Metabolic remodeling during early murine early embryo development
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ABSTRACT:
PROVIDER: PRJNA752870 | ENA |
REPOSITORIES: ENA
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Project description:During early mammalian embryogenesis, dynamic changes in cell growth and proliferation are tightly linked to the underlying genetic and metabolic regulation. However, our understanding of metabolic reprogramming and its impact on epigenetic regulation in early embryo development remains elusive. We reconstruct their metabolic landscapes from the 2-cell and blastocyst stages, as well as their transition from totipotency to pluripotency. While 2-cell embryos favor methionine, polyamine and glutathione metabolism and stay in a more reductive state, blastocyst embryos have higher mitochondrial metabolites related to the tricarboxylic acid cycle, and present a more oxidative state. Moreover, we identify a reciprocal relationship between α-ketoglutarate (α-KG) and the competitive inhibitor of α-KG-dependent dioxygenases, L-2-hydroxyglutarate (2-HG), where 2-cell embryos inherited from oocytes and 1-cell zygotes display higher L-2-HG, whereas blastocysts show higher α-KG.Supplementing 2-HG or knocking down L2hgdh, a gene encoding the 2-HG consuming enzyme L-2-hydroxyglutarate dehydrogenase impeded erasure of global histone methylation markers . Together, our data demonstrate dynamic and interconnected metabolic, transcriptional and epigenetic network remodeling during murine early embryo development.
2021-10-14 | GSE181648 | GEO
Project description:Metabolic remodeling during Bacillus subtilis biofilm development
| PRJNA529199 | ENA
Project description:Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report a surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm-associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following these results, we demonstrate that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This study represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful roadmap for future studies on biofilm physiology.
2019-03-27 | GSE128875 | GEO
Project description:Stressors during early embryogenesis influence embryo developmental trajectories and have long-term metabolic effect on offspring, but the underlying mechanism remains elusive. We performed RNA-Seq to identify transcriptional differences among control and IVF embryos. Results revealed that DNA damage and the resulting activation of Fzr1 play a central role in early embryo stress responses and subsequently affect metabolic reprogramming in offspring. To investigate the underlying molecular mechanism by which Fzr1 affected embryo development and adult metabolism. We performed RNA-Seq and H3K9me3 ChIP-seq experiments to identify transcriptional and histone modification differences among control and Fzr1-OE blastocysts. To explore the underlying mechanisms of Fzr1 activation-induced metabolic disorder, we performed RNA-Seq on the subcutaneous fat tissues of 4-month-old control and Fzr1-OE mice. We further performed reduced-representation bisulfite sequencing (RRBS) of subcutaneous fat tissues to identify possible DNA methylation alterations that could potentially mediate the intergenerational transmission of the obesity phenotype. Our findings therefore provide a new perspective on the mechanisms underlying transgenerational metabolic reprogramming and will help improve offspring health.
2023-12-31 | GSE182567 | GEO
Project description:Biofilms are structured communities of tightly associated cells that constitute thepredominant state of bacterial growth in naturaland human-madeenvironments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilishas been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, weperformed a time-resolved analysisof the metabolic changes associated with pellicle biofilm formation and development inB. subtilisby combining metabolomic, transcriptomic, and proteomic analyses. We report a surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hithertounrecognized as biofilm-associated.For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was generally controlled at the transcriptional level. Our resultsalsoprovide insights into the transcription factors and regulatory networks involved in thiscomplexmetabolic remodeling. Following upon these results, we demonstrate that acetoin production via acetolactate synthase is essential for robust biofilm growthand has the dual role of conservingredox balance and maintaining extracellularpH.This study represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilisbiofilm development that will serve as a useful roadmap for future studies on biofilm physiology.
2019-04-30 | PXD013307 | Pride
Project description:Time course expression data from early Bovine embryo, Human embryo, and Mouse embryo
| PRJNA117925 | ENA
Project description:Enhancer RNAs (eRNAs) play critical roles in diverse biological processes by mediating the activation of their target genes. However, the systematic landscape and potential regulations and functions of eRNAs during mammalian early embryo development remains elusive. Here, we present the comprehensive detection and characterization of eRNAs during mouse early embryo development. We demonstrated the spatiotemporal and allelic landscape of eRNA expression. We found the asymmetric activation of paternal-specific eRNAs during zygotic genome activation (ZGA). We identified TFs and their cooperation in regulating dynamic eRNA expression. eRNA are involved in multiple developmental signaling pathways through putatively regulating their target genes. Interestingly, we observed that the transcriptions of enhancers themselves are also widely modulated by eRNAs during mouse early embryo development. Critically, we de novo identified a novel eRNA transcribed from a super-enhancer region exclusively expressed at 2-cell stage of mouse early embryos and experimentally validated its key functional role in regulating ZGA and early embryo development.
2024-02-27 | GSE213211 | GEO
Project description:Translation is critical for development as transcription in the oocyte and early embryo is silenced. To illustrate the translational changes during meiosis and consecutive two mitoses of the oocyte and early embryo, we performed a genome-wide translatome analysis. Acquired data showed significant and uniform activation of key translational initiation and elongation axes specific to M-phases. Although global protein synthesis decreases in M-phases, translation initiation and elongation activity increases in a uniformly fluctuating manner, leading to qualitative changes in translation regulation via the mTOR1/4F/eEF2 axis. Overall, we have uncovered a highly dynamic and oscillatory pattern of translational reprogramming that contributes to the translational regulation of specific mRNAs with different modes of polysomal occupancy/translation that are important for oocyte and embryo developmental competence. Our results provide new insights into the regulation of gene expression during oocyte meiosis as well as the first two embryonic mitoses and show, how temporal translation can be optimized. This study is the first step towards a comprehensive analysis of the molecular mechanisms that not only control translation during early development, but also regulate translation-related networks employed in the oocyte-to-embryo transition and embryonic genome activation.
2023-05-29 | GSE230016 | GEO
Project description:H3K9me3-dependent heterochromatin is considered as one of the major barriers for cell fate changes, and must be reprogrammed during fertilization to reactivate highly specialized paternal and maternal genome to establish totipotency. However, the molecular details are lacked for early embryos due to the limited materials. Here we map the genome-wide distribution of H3K9me3 modification in the early embryo as well as in the cell fate determined embryonic tissues after implantation. We find that H3K9me3 exhibits distinct dynamic features in promoters and retro-transposons. Both maternal and paternal genome undergo large scale of H3K9me3 reestablishment after fertilization, and the imbalance of maternal H3K9me3 signal over paternal last until the blastocyst stage. The rebuilding of H3K9me3 on LTR retro-transposons maintains its repression state after the global DNA demethylation, and we further discover that Chaf1a is essential for the establishment of H3K9me3 on LTRs and the loss function of Chaf1a leads to embryo development failure. Finally, we find that lineage specific H3K9me3 is established after lineage commitment in post-implantation embryos. Thus, our data demonstrate that H3K9me3-dependent heterochromatin undergoes dramatic reprogramming during early embryo development and the establishment of H3K9me3 on LTRs is essential for proper embryo development. This SuperSeries is composed of the SubSeries listed below.
2018-04-13 | GSE97778 | GEO
Project description:Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development
| PRJNA384149 | ENA