Genomic, Transcriptional and Epigenetic Variation Due to Retrotransposition

Symer实验室的研究小组发现， 在区分经典小鼠品系的广泛的基因组和转录变异中， 单核苷酸多态性（SNP）。这些插入/缺失（indel） 多态性已经在一个新的数据库MouseIndelDB中制成表格，并通过一个新的 PolyBrowse网站，与高级生物医学计算中心合作开发 （ABCC）在NCI-Frederick。我们发现转座子插入缺失在某些类别的 基因，包括受体，但显着减少的X染色体和基本 基因，包括那些参与细胞周期、核苷酸代谢和肿瘤发生的基因。我们有 发现在经典近交系小鼠中几乎没有年轻的转座子整合体存在， 菌株存在于野生菌株基因组中相同的染色体位置。- 识别 许多新的转录本结构区分小鼠品系， 直接与这些最近整合的转座子中的一些连接，并以受调节的 在特定发育时间点的特定组织中的时尚。- 开发了一种新的分子 技术来鉴定新动员内源性转座子，并显示人L1 元素在几周内在培养的癌细胞系中活跃地移动。这些结果表明 转座子可以改变正常哺乳动物的基因组，基因表达谱， 戏剧性地在真实的时间里。- 许多新的转录本结构，可直接归因于 到最近的转座子整合体，并从它们内部的启动子启动， 在睾丸、发育中的胚胎和/或脑中表达最显著，但也在其他组织中表达。 组织中类似地，大多数内源性转座子仅在某些组织中表达， 通常在发育的早期，如大脑和睾丸。- 鉴定了数千条 不同经典小鼠含末端重复序列反转录转座子多态性 菌株我们表征了一些多态性LTR反转录转座子的表达， 融合LTR基因转录本在大多数成年小鼠组织中广泛表达。总的来说， 这种表达模式与融合L1基因转录物的表达模式不同。- 发现感觉 和小鼠睾丸中L1反转录转座子的反义25 nt RNA，表明 产生小RNA并可在控制转座子表达和移动中起作用。 - 发现了微RNA仅以融合形式表达的初步证据 转座子-microRNA转录物。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。- 进行了广泛的统计分析， 从DNA甲基转移酶亚型细胞转录表达，比较系列分析 基因表达cDNA文库标签计数与微阵列数据。分析显示， 可能的“签名基因”，其表达与其基因的表达密切相关。 胞嘧啶甲基化。这些基因包括睾丸癌基因、干扰素诱导基因、 组织相容性复合体（MHC）基因和金属硫蛋白基因簇的成员。- 发现新生L1整合子的表观遗传控制在组织培养中非常不同 细胞（其中存在动态组蛋白尾标记，如乙酰化建立）与体细胞 体内组织（在那里它们经历密集的胞嘧啶甲基化）。

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).