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: 7592810
• 负责人: David Eric Symer
• 金额: $ 101.61万
• 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/7592810
• 关键词: Acetylation; Adult; Aging; Biological; Biomedical Computing; Brain; Cancer cell line; Cataloging; Catalogs; Cells; Chromosome Structures; Collaborations; Count; Cytosine; DNA Methylation; DNA Methyltransferase; DNA Modification Methylases; DNA Transposable Elements; Data; Development; Diagnosis; Disease; Epigenetic Process; 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; Long Terminal Repeats; Major Histocompatibility Complex Gene; Malignant Neoplasms; Malignant neoplasm of testis; Metallothionein; Methylation; MicroRNAs; Mobile Genetic Elements; Modeling; Modification; Molecular; Molecular Profiling; Mouse Strains; Movement; Mus; Numbers; Pattern; Play; RNA Interference; Regulation; Retroelements; Retrotransposition; Retrotransposon; Role; Role playing therapy; Single Nucleotide Polymorphism; Small RNA; Structure; Tail; Techniques; 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; practical application; serial analysis of gene expression; tissue/cell culture

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 made public via a new website, PolyBrowse, developed in collaboration with Advanced Biomedical Computing Center (ABCC) at NCI-Frederick. We found increased transposon indels in brain-associated genes, but significantly reduced indel polymorphisms on the X chromosome. We found that virtually none of the young transposon integrants present in classical inbred mouse strains are present 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. - Found that a disproportionate number of dimorphic endogenous transposons in mouse strains are located in or near genes expressed in brain. Numerous novel transcript structures, attributable directly to recent transposon integrants, are specifically expressed in brain and/or testis. 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).

Symer实验室小组- -发现内源性逆转录因子的转座导致了广泛的基因组和转录变异，从而区分了经典小鼠品系，超过了单核苷酸多态性（SNP）。这些插入/缺失（indel）多态性已经通过一个新的网站PolyBrowse公开，该网站与NCI-Frederick的高级生物医学计算中心（ABCC）合作开发。我们发现脑相关基因中的转座子indel增加，但X染色体上的indel多态性显着减少。我们发现，几乎没有年轻的转座子整合体存在于经典的近交系小鼠品系中存在于野生株基因组中。- 鉴定了许多新的转录本结构，区分小鼠品系，这些小鼠品系可直接归因于这些最近整合的转座子中的一些，并且在特定发育时间点在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元件在培养的癌细胞系中在几周内积极移动。这些结果表明，转座子可以改变正常的哺乳动物基因组和基因表达谱，显着和真实的时间。- 发现小鼠品系中不成比例数量的二态内源性转座子位于脑中表达的基因中或附近。许多新的转录本结构，直接归因于最近的转座子整合体，在脑和/或睾丸中特异性表达。大多数内源性转座子仅在某些组织中表达，通常在发育早期，如脑和睾丸。- 在不同的经典小鼠品系中鉴定了数千个含有长末端重复序列（LTR）的逆转录转座子多态性。我们表征了一些多态性LTR反转录转座子的表达，并发现在大多数成年小鼠组织中广泛表达融合LTR基因转录本。一般来说，这种表达模式与融合L1基因转录本的表达模式不同。- 在小鼠睾丸中发现了小鼠L1反转录转座子的正义和反义25 nt RNA，表明小RNA的产生并可能在控制转座子的表达和运动中起作用。- 发现了微小RNA仅作为融合转座子-微小RNA转录物表达的初步证据。这一结果支持了一种新的方法，通过这种方法可以在细胞中建立和调节microRNA的表达。- 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文库标签计数的系列分析与微阵列数据进行了比较。该分析揭示了一组可能的特征基因，其表达与其胞嘧啶甲基化密切相关。这些基因包括睾丸癌基因、干扰素诱导基因、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。- 发现从头L1整合体的表观遗传控制在组织培养细胞中（其中存在动态组蛋白尾标记，如建立的乙酰化）与体内体细胞组织中（其中它们经历密集的胞嘧啶甲基化）非常不同。