-06-17 | GSE247254 | GEO

Nr5a2 is dispensable for ZGA but essential for morula development [ATAC-seq]

Project description:Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. While the TFs specifying the blastocyst’s lineages are well characterised, those playing earlier roles are ill-defined. Using mouse models of the TF Nr5a2, we show that Nr5a2-/- embryos arrest at the early morula stage and exhibit overt phenotypical problems such as altered lineage specification, frequent mitotic failure and substantial chromosome segregation defects. We further show that whilst NR5A2 plays a minor but measurable role during zygotic genome activation, it predominantly acts as a master regulator at the 8-cells stage, controlling expression of lineage-specifying TFs and genes involved in mitosis, telomere maintenance and DNA repair. We conclude that NR5A2 coordinates proliferation, genome stability and lineage specification to ensure proper morula development.

2024-07-12 | GSE267536 | GEO

Genome-wide H3K27me3 profile in in vitro produced bovine morula treated with MAT2A inhibitor

Project description:We obtained genome-wide profiles of histone H3 lysine 27 trimethylation (H3K27me3) in bovine morula which had been in vitro treated with a methionine adenosyltransferase 2A (MAT2A) inhibitor from the 8-16 cell stage. Sequencing center: NODAI Genome Research Center, Tokyo University of Agriculture

2022-05-31 | GSE198293 | GEO

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