Genomic, Transcriptional and Epigenetic Variation Due to Retrotransposition

Symer实验室小组发现，内源性逆转录因子的转位导致了广泛的基因组和转录变异，区分了经典小鼠品系，超过了单核苷酸多态性（snp）。这些插入/删除（indel）多态性已在一个新的数据库MouseIndelDB中制成表格，并通过与NCI-Frederick的高级生物医学计算中心（ABCC）合作开发的新网站PolyBrowse公开。我们发现转座子索引在某些类型的基因（包括受体）中增加，但在X染色体和必需基因（包括参与细胞周期、核苷酸代谢和肿瘤发生的基因）中显著减少。我们发现，在经典近交系小鼠菌株中，几乎没有一个年轻的转座子整合子存在于野生菌株基因组的相同染色体位置。-鉴定出许多新的转录本结构，这些结构可直接归因于这些最近整合的转座子，并在特定组织中以受调节的方式在特定发育时间点表达。-开发了一种新的分子技术来鉴定新动员的内源性转座子，并显示人类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，转座子可以显著地实时改变正常哺乳动物的基因组和基因表达谱。-许多新的转录结构，可直接归因于最近的转座子整合子，并由其内部启动子启动，在睾丸，发育中的胚胎和/或大脑中表达最为突出，但也在其他组织中表达。同样，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LTR的反转录转座子多态性。我们描述了一些多态LTR反转录转座子的表达，并在大多数成年小鼠组织中发现融合LTR基因转录物的广泛表达。一般来说，这种表达模式不同于融合l1基因转录本的表达模式。-在小鼠睾丸中发现小鼠L1逆转录转座子的正义和反义25 nt rna，提示小rna的产生可能在转座子表达和运动的控制中发挥作用。-发现微rna仅作为融合转座子-微rna转录物表达的初步证据。这一结果为在细胞中建立和调控microRNA表达提供了新的途径。-对DNA甲基转移酶亚胚细胞的转录物表达进行了广泛的统计分析，将基因表达cDNA文库标记计数的序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。这些基因包括癌睾丸基因、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。-发现组织培养细胞（有动态组蛋白尾部标记，如乙酰化建立）与体内体细胞组织（它们经历密集的胞嘧啶甲基化）中新生L1整合体的表观遗传控制非常不同。

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).