Regulatory Mechanisms Governing Precision in Vertebral Segmentation

控制椎体分割精度的调节机制

• 批准号: 10584604
• 负责人: Ertugrul M Ozbudak
• 金额: $ 51.68万
• 依托单位: CINCINNATI CHILDRENS HOSP MED CTR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10584604
• 关键词: Anterior; Biochemical Reaction; Body Size; Buffers; Cell Count; Cell Size; Cells; Characteristics; Chemicals; Complex; Congenital Abnormality; Development; Developmental Process; Embryo; Exhibits; Family; Feedback; Gene Expression; Genes; Genetic; Goals; Kinetics; Ligands; Mathematics; Mesoderm; Noise; Pattern Formation; Periodicity; Phase; Phenotype; Population; Reproducibility; Science; Segmentation Clock Pathway; Signal Transduction; Somites; Statistical Models; Stochastic Processes; System; Tail; Time; Tretinoin; cell growth; dosage; gene regulatory network; malformation; notch protein; prevent; programs; somitogenesis; spine bone structure; transcriptome

PROJECT SUMMARY/ABSTRACT The timely and precise progression of a genetic program along a cascade of regulatory steps is critical to execute a developmental process. However, gene expression is a highly stochastic process due to inevitable fluctuations in the kinetics of complex biochemical reactions; this randomness leads to substantial cell-to-cell variability (gene expression noise). The resulting phenotypic fluctuations can only be detected and quantified at the single cell level within isogenic populations. One of the most intriguing questions in science is how developmental pattern formation is executed so precisely and reproducibly despite these unavoidable fluctuations in gene expression. Presumably, mechanisms that buffer stochastic gene expression must exist. Vertebrate somitogenesis provides a paradigm system for studying this question. Somite segments (the embryonic precursors of vertebrae) are produced sequentially and periodically from the presomitic mesoderm (PSM) at the tail end of the embryo. The period of somite segmentation is controlled by the segmentation clock. The segmentation clock exhibits oscillatory expression of Hes/her-family “clock” genes due to an autoinhibitory intracellular negative feedback loop. Oscillating Delta ligands activate Notch receptors in neighboring cells and establish an intercellular positive feedback loop that synchronizes oscillation phases among neighboring cells. Disruption of these synchronized oscillations results in birth defects. The time-course of somite segmentation and epithelization occur along the posteroanterior direction in the PSM. The coordinated expression of multiple genes along the PSM are controlled by three interconnected signaling gradients (Fgf, Wnt and retinoic acid). Somitogenesis is both precise – embryos of a given species develop certain number of segments with species-specific rhythmicity – and versatile –total number of segments and their periodicity vary widely among species. Somitogenesis is also robust as embryos form segments with a certain size distribution, scaling the sizes of segments with body size, even when total cell numbers, cell sizes or growth rates are altered experimentally. These characteristics indicate that the expression noise within the oscillating segmentation network is efficiently buffered. Our overarching goal is to decipher how expression noise in gene regulatory networks is buffered during developmental pattern formation. We aspire to reach a mechanistic understanding of this buffering by combining mathematical/computational/statistical modeling with different genetic and chemical perturbations to modify dosage of multiple genes or modulate signal feedback strength.

项目摘要/摘要 遗传程序沿一系列监管步骤的及时，准确的进展对于 执行发展过程。但是，由于不可避免，基因表达是一个高度随机的过程 复杂的生化反应动力学的波动；这种随机性导致大量细胞到细胞 变异性（基因表达噪声）。只能在 等生群中的单细胞水平。科学中最有趣的问题之一是如何 发育模式的形成是如此精确且可重复的，这些不可避免的 基因表达的波动。据推测，必须存在缓冲随机基因表达的机制。 脊椎动物的物质发生提供了一个用于研究此问题的范式系统。 somite段（ 椎骨的胚胎前体是由前中胚层依次和定期产生的 （PSM）在胚胎的尾端。节分割的周期由分割控制 钟。分割时钟表现出HES/HER家庭“时钟”基因的振荡表达 自身抑制性细胞内负反馈回路。振荡三角体配体激活Notch受体 相邻的细胞并建立一个同步振荡阶段的细胞间正反馈回路 在相邻细胞中。这些同步振荡的破坏会导致出生缺陷。时间表 沿PSM的后方向发生了节段和上层化。 沿PSM的多个基因的协调表达由三个互连信号传导控制 梯度（FGF，WNT和视黄酸）。体体发生既是精确的 - 给定物种的胚胎 具有特定规格特定节奏性的某些段数 - 多功能 - 段数和多功能段 它们的周期性在物种之间差异很大。体积发生也很健壮，因为胚胎形式段 某些尺寸分布，即使总细胞数量，细胞大小 或增长率在实验中改变。这些特征表明在 振荡分割网络有效缓冲。 我们的总体目标是破译基因调节网络中的表达噪声如何缓冲 发展模式形成。我们渴望通过对这种缓冲的机械理解 将数学/计算/统计建模与不同的遗传和化学扰动相结合 修改多个基因的剂量或调节信号反馈强度。

项目成果

A 3-D Tail Explant Culture to Study Vertebrate Segmentation in Zebrafish.

• DOI: 10.3791/61981
• 发表时间: 2021-06-30
• 期刊: Journal of visualized experiments : JoVE
• 作者: Simsek MF;Özbudak EM
• 通讯作者: Özbudak EM

Regulatory mechanisms ensuring coordinated expression of functionally related genes.

• DOI: 10.1016/j.tig.2021.07.008
• 发表时间: 2022-01
• 期刊: Trends in genetics : TIG
• 作者: Zinani OQH;Keseroğlu K;Özbudak EM
• 通讯作者: Özbudak EM

Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes.

• DOI: 10.1038/s41467-023-42220-7
• 发表时间: 2023-10-14
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Keseroglu, Kemal;Zinani, Oriana Q. H.;Keskin, Sevdenur;Seawall, Hannah;Alpay, Eslim E.;Ozbudak, Ertugrul M.
• 通讯作者: Ozbudak, Ertugrul M.

Gene copy number and negative feedback differentially regulate transcriptional variability of segmentation clock genes.

• DOI: 10.1016/j.isci.2022.104579
• 发表时间: 2022-07-15
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Zinani, Oriana Q. H.;Keseroglu, Kemal;Dey, Supravat;Ay, Ahmet;Singh, Abhyudai;Ozbudak, Ertugrul M.
• 通讯作者: Ozbudak, Ertugrul M.

Using single-molecule fluorescence in situ hybridization and immunohistochemistry to count RNA molecules in single cells in zebrafish embryos.

• DOI: 10.1016/j.xpro.2022.102020
• 发表时间: 2023-03-17
• 期刊: STAR PROTOCOLS
• 作者: Keseroglu, Kemal;Zinani, Oriana Q. H.;Ozbudak, Ertugrul M.
• 通讯作者: Ozbudak, Ertugrul M.