Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators
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ABSTRACT:
PROVIDER: PRJNA901494 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22286408_1.fastq.gz | Fastqsanger.gz | |||
| SRR22286408_2.fastq.gz | Fastqsanger.gz | |||
| SRR22286409.fastq.gz | Fastqsanger.gz | |||
| SRR22286410.fastq.gz | Fastqsanger.gz | |||
| SRR22286411.fastq.gz | Fastqsanger.gz |
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Project description:Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbor prevalent putative enhancers in fully-grown oocytes linked to oocyte-specific gene and repeat activation. Embryo-specific enhancers are primed prior to zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding, and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis – TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting TFs that underpin the development of mammalian oocytes and early embryos.
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Project description:Differences in follicle-stimulating hormone (FSH) ß-subunit N-glycosylation results in distinct FSH glycoforms. Hypoglycosylated FSH21 is more bioactive and abundant in reproductively young women, whereas fully glycosylated FSH24 shows lower bioactivity and a relative increase with age. To investigate if the coinciding shift in FSH glycoform abundance contributes to the age-dependent decline in oocyte quality, an encapsulated in vitro follicle growth system was utilized to examine the direct effects of FSH glycoforms on folliculogenesis and resulting oocyte quality. Long-term culture (10-12 days) with FSH21 (10 ng/ml) enhanced follicle growth, estradiol secretion, and oocyte quality compared to equivalent FSH24 treatment. FSH21 exhibited enhanced capacity to establish transzonal projections, gap junctions, and cell-to-cell communication within 24 hrs in culture. Transient inhibition of FSH21-mediated bidirectional communication abrogated the positive effects of FSH21 on follicle growth, estradiol secretion and oocyte quality. These findings indicate FSH21 promotes folliculogenesis and oocyte quality in vitro through increasing cell-to-cell communication early in folliculogenesis and that the shift in abundance from FSH21 to FSH24 with reproductive aging could contribute to the age-dependent decline in oocyte quality.
2023-07-15 | GSE236967 | GEO
Project description:Background Correct achievement of early ovarian folliculogenesis is a crucial phase for further ovarian function. This process is closely regulated by cell-cell interactions and coordinated expression of genes from oocyte and granulosa cells. But, despite of the large number of studies, little is known about the precise gene expression patterns driving early folliculogenesis. The experimental limitations concerned the very small size of these follicles and the mixture of the different developmental stages within an ovary that make the study of isolated follicular components much more difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarrays experiments is promising in addressing the molecular specificity of each follicular compartment. Nevertheless, the isolation of unique cells or group of cells is still challenging to maintain RNA quality during this process and to obtain sufficient amount of RNA. In this study, we described a method allowing the analysis of oocyte and granulosa cells gene expression during the first stages of sheep early folliculogenesis. Results First we developed a new fixation protocol using a frizzed 70% ethanol fixation solution that ensures correct single cell capture and RNA integrity during microdissection time. After LCM capture of the compartments and follicular stages, RNA extraction and amplification, the expression of 6 oocyte-specific genes (SOHLH2, MAEL, MATER, VASA, GDF9, BMP15) and 3 granulosa cell-specific genes (KITLG, GATA4, AMH) confirmed the purity of the samples and documented their ovine expression profiles. Then, using bovine Affymetrix chip, we identified for the first time, a global gene expression for each follicular compartment during early developmental stages. Particularly the granulosa cell data set is quite unique. 1050 granulosa cell specific transcripts compared to oocyte and 759 oocyte specific transcripts were detected. The analysis of the expression of 2 genes (SIRT7, FST) confirmed this specificity of expression. Finally, the integration of the data stated the 3 main physiological events involved in early folliculogenesis and provided descriptive elements that confirmed the relevance and the potential of the LCM-derived RNAs. Conclusions This method should contribute through an additional genome wide expression profiling to give insights on molecular mechanisms involved in stage transitions and cell type interplays.
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Project description:Despite improved 5-year overall survival rates in B-cell acute lymphoblastic leukemia (B-ALL) due to therapy escalation, effective treatments for relapsed and treatment-resistant disease, especially in specific subtypes like those with TCF3 (formerly E2A) fusions, remain scarce. TCF3, a key regulator of B-cell development, is implicated in various chromosomal translocations linked to lymphoid malignancies, such as TCF3::PBX1 fusion (5% of pediatric B-ALL) and TCF3::HLF fusion (~0.5% of pediatric B-ALL). Current omics research predominantly relies on transcriptomics, but it's increasingly recognized that this may not adequately reflect protein expression, the main targets of drugs and functional entities in biological processes. This study comprehensively analyzed proteomic landscapes of TCF3::HLF+ (n=6) and TCF3::PBX1+ (n=5) B-ALL using primary patient-derived xenografts (PDX), liquid chromatography tandem mass spectrometry, and data-dependent acquisition.
2024-07-05 | PXD053677 | Pride
Project description:Background Correct achievement of early ovarian folliculogenesis is a crucial phase for further ovarian function. This process is closely regulated by cell-cell interactions and coordinated expression of genes from oocyte and granulosa cells. But, despite of the large number of studies, little is known about the precise gene expression patterns driving early folliculogenesis. The experimental limitations concerned the very small size of these follicles and the mixture of the different developmental stages within an ovary that make the study of isolated follicular components much more difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarrays experiments is promising in addressing the molecular specificity of each follicular compartment. Nevertheless, the isolation of unique cells or group of cells is still challenging to maintain RNA quality during this process and to obtain sufficient amount of RNA. In this study, we described a method allowing the analysis of oocyte and granulosa cells gene expression during the first stages of sheep early folliculogenesis. Results First we developed a new fixation protocol using a frizzed 70% ethanol fixation solution that ensures correct single cell capture and RNA integrity during microdissection time. After LCM capture of the compartments and follicular stages, RNA extraction and amplification, the expression of 6 oocyte-specific genes (SOHLH2, MAEL, MATER, VASA, GDF9, BMP15) and 3 granulosa cell-specific genes (KITLG, GATA4, AMH) confirmed the purity of the samples and documented their ovine expression profiles. Then, using bovine Affymetrix chip, we identified for the first time, a global gene expression for each follicular compartment during early developmental stages. Particularly the granulosa cell data set is quite unique. 1050 granulosa cell specific transcripts compared to oocyte and 759 oocyte specific transcripts were detected. The analysis of the expression of 2 genes (SIRT7, FST) confirmed this specificity of expression. Finally, the integration of the data stated the 3 main physiological events involved in early folliculogenesis and provided descriptive elements that confirmed the relevance and the potential of the LCM-derived RNAs. Conclusions This method should contribute through an additional genome wide expression profiling to give insights on molecular mechanisms involved in stage transitions and cell type interplays. The 2 ovine follicular compartments (i.e. granulosa cells (G) and oocytes (O) were captured using LCM technology for each early stage (primordial (Pd), primary (Pm), secondary (Sec) follicles. The RNA of each group was extracted using Picopure RNA Isolation kit (Arcturus) and subjected to 2 round T7 amplification (RiboAmp®HS PLUS kit, Arcturus). Ovine microarray experiments were performed using the Affymetrix Bovine Expression Array. First the quality of the cross-species hybridizations was checked by comparison of hybridization data of ovine fetal ovary RNA with bovine fetal ovary ones, generated with the Affymetrix standard protocol (protocole 1). Then, three biotin-labeling protocols were compared from ovine fetal ovary total RNA: protocol 1; protocol 2 (Biotin-labeled cRNAs were synthesized following Affymetrix protocol using the second-round cDNAs from RiboAmp®HS kit as templates); protocol 3 (Arcturus biotin turboTM labeling kit from aRNA after the 2 round amplification using RiboAmp®HS kit). Last , one LCM-derived aRNA sample of each group was labeled using the Arcturus biotin turboTM labeling kit (protocol 3) and hybridized to Affymetrix Bovine Expression arrays. Images were interpreted using Microarray Suite version 5.0 (MAS 5.0) in GCOS with scaling (100) and without normalization.
2011-07-01 | E-GEOD-25652 | biostudies-arrayexpress
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2011-02-24 | E-GEOD-27455 | biostudies-arrayexpress
Project description:The observation that Tcf3 (MGI name: Tcf7l1) bound the same genes as core stem cell transcription factors, Oct4 (MGI name:Pou5f1), Sox2 and Nanog, revealed a potentially important aspect of the poorly understood mechanism whereby Wnts stimulate self renewal of pluripotent mouse embryonic stem (ES) cells. Although the conventional view of Tcf proteins as the β-catenin-binding effectors of Wnt signaling suggested Tcf3 should activate target genes in response to Wnts, here we show that Wnt3a and Tcf3 effectively antagonize each other’s effects on gene expression. Genetic ablation of Tcf3 caused similar effects as treating cells with recombinant Wnt3a. Moreover, Tcf3 was not necessary for Wnt3a-stimulation of gene expression as the majority of Wnt3a-stimulated genes exhibited a greater increase in Tcf3-/- ES cells than in Tcf3+/+ ES cells. These expression data, together with genetic experiments, show that Wnt3a stimulates ES cell self renewal by inhibiting Tcf3.
2011-02-24 | GSE27455 | GEO