mRNA端到端距离和形状的有效预测模型:三维RNA插图程序 (TRIP)
1Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, University Town of Shenzhen, Shenzhen, Guangdong, China.
Methods in molecular biology (Clifton, N.J.)
|March 19, 2024
概括
这项研究介绍了TRIP,一种用于预测RNA3D结构的新计算模型. TRIP有效地可视化了长信使RNA (mRNA) 构造,有助于理解RNA结构和功能.
科学领域:
- 分子生物学分子生物学
- 计算生物学 计算生物学
- 生物物理学的生物物理.
背景情况:
- RNA的二级和三级结构对于生物调节至关重要.
- 在模型越来越多地预测RNA结构,从热力学发展到深度学习方法.
- 预测长信使RNA (mRNA) 形状仍然具有挑战性.
研究的目的:
- 介绍一种新的计算模型,即三维RNA插图程序 (TRIP).
- 为了能够有效地预测和可视化长mRNA的3D形状.
- 为估计RNA端到端距离提供一个工具.
主要方法:
- 开发了一个基于单链模型的计算机模拟模型TRIP.
- 从单分子光 in situ 杂交 (smFISH) 实验中结合了珠子组件的角度限制.
- 设计TRIP作为一个快速,高效的应用程序,需要最小的投入.
主要成果:
- TRIP提供了RNA3D形状的粗略可视化.
- 该模型是高效的,只需要最多三个输入输出.
- TRIP对于预测RNA端到端距离非常有价值.
结论:
- TRIP提供了一种新的,有效的方法来预测长mRNA的3D结构.
- 该模型的可视化功能有助于理解RNA构造.
- 在RNA结构研究中,TRIP是一个有价值的工具.
相关概念视频
02:22Regulated mRNA Transport
6.3K
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
6.3K
02:51mRNA Stability and Gene Expression
5.6K
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
Cis-acting Elements involved in mRNA stability
5.6K
02:07Improving Translational Accuracy
10.3K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
10.3K
02:27Nonsense-mediated mRNA Decay
10.6K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.6K
01:53RNA Stability
33.5K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.5K
02:31Nuclear Export of mRNA
7.7K
Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
7.7K