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相关概念视频

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

15.3K
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...
15.3K
DNA-only Transposons02:57

DNA-only Transposons

14.4K
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.
The donor site from where the transposon is excised is either degraded or...
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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...
11.4K
LTR Retrotransposons03:08

LTR Retrotransposons

17.4K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
17.4K

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MATES:一种基于深度学习的模型,用于在单细胞中对可转移元素进行特定位置的量化.

Ruohan Wang1,2,3, Yumin Zheng2,3,4, Zijian Zhang5

  • 1School of Computer Science, McGill University, Montreal, Quebec, Canada.

Nature communications
|October 11, 2024
PubMed
概括

可移植元素 (TE) 对遗传多样性至关重要. 我们的新深度学习工具MATES准确地量化TEs在单细胞omics数据中的特定位置,改进生物洞察力.

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科学领域:

  • 基因组学就是基因组学.
  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 可转移元素 (TE) 对遗传多样性和基因调节做出了重大贡献.
  • 目前对TEs的单细胞量化方法往往缺乏位置特异性,并且仅限于转录组学数据.
  • 精确的,特定于位点的TE量化对于理解它们在生物过程中的作用至关重要.

研究的目的:

  • 开发一种新的深度学习方法,用于准确,特定于位置的可转换元素在单细胞的数据中的定量化.
  • 为了克服现有方法在处理多映射读取和多种数据模式方面的局限性.
  • 加强对单细胞异质性和受TE影响的基因调节的探索.

主要方法:

  • 介绍MATES,一种深度学习方法,用于将多重映射读数分配到特定的可转移元素位置.
  • 利用相邻读取对齐的上下文来改善TE位置识别.
  • 应用和验证 MATES 跨多种单细胞数据集的数据.

主要成果:

  • 与现有方法相比,MATES在TE量化准确度方面表现优越.
  • 该工具有效地将多重映射读数分配给特定的TE位置.
  • MATES有助于识别特定细胞群的标记TE,揭示细胞异质性.

结论:

  • 在单细胞基因组学中,MATES提供了一种准确且可适应的工具,用于转移元素量化.
  • 这一进步有助于更深入地探索TE在基因调节和细胞多样性中的功能.
  • 马特斯为单细胞基因组学社区提供了宝贵的资源.