Analysis of Nematode Sex Determination and Dosage Compensation

线虫性别决定和剂量补偿分析

基本信息

批准号：
10598121
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
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-04-01 至 2025-03-31
项目状态：
未结题

项目摘要

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.

项目概要拟议的研究旨在剖析大多数人所采取的基本的二元发展决策之一。后生动物制造：它们的性别。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) 的比率信号男性命运，而 3X:4A (0.75) 和 2X:2A (1.0) 的比率则信号雌雄同体命运。我们发现关于 X:A 信号及其直接目标（主要性别决定开关基因）的性质和作用的更多信息它还控制 X 染色体剂量补偿。然而，一个根本问题依然存在：如何以“全部或全部”的方式重复解释信号以引发可育的雄性或雌雄同体发育，从不两性发育？我们开创了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基因表达方面的作用染色体区域。线虫中的 X 染色体剂量补偿是本分析的典范：我们最近发现，剂量补偿的 X 染色体 (i) 修饰组蛋白水平升高 H4K20me1 与常染色体相比以及 (ii) 独特的三维架构。两者均由剂量补偿复合物（DCC）。 H4K20me1 缺失会破坏 3D 架构并提升 X 基因表达。在线虫 DCC 中，一个亚基是 H4K20me2 去甲基酶，五个亚基是同系物凝缩蛋白亚基，压缩并分解有丝分裂和减数分裂染色体。所有 DCC 亚基均为由 XX 特异性亚基特异性招募到雌雄同体 X 染色体，触发与顺式结合作用于 X (rex) 的调控元件可将基因表达量减少一半。 DCC重塑X的结构使用其最高亲和力的雷克斯位点进入拓扑关联域（TAD）来建立域边界。尽管有了这些知识，剂量补偿机制背后的重要问题仍然存在。哪些 DCC 亚基可识别 rex 位点中富含 X 的基序以直接结合 X？ DCC如何监管 RNA聚合酶II抑制基因表达？ H4K20me1 控制的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？我们的研究结果应该具有广泛的意义，因为（i）凝缩蛋白复合物控制染色体结构细菌对人类的影响，(ii) H4K20me1 在雌性哺乳动物的非活性 X 上富集，(iii) 去甲基酶与肿瘤进展，以及 (iv) H4K20me2 去甲基酶调节线虫生长、代谢和进入静止的多尔状态。最后，我们将利用我们的意外发现，即霸王龙的站点已经分散 Caenorhabditis 物种相距 30 MYR，尽管对物种进行了强有力的保护，但没有保留功能重叠核心DCC机械。这种分歧提供了一个不寻常的机会来研究协调一致的合作之路 X 染色体上数百个目标位点以及结合它们的蛋白质复合物的进化变化。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Life 2.0-A CRISPR path to a sustainable planet.

生命 2.0-通往可持续地球的 CRISPR 之路。

DOI：
10.1073/pnas.2107418118
发表时间：
2021
期刊：
Proceedings of the National Academy of Sciences of the United States of America
影响因子：
11.1
作者：
Carroll,Dana;Meyer,BarbaraJ
通讯作者：
Meyer,BarbaraJ

Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans.

DOI：
10.1101/gr.270082.120
发表时间：
2021-07
期刊：
Genome research
影响因子：
7
作者：
Krassovsky K;Ghosh RP;Meyer BJ
通讯作者：
Meyer BJ

Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development.

DOI：
10.1146/annurev-cellbio-032321-035734
发表时间：
2021-10-06
期刊：
Annual review of cell and developmental biology
影响因子：
11.3
作者：
Ghosh RP;Meyer BJ
通讯作者：
Meyer BJ

Combinatorial clustering of distinct DNA motifs directs synergistic binding of Caenorhabditis elegans dosage compensation complex to X chromosomes.

DOI：
10.1073/pnas.2211642119
发表时间：
2022-09-13
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Fuda, Nicholas J.;Brejc, Katjusa;Kruesi, William S.;Ralston, Edward J.;Bigley, Rachel;Shin, Aram;Okada, Miki;Meyer, Barbara J.
通讯作者：
Meyer, Barbara J.

X-chromosome target specificity diverged between dosage compensation mechanisms of two closely related Caenorhabditis species.