Heterochromatin on the human inactive X chromosome

人类失活 X 染色体上的异染色质

• 批准号: 8327212
• 负责人: Brian P. Chadwick
• 金额: $ 30.56万
• 依托单位: FLORIDA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-02-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8327212
• 关键词: Antisense RNA; Binding; Binding Sites; Biological; Biological Models; Biology; CCCTC-binding factor; Cell Line; Cell division; Cells; Centromere; Chemicals; Chromatin; Chromatin Fiber; Chromosomes; Chromosomes, Human, Pair 4; Communication; Complex; Custom; D4Z4; DNA; DNA Methylation Inhibition; DNA Methyltransferase; DNA Modification Methylases; DNA Packaging; DNA Sequence; DNA-Binding Proteins; Data; Deoxyribonucleases; Disease; Distal; Drug Formulations; ES Cell Line; Employee Strikes; Enhancers; Ensure; Epigenetic Process; Equilibrium; Euchromatin; Excision; Facioscapulohumeral Muscular Dystrophy; Family member; Female; Fiber FISH; Fission Yeast; Foundations; Functional RNA; Future; Gene Expression; Gene Silencing; Genes; Genetic Transcription; Genome; Genomics; Goals; HCT116 Cells; Health; Hereditary Disease; Heterochromatin; Histone Deacetylation; Histone H3; Histones; Homologous Gene; Human; In Vitro; Insulator Elements; Interphase; Investigation; Knock-out; Link; Location; Lysine; Maintenance; Malignant Neoplasms; Mammals; Maps; Mediating; Modeling; Modification; Molecular; Monitor; Mus; Mutation; Nucleosomes; Nucleotides; Pathway interactions; Pattern; Polycomb; Primates; Process; Proteins; RNA; RNA Interference; Regulatory Element; Reporting; Research; Research Design; Resolution; Rett Syndrome; Role; Sequence Homology; Sex Chromatin; Side; Signal Transduction; Site; Small RNA; Solid; Somatic Cell; Structure; Syndrome; Testing; Transcript; Transcriptional Regulation; Ursidae Family; Variant; X Chromosome; X Inactivation; Yin-Yang; base; chemical genetics; chromatin immunoprecipitation; chromatin modification; chromatin protein; dosage; embryonic stem cell; genetic manipulation; histone methyltransferase; histone modification; imprint; insight; male; monomer; novel; promoter; recombinase; research study; sex; spatial relationship; transcription factor

DESCRIPTION (provided by applicant): X chromosome inactivation is an essential mammalian epigenetic process that serves to balance the levels of X-linked gene expression between the sexes. The inactive X chromosome (Xi) is the most extensive example of developmentally regulated gene silencing, and provides a model to explore in depth the epigenetic features of heterochromatin and to relate these to the underlying genomic DNA sequence. Unexpectedly, the X-linked macrosatellite DXZ4 is packaged into the opposite chromatin arrangement than that of the surrounding chromosome. Consequently, DXZ4 on the Xi is organized into euchromatin, whereas the array on the active X chromosome (Xa) is heterochromatic. DXZ4 is bi-directionally transcribed on both the Xa and Xi, but the processing of the non-coding RNAs differs between the two chromosomes. Cleavage of the antisense transcript into small RNAs coincides with the heterochromatic form of DXZ4, and the small RNAs themselves directly align with nucleosomes bearing the heterochromatin modification H3K9me3. Meanwhile, antisense RNA originating from the Xi is sufficiently stable that it can be detected as a longer transcript. Intriguingly, the chromatin insulator and epigenetic organizer protein CTCF binds specifically to the Xi array, immediately adjacent to the DXZ4 bi-directional promoter. To what extent CTCF is involved in establishing and maintaining DXZ4 chromatin on the Xi, and the impact this unusual organization has on flanking chromatin is unknown. However, the contrasting arrangement of DXZ4 chromatin between the X chromosomes and the specific binding of CTCF to the Xi is conserved at the functional homologue of DXZ4 on the mouse X chromosome (Dxz4), suggesting that this organization serves an important function. Our long-term goal is to understand the role of DXZ4 on the Xa and Xi and the extent to which it is involved in organizing and maintaining flanking chromatin and gene expression. We hypothesize that (A) The Xa processed antisense small RNAs are intimately linked to H3K9me3, via a mammalian pathway similar to RNAi mediated heterochromatin formation described for S.pombe, and (B) The Xi specific association of CTCF with DXZ4 ensures stabilization of antisense transcripts, packaging of the array into euchromatin and maintenance of flanking heterochromatin. In order to test these hypotheses, we propose three specific aims: (i) To define in detail the chromatin organization of DXZ4/Dxz4 on the Xa and Xi, (ii) To understand the role of DXZ4 features in maintaining chromatin and expression of both the array and flanking genomic interval on the Xa and Xi and (iii) To assess the role of Dxz4 on the mouse X. Taken together, these studies are designed to explore the mechanisms that direct packaging of DNA into euchromatin and heterochromatin and will provide valuable insight into the role of RNA in chromatin organization in complex genomes. As such, this research has direct relevance to all forms of epigenetic abnormalities including imprinting disorders, genetic disease involving mutation of chromatin proteins, and the many chromatin alterations observed in cancer. PUBLIC HEALTH RELEVANCE: The proposed studies aim to investigate an unusual epigenetic phenomena involving the macrosatellite sequence DXZ4 on the inactive X chromosome. DXZ4 is a paradigm to explore in depth the interplay between epigenetic features in establishing and maintaining chromatin organization. Therefore, this research has direct relevance to all forms of epigenetic abnormalities including imprinting disorders such as Prader-Willi/Angleman syndrome or Beckwith-Weidemann syndrome, genetic disease involving mutation of chromatin proteins such as Rett syndrome, and the many chromatin changes observed in cancer. Furthermore, understanding the packaging and organization of DXZ4 will have direct impact on Facioscapulohumeral Muscular Dystrophy research, a devastating macrosatellite contraction disorder.

描述（由申请人提供）：X 染色体失活是哺乳动物重要的表观遗传过程，用于平衡两性之间 X 连锁基因表达的水平。失活的 X 染色体 (Xi) 是发育调控基因沉默的最广泛的例子，并提供了一个模型来深入探索异染色质的表观遗传特征并将其与潜在的基因组 DNA 序列联系起来。出乎意料的是，X连锁大卫星DXZ4被包装成与周围染色体相反的染色质排列。因此，Xi 上的 DXZ4 被组织成常染色质，而活性 X 染色体 (Xa) 上的阵列是异染色质的。 DXZ4 在 Xa 和 Xi 上双向转录，但两条染色体之间非编码 RNA 的处理不同。反义转录物裂解成小RNA与DXZ4的异染色质形式一致，并且小RNA本身直接与带有异染色质修饰H3K9me3的核小体对齐。同时，源自 Xi 的反义 RNA 足够稳定，可以作为更长的转录本被检测到。有趣的是，染色质绝缘体和表观遗传组织蛋白 CTCF 特异性结合 Xi 阵列，紧邻 DXZ4 双向启动子。 CTCF 在多大程度上参与 Xi 上 DXZ4 染色质的建立和维持，以及这种不寻常的组织对侧翼染色质的影响尚不清楚。然而，X 染色体之间 DXZ4 染色质的对比排列以及 CTCF 与 Xi 的特异性结合在小鼠 X 染色体上 DXZ4 的功能同源物 (Dxz4) 上是保守的，表明该组织发挥着重要的功能。我们的长期目标是了解 DXZ4 对 Xa 和 Xi 的作用以及它参与组织和维持侧翼染色质和基因表达的程度。我们假设 (A) Xa 加工的反义小 RNA 通过类似于 RNAi 介导的粟酒裂殖酵母异染色质形成的哺乳动物途径与 H3K9me3 密切相关，(B) CTCF 与 DXZ4 的 Xi 特异性关联确保了反义的稳定性转录本、将阵列包装成常染色质并维持侧翼异染色质。为了检验这些假设，我们提出了三个具体目标：（i）详细定义 DXZ4/Dxz4 在 Xa 和 Xi 上的染色质组织，（ii）了解 DXZ4 特征在维持染色质和两者表达中的作用Xa 和 Xi 上的阵列和侧翼基因组间隔，以及 (iii) 评估 Dxz4 对小鼠 X 的作用。总而言之，这些研究旨在探索直接将 DNA 包装成常染色质和异染色质，将为复杂基因组中 RNA 在染色质组织中的作用提供有价值的见解。因此，这项研究与所有形式的表观遗传异常直接相关，包括印记疾病、涉及染色质蛋白突变的遗传病以及在癌症中观察到的许多染色质改变。公共健康相关性：拟议的研究旨在调查涉及失活 X 染色体上的大卫星序列 DXZ4 的不寻常表观遗传现象。 DXZ4 是深入探索表观遗传特征在建立和维持染色质组织中相互作用的范例。因此，这项研究与所有形式的表观遗传异常有直接关系，包括印记疾病，如 Prader-Willi/Angleman 综合征或 Beckwith-Weidemann 综合征，涉及染色质蛋白突变的遗传病，如 Rett 综合征，以及在癌症中观察到的许多染色质变化。此外，了解 DXZ4 的包装和组织将对面肩肱型肌营养不良症（一种破坏性的大卫星收缩障碍）的研究产生直接影响。