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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

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Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

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Published on: September 30, 2016

The YTH domain is a novel RNA binding domain.

Zhaiyi Zhang1, Dominik Theler, Katarzyna H Kaminska

  • 1Institute for Biochemistry, Universität Erlangen-Nuremberg, Fahrstrasse 17, 91054 Erlangen, Germany.

The Journal of Biological Chemistry
|February 20, 2010
PubMed
Summary

The YT521-B homology (YTH) domain is a novel RNA-binding domain found in eukaryotic proteins. It recognizes a specific RNA motif, influencing alternative splicing of vertebrate-specific exons.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • The YT521-B homology (YTH) domain is conserved across eukaryotes, present in 174 proteins.
  • This domain features 14 invariant residues within a characteristic alpha-helix/beta-sheet structure.

Purpose of the Study:

  • To identify the function of the YTH domain.
  • To characterize the RNA-binding properties and structural features of the YTH domain.
  • To investigate the role of YTH domain-containing proteins in gene regulation.

Main Methods:

  • Sequence comparison and structural analysis.
  • RNA binding assays, including NMR titration.
  • In vivo splice site selection assays and array analyses.

Main Results:

  • The YTH domain is a novel RNA-binding domain recognizing a specific single-stranded RNA motif.
  • YT521-B directly influences splice site selection of alternative exons containing this motif.
  • YT521-B primarily regulates vertebrate-specific exons.
  • Structural analysis reveals YTH domain similarity to the PUA domain.

Conclusions:

  • The YTH domain confers RNA-binding capability to a new class of eukaryotic proteins.
  • This domain plays a significant role in post-transcriptional gene regulation, particularly alternative splicing.