通过CLASH绘制人类miRNA互动组图,揭示了频繁的非正规结合
Aleksandra Helwak1, Grzegorz Kudla, Tatiana Dudnakova
1Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK.
Cell
|April 30, 2013
概括
识别微RNA (miRNA) 目标是一个挑战. 这项研究引入了绘制人类miRNA-mRNA相互作用的新方法,揭示了复杂的结合模式和新的点.
科学领域:
- 分子生物学分子生物学
- 遗传学 是一个遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 微RNAs (miRNAs) 是基因表达的关键调节者.
- 精确识别miRNA目标是必不可少的,但在实验上很困难.
- 现有的方法缺乏全面目标发现所需的公正范围.
研究的目的:
- 开发一种无偏见的实验方法来识别人类microRNA目标.
- 描述miRNAs及其目标信使RNAs (mRNAs) 之间的结合模式和相互作用.
- 为了生成一个大规模的数据集的高可靠性miRNA-mRNA相互作用.
主要方法:
- 为miRNA-目标RNA复合体开发一个结合和测序技术.
- 复合体与人类阿尔戈诺特1 (AGO1) 蛋白质的关联.
- 对18000多个已识别的miRNA-mRNA相互作用进行了生物信息分析.
主要成果:
- 发现了超过18000个高可信度miRNA-mRNA相互作用.
- 主要非正规的种子区域结合 (60%) 与伴随的非种子配对的特征.
- 在18%的相互作用中确定3'端miRNA的参与,其中一些功能性验证.
- 在miRNA的系统差异:在不同miRNA家族的mRNA基配对.
- 在特定miRNA的相互作用部位中发现过度表现的图案.
结论:
- 开发的方法提供了对人类miRNA点相互作用的无偏见.
- 密RNA结合比以前认为的要复杂得多,频繁存在非正规的相互作用.
- 特定的基配对模式和图案可能会影响目标识别和RISC活动.
相关概念视频
MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...


