Background: Transposable elements (TEs) in eukaryote genomes are quantitatively the main components affecting genome size, structure and expression. The dynamics of their insertion and deletion depend on diverse factors varying in strength and nature along the genome. We address here how TE sequence evolution is affected by neighboring genes and the chromatin status (euchromatin or heterochromatin) at their insertion site. Results: We estimated ages of TE sequences in Arabidopsis thaliana, and found that they depend on the distance to the nearest genes: TEs located close to genes are older than those that are more distant. Consequently, TE sequences in heterochromatic regions, which are gene-poor regions, are surprisingly younger and longer than that elsewhere. Conclusions: We provide evidence for biased TE age distribution close or near to genes. Interestingly, TE sequences in euchromatin and those in heterochromatin evolve at different rates, and as a result, could explain that TE sequences in heterochromatin tend to be younger and longer. Then, we revisit models of TE sequence dynamics and point out differences for TE-rich genomes, such as maize and wheat, compared to TE-poor genomes such as fly and A. thaliana.
Identification and characterization of unique to human regulatory sequences in embryonic stem cells reveal associations with transposable elements, distal enhancers, non-coding RNA, and DNA methylation-driven mechanisms of genome editing
The Stanford University School of Medicine（斯坦福大学医学院）；Sanford-Burnham Medical Research Institute（桑福德-伯纳姆医学研究所）；Genlight Technology Corporation（Genlight科技有限公司）
SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
背景资料：已知转座元件（TE）会影响转录组，因为新的外显子是从内含子转座元件产生的（这称为外显子化），或者元件插入外显子，导致新的转录本。文献中的几个例子表明，由外切作用产生的同种型对某种组织（例如心肌）是特异性的，或者会引起疾病。因此，外切作用可能对生物体的转录组具有负面影响。结果如下：由于我们的目的是检测人类和小鼠基因组中通过转座元件的外切产生的其他组织或肿瘤特异性亚型，我们设计了自动分析管道SERpredict（SER = Specific Exonized Retroelement），利用贝叶斯统计。通过这个管道，我们发现了几个基因，其中一个转座元件形成了组织或肿瘤特异性同种型。结论：我们的研究结果表明，SERpredict产生了相关的结果，证明了转座元件在塑造人类和小鼠转录组中的重要性。转座元件对人类转录组的影响比对小鼠转录组的影响高几倍，这是由于灵长类动物特异性Alu元件的贡献
Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function
SINE VNTR Alu（SVA）是人类基因组中最年轻的转座因子。最古老的SVA A型的传播发生在大约一千三百万年前，而最年轻的SVA类型在黑猩猩分化后出现在人类基因组中。与SVA插入相关的基因的功能富集分析表明，它们与归因于脑功能和疾病的多个本体论类别有很强的联系。SVA类型，扩大其存在于人类基因组中的不同阶段的类人猿生活史也与逐步演变的行为特征，表明一个潜在的影响SVA传播的认知能力的现代人。SVA相关基因在功能网络中高度交联，表明SVA插入可能引起的功能改变的累积影响。我们的分析揭示了SVA在人类CNS进化中的潜在作用，特别是与社会和父母行为相关的功能趋势的出现。它还支持的模型，部分解释了大脑功能如何可以调制的免疫和生殖系统的基础上的基因表达模式和基因途径可能改变SVA插入。
Highly conserved sequence-specific double-stranded DNA binding networks contributing to divergent genomic evolution of human and chimpanzee brain development
Institute of Engineering in Medicine University of California, San Diego（加州大学圣地亚哥分校工程医学院）
The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae
Hunan University of Arts and Science（湖南文理学院）；Chinese Medicine Research Institute of Beijing Tcmages Pharmaceutical Co., Ltd.（北京同仁堂制药有限公司中药研究所）；College of Forestry, Central South University of Forestry and Technology（中南林业科技大学林学院）；Huaihua University（怀化学院）；Hunan Normal University（湖南师范大学）
