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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...
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.
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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
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...
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,...

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The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis.

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Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis
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Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis

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MODOMICS: a database of RNA modification pathways--2013 update.

Magdalena A Machnicka1, Kaja Milanowska, Okan Osman Oglou

  • 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.

Nucleic Acids Research
|November 3, 2012
PubMed
Summary
This summary is machine-generated.

The MODOMICS database now offers enhanced features for RNA modifications, including human and yeast snoRNAs, 5'-end capping, and chemical synthesis building blocks. This update expands information on modified ribonucleosides and RNA-modifying enzymes for better research accessibility.

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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing
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2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing
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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA modifications are crucial for diverse cellular functions.
  • Databases cataloging these modifications are essential for research.
  • Previous versions of MODOMICS provided foundational data on RNA modifications.

Purpose of the Study:

  • To update and expand the MODOMICS database with new features and data.
  • To enhance the accessibility and utility of RNA modification information for researchers.
  • To incorporate new findings in RNA modification, enzymes, and sequences.

Main Methods:

  • Database curation and integration of new data on RNA modifications.
  • Inclusion of human and yeast small nucleolar RNAs (snoRNAs) involved in RNA-guided modification.
  • Addition of a section on the 5 -end capping process and chemical synthesis building blocks.

Main Results:

  • The updated MODOMICS database includes newly identified modified ribonucleosides and over 100 characterized proteins.
  • Expanded collections of rRNA, tRNA, snRNA, and snoRNA sequences with mapped modifications.
  • New search functionalities, including BLAST for protein sequences and PARALIGN for nucleic acid sequences, have been implemented.

Conclusions:

  • The enhanced MODOMICS database serves as a comprehensive resource for RNA modification research.
  • New features facilitate the study of RNA-guided modifications, capping, and chemical synthesis.
  • Improved search capabilities enhance literature discovery and data retrieval for RNA modification studies.