Genomic, Transcriptional and Epigenetic Variation Due to Retrotransposition

逆转录转座引起的基因组、转录和表观遗传变异

• 批准号: 7733119
• 负责人: David Eric Symer
• 金额: $ 59.35万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7733119
• 关键词: Acetylation; Adult; Aging; Biological; Biomedical Computing; Brain; Cancer cell line; Cataloging; Catalogs; Categories; Cell Cycle; Cells; Chromosome Structures; Collaborations; Count; Cytosine; DNA Methylation; DNA Methyltransferase; DNA Modification Methylases; DNA Transposable Elements; Data; Databases; Development; Diagnosis; Disease; Embryo; Epigenetic Process; Essential Genes; Gene Cluster; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic Polymorphism; Genetic Variation; Genome; Genomics; Goals; Histones; Human; Inbred Strains Mice; Individual; Interferons; Knowledge; L1 Elements; Laboratories; Link; Location; Long Terminal Repeats; Major Histocompatibility Complex Gene; Malignant Neoplasms; Malignant neoplasm of testis; Mammals; Metallothionein; Methylation; MicroRNAs; Mobile Genetic Elements; Modeling; Modification; Molecular; Molecular Profiling; Mouse Strains; Movement; Mus; Pattern; Play; RNA Interference; Regulation; Retroelements; Retrotransposition; Retrotransposon; Role; Role playing therapy; Single Nucleotide Polymorphism; Small RNA; Structure; Tail; Techniques; Terminal Repeat Sequences; Testing; Testis; Testis Brain; Time; Tissues; Transcript; Variant; Week; X Chromosome; cDNA Library; epigenetic variation; human disease; in vivo; insertion/deletion mutation; mammalian genome; man; member; novel; nucleotide metabolism; practical application; promoter; receptor; serial analysis of gene expression; tissue/cell culture; tumorigenesis

The Symer lab group - - Found that transposition of endogenous retroelements resulted in extensive genomic and transcriptional variation distinguishing classical mouse strains, exceeding that from single nucleotide polymorphisms (SNPs). These insertion / deletion (indel) polymorphisms have been tabulated in a new database, MouseIndelDB, and made public via a new website, PolyBrowse, developed in collaboration with Advanced Biomedical Computing Center (ABCC) at NCI-Frederick. We found transposon indels are increased in certain categories of genes including receptors, but significantly reduced on the X chromosome and in essential genes including those involved in cell cycle, nucleotide metabolism, and oncogenesis. We have found that virtually none of the young transposon integrants present in classical inbred mouse strains are present at the same chromosomal locations in wild strain genomes. - Identified numerous novel transcript structures distinguishing mouse strains that are attributable directly to some of these recently integrated transposons and are expressed in a regulated fashion in specific tissues at specific developmental time points. - Developed a new molecular technique to identify newly mobilized endogenous transposons, and showed that human L1 elements actively move in cultured cancer cell lines within a few weeks. These results show that transposons can alter the normal mammalian genome, and gene expression profiles, dramatically and in real time. - Numerous novel transcript structures, attributable directly to recent transposon integrants and initiated from internal promoters within them, are expressed most prominently in testis, developing embryos and/or brain, but also in other tissues. Similarly, most endogenous transposons are expressed in only certain tissues, typically early in development, such as brain and testis. - Identified thousands of long terminal repeat (LTR)-containing retrotransposon polymorphisms in different classical mouse strains. We characterized expression of some polymorphic LTR retrotransposons and found extensive expression of fusion LTR-gene transcripts in most adult mouse tissues. In general, this pattern of expression is distinct from that for fusion L1-gene transcripts. - Found sense and antisense 25 nt RNAs from mouse L1 retrotransposons in mouse testis, suggesting that small RNAs are generated and may play a role in control of transposon expression and movement. - Found preliminary evidence for expression of micro RNAs exclusively as fusion transposon-microRNA transcripts. This result supports a new way by which microRNA expression can be established and regulated in cells. - Conducted extensive statistical analysis of transcript expression from DNA methyltransferase hypomorphic cells, comparing serial analysis of gene expression cDNA library tag counts with microarray data. This analysis revealed a set of possible "signature genes" whose expression is closely linked to their cytosine methylation. These include cancer testis genes, interferon-inducibile genes, major histocompatibility complex (MHC) genes, and members of the metallothionein gene cluster. - Found that epigenetic controls of de novo L1 integrants are very different in tissue culture cells (where there are dynamic histone tail marks such as acetylation established) vs. somatic tissues in vivo (where they undergo dense cytosine methylation).

Smer实验室小组发现，内源性逆转录元件的转位导致了区别于经典小鼠品系的广泛的基因组和转录变异，超过了单核苷酸多态(SNPs)。这些插入/缺失(Indel)多态已经在一个新的数据库MouseIndelDB中列出，并通过一个新的网站PolyBrowse公开，该网站是与NCI-Frederick的先进生物医学计算中心(ABCC)合作开发的。我们发现转座子INDELs在包括受体在内的某些基因类别中增加，但在X染色体和必要基因中显著减少，包括那些参与细胞周期、核苷酸代谢和肿瘤发生的基因。我们发现，在经典近交系小鼠基因组中，几乎没有一个年轻的转座子整合子存在于野生品系基因组中相同的染色体位置。-鉴定了许多新的转录本结构，区分了直接归因于一些最近整合的转座子的小鼠品系，并在特定发育时间点的特定组织中以受调控的方式表达。-开发了一种新的分子技术来识别新动员的内源性转座子，并表明人类L1元件在几周内就能在培养的癌细胞系中活跃地移动。这些结果表明，转座子可以戏剧性地实时改变正常哺乳动物的基因组和基因表达谱。-许多新的转录本结构，直接归因于最近的转座子整合子，并由它们内部的启动子启动，最显著地在睾丸、发育中的胚胎和/或脑中表达，但也在其他组织中表达。同样，大多数内源性转座子只在某些组织中表达，通常是在发育早期，如大脑和睾丸。-在不同的经典小鼠品系中鉴定了数千个包含长末端重复序列(LTR)的反转录转座子多态。我们鉴定了一些多态的LTR反转录转座子的表达，并发现融合的LTR基因转录本在大多数成年小鼠组织中广泛表达。一般来说，这种表达模式不同于融合的L1基因转录本。-在小鼠睾丸中发现了来自小鼠L1反转录转座子的正义和反义25NT RNA，表明产生了小RNA，并可能在控制转座子的表达和运动中发挥作用。-发现了仅作为融合转座子-microRNA转录本表达microRNA的初步证据。这一结果支持了一种在细胞中建立和调节microRNA表达的新方法。-对DNA甲基转移酶亚型细胞的转录本表达进行了广泛的统计分析，将基因表达cDNA库标签计数的系列分析与微阵列数据进行了比较。这项分析揭示了一组可能的“标志性基因”，它们的表达与胞嘧啶甲基化密切相关。这些基因包括癌症睾丸基因、干扰素诱导胆汁基因、主要组织相容性复合体(MHC)基因和金属硫蛋白基因簇的成员。-发现在组织培养细胞(有动态的组蛋白尾标，如乙酰化已建立)和体内的体细胞组织(在体内，它们经历密集的胞嘧啶甲基化)中，从头L1整合体的表观遗传控制非常不同。