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相关概念视频

Riboswitches01:56

Riboswitches

8.0K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.0K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
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...
3.5K
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

1
Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
1
Types of RNA01:23

Types of RNA

63.2K
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
63.2K
Leaky Scanning02:28

Leaky Scanning

5.1K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.1K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.5K
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,...
10.5K

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相关实验视频

Updated: Jun 5, 2025

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells
07:19

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

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在Homo SapiensmRNA 5'UTR序列中识别潜在的 рибо开关元素,使用正无标记机器学习.

William S Raymond1, Jacob DeRoo1, Brian Munsky1,2

  • 1School of Biomedical Engineering, Colorado State University Fort Collins, CO 80523, USA.

bioRxiv : the preprint server for biology
|December 16, 2024
PubMed
概括

研究人员使用机器学习来识别人类mRNA中的潜在核糖突变. 这项研究提供了5'未翻译区域 (5'UTR) 的数据库,以指导未来人类核糖突变的实验发现.

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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相关实验视频

Last Updated: Jun 5, 2025

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells
07:19

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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科学领域:

  • *RNA生物学 *RNA生物学
  • * 计算生物学 * 计算生物学
  • * 基因组学 是一个学科.

背景情况:

  • * рибо开关是常见于原核生物,真菌,植物和酵母中的调节性RNA分子,但尚未在人类中发现.
  • *最近的发现表明,人类转基因组中的类似于核糖突变器的机制引发了关于Homo sapiens中小分子依赖核糖突变器的问题.

研究的目的:

  • *以计算方式识别人类mRNA5'未翻译区域 (5'UTRs) 中潜在的小分子依赖的核糖开关.
  • * 开发和应用机器学习分类器来选人类5'UTR的大型数据集,以寻找riboswitch元素.

主要方法:

  • *对来自RNAcentral (67,683个示例) 的已知 рибо开关序列和来自UTRdb (48,031个示例) 的人类5'UTR进行了训练,对20个未标记的正机器学习分类器进行了训练.
  • * 使用序列和二次结构特征,使用交叉验证进行准确性评估 (75%-99%).
  • *分析并根据分类器协议和与已知 рибо开关的相似性对已识别的5'UTR进行排名.

主要成果:

  • *通过至少一个分类器,确定了15333个人类5'UTR作为潜在的 рибо交换机.
  • * 发现436个5'UTR被所有20个分类器一致标记为潜在的 рибо开关.
  • *将这些436个序列映射到类似的已知核糖突变器中,并将结果编译成在线数据库.

结论:

  • *这项研究提出了一种计算方法,用于在人类基因组中发现新的核突变开关.
  • * 为促进实验验证,提供了一个对潜在的人类核链开关的精心策划的数据库.
  • * 这项工作显著推进了在Homo sapiens中寻找功能性核突开关的研究.