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 研究建议剖析一个基本的，二元的发展决定， 后生动物的性别。线虫C. elegans通过计算X-来极其精确地确定性别 相对于常染色体组的染色体数目（X：A信号）：1X：2A（0.5）和2X：3A（0.67）的比率 信号为雄性命运，而3X：4A（0.75）和2X：2A（1.0）的比例信号为雌雄同体命运。我们已经发现 关于X的本质和作用：一个信号及其直接目标，一个主要的性别决定开关基因 也控制着X染色体的剂量补偿然而，一个基本问题仍然存在： 以“全或无”的方式可再现地解释信号以引起可育雄性或雌雄同体发育， 中间性发育？我们开创了使用机器学习神经网络来解决这个问题的新方法 单分子和单细胞分辨率的问题。我们还建议剖析功能的相互作用 染色质修饰和染色体结构在调节基因表达中的作用 染色体区域C. X染色体剂量补偿elegans是这种分析的典范：我们 最近发现，剂量补偿的X染色体（i）修饰的组蛋白水平升高 H4 K20 me 1相比，常染色体和（ii）一个独特的三维结构。两者都是由 剂量补偿复合物（DCC）。H4 K20 me 1的缺失破坏了3D结构并提升了X基因 表情在线虫DCC中，一个亚基是H4 K20 me 2脱甲基酶，五个亚基是同源物 压缩和分解有丝分裂和减数分裂染色体的凝聚素亚基。所有DCC子单元均为 通过一个XX特异性亚基特异性地募集到两性X染色体上，该亚基触发与顺式 作用于X（雷克斯）上的调节元件以使基因表达减少一半。DCC重塑了X的结构 使用其最高亲和力的雷克斯位点将其转化为拓扑关联结构域（TADs）以建立结构域边界。 尽管有这些知识，剂量补偿机制的重要问题仍然存在。 什么样的DCC亚基能够识别雷克斯位点上富含X的基序并直接与X结合？DCC如何监管 RNA聚合酶II抑制基因表达？H4 K20 me 1的控制机制是什么？ 染色体结构，以及DCC介导的高阶结构如何影响基因表达？我们 这些发现应该具有广泛的意义，因为（i）凝聚素复合物控制染色体结构， （ii）H4 K20 me 1在雌性哺乳动物的无活性X上富集，（iii）脱甲基酶与 肿瘤进展，和（iv）H4 K20 me 2脱甲基酶调节线虫生长、代谢和进入肿瘤细胞。 静止的状态。最后，我们将利用我们的意外发现，雷克斯网站已经分歧， 小杆线虫物种被30 MYR分开，尽管它们具有很强的保守性，但没有保留功能重叠。 核心DCC机械。这种分歧提供了一个不同寻常的机会，研究协调一致的共同努力的道路。 X染色体上的数百个靶位点以及与它们结合的蛋白质复合物的进化变化。