Establishment and visualization of nuclear architecture at the onset of mammalian development

哺乳动物发育初期核结构的建立和可视化

• 批准号: 10704049
• 负责人: Maria Elena Torres Padilla
• 金额: $ 39.39万
• 依托单位: HELMHOLTZ ZENTRUM MUENCHEN - GMBH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-16 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10704049
• 关键词: 3-Dimensional; Address; Affect; Architecture; Biological Models; CRISPR imaging; Cell Cycle; Cell Nucleus; Cell physiology; Cells; Chromatin; Chromosomes; Communities; Competence; DNA; DNA Folding; Data; Dependence; Development; Developmental Process; Elements; Embryo; Epigenetic Process; Fertilization; Gene Expression; Gene Expression Regulation; Genetic Recombination; Genome; Genomic Instability; Genomic Segment; Genomic approach; Genomics; Goals; Grant; Hereditary Disease; Image; KDM5B gene; Knowledge; Mammals; Methodology; Methods; Molecular; Mus; Nuclear; Nuclear Lamina; Nuclear Matrix; Organism; Pathway interactions; Physiological; Play; Pre-implantation Embryo Development; Process; Proteins; Regulation; Role; Structural Protein; Structure; Technology; Time; Transcription Process; Validation; Visualization; biophysical properties; blastocyst; design; epigenome; epigenomics; imaging approach; imaging system; in vivo; in vivo imaging; innovation; insight; mammalian genome; mechanical properties; novel; programs; scaffold; screening; tool; tool development; zygote

Project Summary/Abstract “Establishment and visualization of nuclear architecture at the onset of mammalian development” Nuclear organization is a key feature of our epigenome. The way in which our DNA is folded into the cell nucleus can affect gene expression and determine cellular identity, but it can also regulate recombination and genome instability. Indeed, the disruption of key elements underlying the architecture of the nucleus, such as Topologically-Associated Domain (TAD) boundaries, has been shown to be the cause of genetically inherited diseases in some instances. How nuclear organization is first established after fertilization in mammals is largely unknown. In particular, the lack of approaches to observe in real time the different layers of nuclear organization has been a barrier for the full understanding of the dynamics and the impact of nuclear organization in vivo. Most importantly, the chromatin and structural pathways that regulate the initial folding of our genome into the nucleus as well as the impact of the resulting genome organization for key developmental and transcriptional processes in vivo, is largely unknown. We have recently shown that nuclear organization, particularly the association of specific genomic regions to the nuclear lamina, is established de novo in the newly formed embryo immediately after fertilization. Lamina- Associated Domains (LADs) precede the consolidation of TADs and compartments, suggesting that the association with the nuclear lamina may be the first nuclear architectural scaffold and set the framework for nuclear architecture. Here, to fulfill the outstanding need for methodologies to visualize specific chromosome domains, we will establish “LivePaint”, a technology to visualize the fundamental pillars of genome organization and their dynamics in real time (Aim 1). We propose to image the process of establishment of nuclear architecture by applying this tool to the mouse pre-implantation embryo, a full organism amenable to imaging and in which real time dynamics can be studied in their natural context. In parallel, we will deploy low input genomic approaches, such as DamID to identify the regulators of LAD establishment (Aim 2). Finally, using this information, we will perform perturbations to establish the role of LADs in regulating the establishment of nuclear architecture through both imaging and genomics approaches (Aim 3). We will also identify the impact of the disruption to the establishment of nuclear organization in vivo on epigenetic features, such as replication timing and gene expression and ultimately their impact on developmental competence. Through the perturbation and live imaging of the main determinants of nuclear organization in vivo, this proposal will establish the functional dependencies between the different layers of nuclear organization and will reveal their role in cellular function, gene expression and developmental progression at the beginning of mammalian development. The knowledge generated through these Aims will address outstanding challenges for our understanding of how the mammalian genome folds within the nuclear space in a physiological context and will reveal molecular regulators of this process.

项目总结/文摘

项目成果

Regulation of mammalian totipotency: a molecular perspective from in vivo and in vitro studies.

• DOI: 10.1016/j.gde.2023.102083
• 发表时间: 2023-07
• 期刊: Current opinion in genetics & development
• 影响因子: 4
• 作者: Tsunetoshi Nakatani;M. Torres-Padilla

Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging.

• DOI: 10.1016/j.devcel.2023.02.018
• 发表时间: 2023-03
• 期刊: Developmental cell
• 影响因子: 11.8
• 作者: Federico Pecori;M. Torres-Padilla

Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity.

早期小鼠胚胎中核纤层相关结构域的重组受 RNA 聚合酶 II 活性的调节。

• DOI: 10.1101/gad.350799.123
• 发表时间: 2023
• 期刊: Genes & development
• 影响因子: 10.5
• 作者: Pal,Mrinmoy;Altamirano-Pacheco,Luis;Schauer,Tamas;Torres-Padilla,Maria-Elena
• 通讯作者: Torres-Padilla,Maria-Elena