扩展了RNA基编辑器的调色板,用于全面的RBP-RNA互动原子研究
Hugo C Medina-Munoz1,2,3, Eric Kofman1,2,3,4, Pratibha Jagannatha1,2,3,4
1Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
bioRxiv : the preprint server for biology
|October 9, 2023
概括
研究人员开发了PRINTER,以寻找新的RNA基编辑器 (rBEs),用于研究RNA结合蛋白 (RBPs). 这扩展了绘制RBP-RNA相互作用的工具,改善了RNA目标发现.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 生物化学 生物化学
背景情况:
- RNA结合蛋白 (RBPs) 对于RNA处理和细胞功能至关重要.
- 像TRIBE和STAMP这样的当前方法使用RNA基编辑器 (rBEs) 来识别RBP目标,但可用的rBE目录有限.
- 基于免疫沉 (CLIP) 的方法有局限性,包括酶消化和高投入材料要求.
研究的目的:
- 扩大用于RBP-RNA相互作用研究的RNA基编辑器 (rBE) 的范围.
- 开发一个系统的框架来评估和选择合适的RBE用于RBP目标发现.
- 确定可以描述各种RBP的绑定模式的rBE,包括序列特定和宽绑定类型.
主要方法:
- 开发了PRINTER (编辑RNA的酶的基于蛋白质-RNA相互作用的分类) 框架.
- 采用实验和计算分析来评估30多个A-to-I和C-to-UrBE.
- 根据编辑偏差和单个和双个RBP应用程序的RBP约束偏好,评估rBE的适用性.
主要成果:
- 确定了新的rBEs,这些rBEs增强了RBP-RNA结合模式的表征.
- 证明rBE的选择取决于其编辑偏见和RBP的约束性偏好.
- 提出适用于双RBP相互作用研究的特定rBE,扩大实验可能性.
结论:
- PRINTER框架简化和增强了用于RBP-RNA目标发现的rBE的选择.
- 这项研究扩大了下一代RBP-RNA相互作用研究可用的rBEs的范围.
- 这些发现有助于更全面地描述RBP结合模式和RNA标场景.
相关概念视频
02:23RNA Editing
9.0K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.0K
02:24Ribosome Profiling
3.6K
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...
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...
3.6K
00:58Eukaryotic RNA Polymerases
24.3K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
24.3K