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Related Concept Videos

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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

Updated: Oct 9, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Two novel RNA-binding proteins identification through computational prediction and experimental validation.

Juan Xie1, Xiaoli Zhang1, Jinfang Zheng1

  • 1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

Genomics
|December 18, 2021
PubMed
Summary

Researchers identified CLIP1 and DMD as RNA-binding proteins (RBPs) using iRIP-seq and CLIP-seq. Their RNA-binding motifs and potential links to muscular dystrophies and cancer were revealed.

Keywords:
CLIP-seqCLIP1CancerClinVarDMDRBPPredRNA-binding proteiniRIP-seq

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • RNA-binding proteins (RBPs) are crucial for cellular functions.
  • Identifying novel RBPs is essential for understanding gene regulation.
  • RBPPred software predicts potential RNA-binding proteins.

Purpose of the Study:

  • To experimentally validate CLIP1 and DMD as RNA-binding proteins (RBPs).
  • To identify RNA-binding motifs associated with CLIP1 and DMD.
  • To explore the functional and disease-related implications of CLIP1 and DMD.

Main Methods:

  • RNA immunoprecipitation followed by sequencing (iRIP-seq).
  • Crosslinking immunoprecipitation followed by sequencing (CLIP-seq).
  • Bioinformatic analyses including motif enrichment, KEGG, and Gene Ontology (GO) analysis.
  • Analysis of Single Nucleotide Polymorphisms (SNPs) and cancer genomic data.

Main Results:

  • CLIP1 and DMD were confirmed to possess RNA-binding activity.
  • Enriched RNA-binding motifs: UGGGGAGG for CLIP1 (iRIP-seq), CUUCCG and CCCGU for DMD (iRIP-seq and CLIP-seq, respectively).
  • CLIP1 and DMD share biological processes and functions.
  • SNPs in DMD and its RNA partners are potentially linked to muscular dystrophies and cardiovascular conditions.
  • CLIP1 co-occurs with 300 oncogenes in thirteen cancer datasets, with 123 interacting genes.

Conclusions:

  • CLIP1 and DMD are validated as RBPs with distinct binding motifs.
  • These RBPs are implicated in muscular dystrophies, cardiovascular diseases, and cancer.
  • Further research into CLIP1 and DMD interactions may reveal new therapeutic targets.