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Related Concept Videos

Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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.
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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,...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Related Experiment Video

Updated: Jun 29, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

MODOMICS: a database of RNA modification pathways. 2008 update.

Anna Czerwoniec1, Stanislaw Dunin-Horkawicz, Elzbieta Purta

  • 1Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.

Nucleic Acids Research
|October 16, 2008
PubMed
Summary

The MODOMICS database now offers enhanced systems biology insights into RNA modifications. It includes expanded RNA sequence data, new modifying enzymes, and improved search functionalities for RNA research.

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Last Updated: Jun 29, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis
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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing

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Area of Science:

  • Systems biology
  • Molecular biology
  • Bioinformatics

Background:

  • RNA modifications are crucial for cellular function and gene regulation.
  • Databases are essential for organizing and accessing complex biological information.
  • The MODOMICS database previously provided curated data on RNA modifications.

Purpose of the Study:

  • To substantially improve and expand the MODOMICS database.
  • To enhance its utility for systems biology research on RNA modification.
  • To provide comprehensive and updated information on modified nucleosides, enzymes, and RNA sequences.

Main Methods:

  • Curating and integrating data on modified nucleosides, biosynthesis pathways, RNA sequences, and modifying enzymes.
  • Expanding the database to include additional tRNAs, rRNAs, and RNAs with known 3D structures.
  • Annotating a large number of modified bases across various organisms.
  • Incorporating homology models for RNA-modifying enzymes where structures are known.
  • Developing new search and query options.

Main Results:

  • MODOMICS now provides comprehensive information on chemical structures, biosynthesis pathways, RNA sequences with modifications, and RNA-modifying enzymes.
  • The database includes 3460 annotated modified bases in RNA sequences from diverse organisms.
  • Additional tRNAs, rRNAs, and 3D-structured RNAs containing modified nucleosides have been incorporated.
  • New RNA-modifying enzymes have been added, with homology models for uncharacterized proteins.
  • Enhanced search and querying functionalities are now available.

Conclusions:

  • The improved MODOMICS database serves as a valuable resource for systems biology research on RNA modifications.
  • It offers a centralized and expanded platform for exploring RNA modification data.
  • The database facilitates deeper understanding of the roles and mechanisms of RNA modifications across different species.