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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Termination of Translation01:44

Termination of Translation

The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Feature-based 3D motif filtering for ribosomal RNA.

Ying Shen1, Hau-San Wong, Shaohong Zhang

  • 1Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.

Bioinformatics (Oxford, England)
|August 30, 2011
PubMed
Summary

Feature-based RNA Motif Filtering (FRMF) identifies RNA 3D motifs using moment invariants and Earth Mover's Distance. This method successfully detects known motifs and discovers new ones, enhancing RNA structure analysis.

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Area of Science:

  • Structural Biology
  • Bioinformatics

Background:

  • RNA 3D motifs are crucial substructures for RNA architecture, protein binding, and tertiary structure stabilization.
  • RNA 3D motif searching involves candidate generation and filtering.

Purpose of the Study:

  • To introduce a novel method, Feature-based RNA Motif Filtering (FRMF), for efficient and accurate RNA 3D motif identification.
  • To validate the FRMF method using a compiled set of RNA motifs.

Main Methods:

  • The FRMF method utilizes moment invariants and Earth Mover's Distance for candidate filtering in RNA motif searching.
  • A positive set of RNA motifs, including six characteristic types and eight subtypes from HM 50S, was compiled for validation.

Main Results:

  • FRMF successfully identified most of the positive RNA motif fragments in the validation set.
  • The study recognized novel motifs, including a π-turn and non-standard A-minor motifs.
  • The newly discovered motifs offer additional insights into RNA structure conformation.

Conclusions:

  • The FRMF method provides an effective approach for RNA 3D motif identification.
  • The compiled dataset and newly identified motifs contribute valuable information to the field of RNA structure research.