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相关概念视频

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

15.2K
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...
15.2K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

11.4K
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
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...
14.4K
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
piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

6.8K
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...
6.8K
RNA-seq03:21

RNA-seq

9.8K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.8K

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相关实验视频

Updated: Jun 7, 2025

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR

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使用sTELLeRR检测长读基因组中的可转移元素.

Kristine Bilgrav Saether1,2, Jesper Eisfeldt1,2,3

  • 1Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm 171 76, Sweden.

Bioinformatics (Oxford, England)
|November 19, 2024
PubMed
概括
此摘要是机器生成的。

使用长读基因组测序,sTELLeR准确地检测可转移元素 (TE). 这种快速而精确的工具改进了分析重复性DNA序列的现有方法,这对于理解基因组功能和疾病至关重要.

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
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相关实验视频

Last Updated: Jun 7, 2025

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

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Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
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Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

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科学领域:

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

背景情况:

  • 可移植元素 (TE) 占基因组的50%左右,可以通过破坏基因功能来引起疾病.
  • 短读测序难以表征重复的TEs,阻碍了准确的分析.
  • 长读基因组测序 (lrGS) 为TE检测提供了更好的分辨率.

研究的目的:

  • 开发一种新的工具,以使用irrgs进行准确,快速和有效的TE检测.
  • 提高重复性DNA序列的特征,包括与疾病相关的TE.
  • 为研究和临床环境中TE分析提供计算效率高和兼容的解决方案.

主要方法:

  • 开发了sTELLeR,这是一个基于Python的工具,用于长读的可转换元素检测.
  • 评估了STELLeR与现有的TE呼叫者之间的表现.
  • 为下游分析兼容性确保了哈普洛型的认识和VCF输出.

主要成果:

  • 与类似的工具相比,sTELLeR在Alu元素调用方面表现出更高的精度和灵敏度.
  • 该工具显著更快 (5-48倍),使用较少的计算资源 (<2%的CPU小时).
  • 具有哈普类型意识的VCF输出方便集成到现有的变量调用工作流中.

结论:

  • sTELLeR是一种快速,灵敏和精确的呼叫器,用于使用lrGS检测TE.
  • 该工具可以很容易地应用于变异调用管道,以改进基因组分析.
  • sTELLeR推进了对TEs及其相关疾病的临床检测的潜力.