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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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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.
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RNA-seq03:21

RNA-seq

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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. 
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RNA Stability01:53

RNA Stability

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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...
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RNA Structure01:23

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Leaky Scanning02:28

Leaky Scanning

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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...
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Related Experiment Video

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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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Live-Cell Covalent Profiling Reveals Principles of RNA-Small Molecule Recognition across the Human Transcriptome.

Yuquan Tong, Amirhossein Taghavi, Xiaoxuan Su

    Biorxiv : the Preprint Server for Biology
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    Researchers developed a live-cell method to map small molecules binding to RNA, identifying new targets and creating selective RNA degraders. This approach enables the rational design of RNA-targeted therapeutics for diseases like cancer.

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    iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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    iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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    Area of Science:

    • Chemical Biology
    • Molecular Biology
    • Genomics

    Background:

    • RNA molecules are abundant in cells but challenging to target with small molecules.
    • Understanding RNA-small molecule interactions is crucial for developing new therapeutics.

    Purpose of the Study:

    • To develop a live-cell pipeline for mapping small molecule-RNA interactions across the human transcriptome.
    • To convert identified RNA binders into selective RNA degraders.

    Main Methods:

    • A scalable, unbiased live-cell pipeline using fragment libraries and Chem-CLIP-Map-Seq.
    • Machine learning models to predict RNA binders based on molecular features.
    • Development of RiboTACs (RNA-targeted chimera) for selective RNA degradation.

    Main Results:

    • Identified 723 RNA targets and binding sites, with a bias towards 5' and 3' UTRs of mRNAs.
    • Developed a machine learning model to distinguish binders and identify favorable chemical features.
    • Created selective RiboTACs that degrade specific mRNAs (e.g., MPP7, SSC4D) and reduce protein levels, impacting cell migration.

    Conclusions:

    • Established practical principles for identifying ligandable RNA sites in cells.
    • Demonstrated a framework for the rational design of RNA-targeted small molecules and degraders.
    • Showcased the potential of selective RNA degradation for therapeutic applications, such as in breast cancer.