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相关概念视频

Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
RNA-seq03:21

RNA-seq

11.7K
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...
11.7K
Ribozymes02:47

Ribozymes

13.3K
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can...
13.3K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

7.1K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.1K
Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

16.6K
The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
16.6K
Rab Proteins01:14

Rab Proteins

4.9K
Rab proteins constitute the largest family of monomeric GTPases, of which 70 members are present in humans. Rab proteins and their effectors regulate consecutive stages of vesicle transport such as vesicle transport, docking, and fusion to the correct recipient membrane.
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
4.9K

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相关实验视频

Updated: Jan 11, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

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基于结构的RiPP识别元素的发现和定义.

Miriam H Bregman1, Dillon P Cogan2, Kyle E Shelton1

  • 1Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

mSystems
|November 18, 2025
PubMed
概括

这项研究通过将基于结构的搜索与AlphaFold预测相结合来增强RiPP发现,识别了9万多个RiPP识别元素 (RRE) 和13个识别动机. 这提高了基因组挖掘的准确性,并扩大了对隐藏的RiPP生物合成途径的访问.

关键词:
这就是RiPPs.基因组采矿是如何进行的分子识别分子识别自然产品是自然产品的产品.蛋白质:相互作用核糖体酸是一种体.

更多相关视频

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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相关实验视频

Last Updated: Jan 11, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
13:34

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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科学领域:

  • 自然产品的发现自然产品的发现.
  • 生物信息学是一种生物信息学.
  • 结构生物学是结构生物学.
  • 基因组学就是基因组学.

背景情况:

  • 核糖体合成和翻译后改性 (RiPPs) 是各种自然产物,在各种生物过程中至关重要.
  • RiPP识别元素 (RRE) 是RiPP生物合成和基因组挖掘所必需的关键结域.
  • 现有的RRE-Finder工具面临的局限性是由于高假阳性率和难以识别序列分离的RRE.

研究的目的:

  • 通过加强RRE识别来提高RiPP基因组挖掘的准确性和范围.
  • 利用基于结构的搜索 (Foldseek) 和AlphaFold预测来发现序列分离的RRE及其相关的前体.
  • 完善生物信息工具,以便更全面地识别依赖RRE的生物合成途径.

主要方法:

  • Employed Foldseek用于对AlphaFold数据库进行基于结构的搜索,以识别不同的RRE.
  • 开发了11个新的Foldseek衍生的隐藏马尔科夫模型 (HMM),并为RRE-Finder改进了现有的模型.
  • 利用AlphaFold 3来预测RRE-复合体,使识别序列的映射成为可能.

主要成果:

  • 更新的工作流确定了超过9万个高可信度RRE,与原始模型相比,UniProt的检索率几乎翻了一番.
  • 发现了新的RRE域融合和5000个以前未知的RRE域,保留了正规折叠,但提供了新的生物信息处理.
  • 通过预测RRE-前体相互作用,在RiPP类中映射出13个不同的识别序列动图.

结论:

  • 基于结构的搜索和高级建模的整合显著提高了RiPP基因组挖掘的准确性和效率.
  • 这种改进的方法扩大了已知依赖RRE的生物合成途径的范围,提供了以前隐藏的自然产品.
  • 这些发现简化了RiPP前体及其相关RRE的识别,促进了对RiPP多样性和功能的进一步研究.