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Non-LTR Retrotransposons03:18

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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TE-SCALE:一个全面的数据库,用于在单细胞分辨率下在人类癌症中探索可移植元素表达.

Xini Meng1,2,3, Zhi Nie1,2,3,4, Qifei Wang1,2,3

  • 1China National Center for Bioinformation, Beijing 100101, China.

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概括

转移性元素 (TE),通常是沉默的,当调节失调时,可以驱动癌症. TE-SCALE是一个新的数据库,可以对人类癌症中TE表达的单细胞分析,帮助发现生物标志物.

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科学领域:

  • 基因组学就是基因组学.
  • 癌症生物学 癌症生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 可转移元素 (TE) 是重复的DNA序列,在基因组进化中至关重要.
  • TE失调与癌症发展有关,影响瘤基因激活.
  • 现有的单细胞分析由于其重复性,往往省略了TEs,限制了全面的癌症研究.

研究的目的:

  • 开发一个系统的资源来探索人类癌症中单细胞可移植元素的动态.
  • 创建一个全面的数据库,用于整合性分析和可视化跨不同癌症类型的TE表达.
  • 促进用于癌症诊断和治疗的基于TE的新型生物标志物的识别.

主要方法:

  • 开发scTEfinder管道用于单细胞TE量化.
  • 从330个样本中整合了超过130万个细胞,从20种癌症类型中整合到TE-SCALE数据库中.
  • 对差异性TE表达,TE基因共同表达网络分析和功能丰富的分析模块的实施.

主要成果:

  • TE-SCALE提供了一个全癌症TE表达图谱,具有多层次探索能力.
  • 该数据库可以识别具有潜在临床应用的瘤特异性TE.
  • 用户友好的Web界面可方便浏览,搜索,分析和数据下载.

结论:

  • TE-SCALE是了解癌症中TE生物学的宝贵资源.
  • 该平台有助于解码TE在瘤发生和癌症进展中的作用.
  • TE-SCALE加速了TE研究转化为临床应用,包括生物标志物发现和免疫治疗向.