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; 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染色体灭活是一种必不可少的哺乳动物表观遗传学过程，可以平衡性别之间X连锁基因表达的水平。非活性X染色体（XI）是发育调节基因沉默的最广泛的例子，并提供了一个模型，可以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序列相关联。出乎意料的是，与周围染色体的X连锁宏观卫星DXZ4包装到相对的染色质排列中。因此，XI上的DXZ4被组织成白染色质，而活性X染色体（XA）上的阵列是异色素。 DXZ4在XA和XI上均进行双向转录，但是非编码RNA的处理在两个染色体之间有所不同。反义转录物在小RNA中的切割与DXZ4的异颜色形式一致，而小的RNA本身直接与带有异染色质修饰H3K9me3的核小体一致。同时，起源于XI的反义RNA足够稳定，可以将其检测为更长的转录本。有趣的是，染色质绝缘子和表观遗传组织者蛋白CTCF专门与XI阵列结合，紧接于DXZ4 BI方向启动子。 CTCF在多大程度上涉及在XI上建立和维持DXZ4染色质，而该组织对侧翼染色质的影响尚不清楚。然而，X染色体之间DXZ4染色质与CTCF与XI的特异性结合在小鼠X染色体（DXZ4）上的功能同源物中保守，这表明该组织起着重要功能。我们的长期目标是了解DXZ4在XA和XI上的作用，以及它参与组织和维持侧翼染色质和基因表达的程度。 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异染色质。为了检验这些假设，我们提出了三个具体目的：（i）详细定义dxz4/dxz4在XA和XI上的染色质组织，（ii），以了解DXZ4特征在维持染色质和表达中的作用，并在XA和XI xi xi和hey the the Dem of the dxz ins of dex xi the the the the the the the the the the the the the the dxz ins of dxz ins the xi和the xi seplane the xi xi the the xi se x.4探索将DNA将DNA包装到白染色质和异染色质中的机制，并将为RNA在复杂基因组中的染色质组织中的作用提供宝贵的见解。因此，这项研究与各种形式的表观遗传异常有直接相关性，包括印记疾病，涉及染色质蛋白突变的遗传疾病以及在癌症中观察到的许多染色质改变。公共卫生相关性：拟议的研究旨在研究涉及无活性X染色体上的宏​​观阳性层序列DXZ4的异常表观遗传现象。 DXZ4是一个范式，可以深入探索在建立和维持染色质组织中表观遗传特征之间的相互作用。因此，这项研究与所有形式的表观遗传异常具有直接相关性，包括诸如Prader-Willi/Angleman综合征等烙印或Beckwith-Weidemann综合征，涉及染色质蛋白（如RETT综合征）的突变以及许多染色质在癌症中的变化。此外，了解DXZ4的包装和组织将直接影响对毁灭性的巨阳性卫生间收缩障碍的Facioscapulohumeral肌肉营养不良研究。