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相关概念视频

lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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RNA-seq03:21

RNA-seq

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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...
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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
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通过scRNA-seq与ELATUS一起发现功能性lncRNAs.

Enrique Goñi1,2,3, Aina Maria Mas1,2,3, Jovanna Gonzalez1,2,3

  • 1Center for Applied Medical Research, University of Navarra, PIO XII 55 Ave, Pamplona, Spain.

Nature communications
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概括

我们开发了ELATUS,这是一个新的计算框架,用于改进在单细胞RNA测序 (scRNA-seq) 数据中检测长非编码RNA (lncRNA). 埃拉图斯增强了功能性lncRNAs的识别,揭示了乳腺癌等疾病中的新角色.

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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:

  • 长非编码RNAs (lncRNAs) 是细胞功能和疾病中的基因表达的关键调节者.
  • 使用单细胞RNA测序 (scRNA-seq) 研究细胞类型特定的lncRNA是具有挑战性的,因为注释的不准确性和低表达水平.

研究的目的:

  • 在scRNA-seq数据中对lncRNA检测的预处理方法进行基准测试.
  • 开发和验证一个计算框架,ELATUS,用于增强 lncRNA识别.
  • 揭示新型,具有生物学意义的 lncRNA 和它们在病理中的作用.

主要方法:

  • 对scRNA-seq预处理技术的系统基准测试.
  • 开发ELATUS计算框架,将Kallisto伪对齐与选择性功能过相结合.
  • 使用单细胞多组ATAC-seq数据进行验证,并独立确认检测到的lncRNA表达模式.

主要成果:

  • 埃拉图斯显著提高了从scRNA-seq数据中检测功能lncRNA的检测.
  • 与标准方法相比,ELATUS与ATAC-seq配置文件的一致性更高,特别是在不完美的参考注释方面.
  • 该框架确定了以前未经记录的lncRNAs,包括AL121895.1,这是一种涉及乳腺癌进展的新型cis-抑制器lncRNA.

结论:

  • 一个专门为lncRNAs量身定制的scRNA-seq工作流对于全面分析至关重要.
  • 埃拉图斯提供了一种强大的方法来揭示 lncRNAs 在细胞过程和疾病中的多方面的作用.
  • 这项研究强调了ELATUS在发现新生物标志物和治疗点方面的潜力,例如乳腺癌中的AL121895.1.