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相关概念视频

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

15.7K
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 Transposons02:57

DNA-only Transposons

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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.
The donor site from where the transposon is excised is either degraded or...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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相关实验视频

Updated: Jul 18, 2025

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
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奇梅拉TE:一个管道检测基因和可转移元素衍生的奇梅拉转录.

Daniel S Oliveira1,2, Marie Fablet2,3, Anaïs Larue2,4

  • 1São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil.

Nucleic acids research
|August 24, 2023
PubMed
概括

可转移的元素 (TE) 创建嵌合式转录,驱动遗传多样性和适应. ChimeraTE是一个新的管道,可以识别这些关键的TE-基因融合,即使没有参考基因组.

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CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
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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:

  • 可移植元素 (TE) 是遗传变异的重要驱动因素,可以导致结构变异.
  • TE-基因融合转录或嵌合转录与物种适应有关.
  • 目前用于识别嵌合体转录的方法受到规模和依赖参考基因组的限制,忽视了多态TE插入.

研究的目的:

  • 开发一种新的计算管道,ChimeraTE,用于转录组全方位识别嵌合体转录.
  • 为了能够检测出源于参考指导和无参考分析的嵌合式转录.
  • 通过嵌合体转录形成来研究TE在产生遗传多样性的作用.

主要方法:

  • 开发了ChimeraTE,这是一个利用对结 RNA-seq 阅读的管道,用于嵌合体转录识别.
  • 实现了两种模式:用于多态 TE 插入的参考指导方法 (模式 1) 和无参考方法 (模式 2).
  • 使用四个Drosophila melanogaster野生型菌株的RNA-seq数据验证了管道.

主要成果:

  • 确定大约1.12%的所有基因产生了嵌合体转录,主要涉及TE-exonized序列.
  • 发现大约23%的检测到的嵌合体不在参考基因组中,这表明最近或多态TE插入.
  • 证明了ChimeraTE在没有参考基因组的情况下发现嵌合体转录的能力.

结论:

  • 奇美拉TE是第一个能够自动识别奇美拉转录的管道,而不需要参考基因组.
  • 该工具有助于研究TE对转录组可塑性和遗传多样性的贡献.
  • 这些发现强调了多态TE在产生新基因融合和潜在适应过程中的重要性.