Analysis of Nematode Sex Determination and Dosage Compensation

线虫性别决定和剂量补偿分析

• 批准号: 10371895
• 负责人: BARBARA J MEYER
• 金额: $ 46.63万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10371895
• 关键词: 3-Dimensional; Address; Affect; Affinity; Architecture; Bacteria; Binding; Caenorhabditis; Caenorhabditis elegans; Cells; Chromosome Structures; Chromosome Territory; Chromosomes; Complex; Development; Dosage Compensation (Genetics); Female; Gene Expression; Gene Expression Regulation; Growth; Hermaphroditism; Higher Order Chromatin Structure; Histones; Knowledge; Link; Machine Learning; Mammals; Mediating; Meiosis; Metabolism; Methods; Mitotic; Molecular; Nature; Nematoda; RNA Polymerase II; Regulatory Element; Resolution; Signal Transduction; Site; Structure; Switch Genes; Work; X Chromosome; X Inactivation; autosome; chromatin modification; condensin; dosage; histone demethylase; male; man; neural network; protein complex; recruit; sex; sex determination; single molecule; tumor progression

PROJECT SUMMARY Studies are proposed to dissect one of the fundamental, binary development decisions that most metazoans make: their sex. The nematode C. elegans determines sex with remarkable precision by tallying X- chromosome number relative to the sets of autosomes (X:A signal): ratios of 1X:2A (0.5) and 2X:3A (0.67) signal male fate, while ratios of 3X:4A (0.75) and 2X:2A (1.0) signal hermaphrodite fate. We have discovered much about the nature and action of the X:A signal and its direct target, a master sex-determination-switch gene that also controls X-chromosome dosage compensation. However, a fundamental question remains: how is the signal interpreted reproducibly in an "all or none" manner to elicit fertile male or hermaphrodite development, never intersexual development? We pioneer new methods using machine learning neural networks to address this question with single-molecule and single-cell resolution. We also propose to dissect the functional interplay between chromatin modification and chromosome structure in regulating gene expression over vast chromosomal territories. X-chromosome dosage compensation in C. elegans is exemplary for this analysis: we found recently that dosage-compensated X chromosomes have (i) elevated levels of modified histone H4K20me1 compared to autosomes and (ii) a unique three-dimensional architecture. Both are imposed by the dosage compensation complex (DCC). Loss of H4K20me1 disrupts 3D architecture and elevates X gene expression. In the nematode DCC, one subunit is an H4K20me2 demethylase and five subunits are homologs of condensin subunits, which compact and resolve mitotic and meiotic chromosomes. All DCC subunits are recruited specifically to hermaphrodite X chromosomes by an XX-specific subunit that triggers binding to cis- acting regulatory elements on X (rex) to reduce gene expression by half. The DCC remodels the structure of X into topologically associating domains (TADs) using its highest affinity rex sites to establish domain boundaries. Despite this knowledge, important questions underlying the mechanisms of dosage compensation remain. What DCC subunits recognize the X-enriched motifs in rex sites to bind X directly? How does the DCC regulate RNA polymerase II to repress gene expression? What mechanisms underlie H4K20me1's control of chromosome structure, and how does DCC-mediated higher-order structure affect gene expression? Our findings should have broad implications, because (i) condensin complexes control chromosome structure from bacteria to man, (ii) H4K20me1 is enriched on the inactive X of female mammals, (iii) demethylases are linked to tumor progression, and (iv) the H4K20me2 demethylase modulates nematode growth, metabolism, and entry into the quiescent dauer state. Lastly, we will exploit our unexpected finding that rex sites have diverged across Caenorhabditis species separated by 30 MYR, retaining no functional overlap despite strong conservation of the core DCC machinery. This divergence provides an unusual opportunity to study the path for a concerted co- evolutionary change in hundreds of target sites across X chromosomes and the protein complexes that bind them.

项目摘要 提出研究旨在剖析大多数基本的二元发展决策之一 Metazoans Make：他们的性爱。线虫C.秀丽隐杆线虫通过对X-进行X-的精度确定性别 相对于常染色体集的染色体数（x：a信号）：比率为1x：2a（0.5）和2x：3a（0.67）（0.67） 信号男性命运，而比率为3倍：4A（0.75）和2x：2a（1.0）信号雌雄同体命运。我们发现了 关于X的性质和动作的很多内容：一个信号及其直接目标，主要性别确定开关基因 这也控制X染色体剂量补偿。但是，仍然是一个基本问题： 信号以“全部或无”的方式重复解释，以引起肥沃的男性或雌雄同体的发育，从来没有 两性发展？我们使用机器学习神经网络的新方法来解决这个问题 单分子和单细胞分辨率的问题。我们还建议剖析功能相互作用 染色质修饰和染色体结构之间在调节广泛的基因表达中 染色体领土。秀丽隐杆线虫中的X染色体剂量补偿是这种分析的典范：我们 最近发现，剂量补偿的X染色体具有（i）改良的组蛋白水平升高 与常染色体和（ii）独特的三维架构相比，H4K20ME1。两者都是由 剂量补偿复合物（DCC）。 H4K20ME1的损失破坏了3D体系结构并提升X基因 表达。在线虫DCC中，一个亚基是H4K20me2脱甲基酶，五个亚基是同源物 冷凝蛋白亚基，这些亚基紧凑并解决有丝分裂和减数分裂染色体。所有DCC亚基都是 XX特异性亚基特异性亚基专门招募了雌雄同体X染色体，该亚基触发与顺式结合的 X（REX）上的作用调节元素以将基因表达降低一半。 DCC重塑X的结构 使用其最高亲和力雷克斯站点建立拓扑结构域（TADS）以建立域边界。 尽管有这些知识，但仍然存在剂量补偿机制的重要问题。 哪些DCC亚基识别REX位点中X元素的基序直接结合X？ DCC如何调节 RNA聚合酶II抑制基因表达？ H4K20ME1的控制权是什么机制 染色体结构，DCC介导的高阶结构如何影响基因表达？我们的 调查结果应该具有广泛的影响，因为（i）冷凝蛋白配合物控制染色体结构 人类的细菌，（ii）H4K20Me1富集在女性哺乳动物的无活性X上，（iii）脱甲基酶与 肿瘤进展，（iv）H4K20me2脱甲基酶调节线虫的生长，代谢和进入 静止的道尔州。最后，我们将利用我们意外的发现，即雷克斯网站已经分歧 Caenorhabditis种类分别为30 Myr，尽管坚持强烈保护，但仍未保持功能重叠 核心DCC机械。这种差异为研究一致共同的路径提供了一个异常的机会 跨X染色体的数百个靶位点的进化变化以及结合它们的蛋白质复合物。