Related Experiment Video
Updated: Jun 17, 2025
12:29
mRNA Interactome Capture from Plant Protoplasts
Published on: July 28, 2017
9.1K
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites
Veerendra P Gadekar1,2,3,4, Alexander Welford Munk1,2, Milad Miladi5
1Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark.
NAR Genomics and Bioinformatics
|August 12, 2024
Summary
This study links conserved RNA structures in human untranslated regions (UTRs) to specific gene functions. Clustering these RNA structures reveals associations with RNA-binding proteins and biological processes like signal transduction.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- RNA secondary structures are crucial for tertiary structure and function.
- Genome-wide studies suggest significant roles for RNA structures in mammals.
- Assigning functional roles to structured RNAs remains a challenge.
Purpose of the Study:
- To associate conserved RNA structures (CRSs) in human untranslated regions (UTRs) with gene functions.
- To explore the functional potential of clustered CRSs using guilt-by-association analysis.
Main Methods:
- Computationally predicted conserved RNA structures (CRSs) were filtered for UTR overlap.
- CRSs were clustered using RNAscClust for 5' and 3' UTRs.
- Overrepresented RNA-binding protein sites and Gene Ontologies were identified in clustered CRSs.
Main Results:
- 4734 (5' UTR) and 24,754 (3' UTR) CRSs were identified and clustered into 793 and 2403 groups, respectively.
- Overrepresented binding sites for 60 (5' UTR) and 43 (3' UTR) RNA-binding proteins were found.
- 104 (5' UTR) and 441 (3' UTR) clusters showed enrichment for Gene Ontologies, including 'signal transduction' and 'synapse'.
Conclusions:
- Clustering conserved RNA structures provides significant functional insights.
- This approach links RNA structural characteristics to biological functions and protein interactions.
Related Concept Videos
01:19RNA Structure
4.7K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
4.7K
01:53RNA Stability
33.4K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.4K
02:13Cooperative Binding of Transcription Regulators
6.4K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.4K
01:49Conserved Binding Sites
4.2K
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...
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...
4.2K
02:51Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
02:26Conservation of Protein Domains Over Different Proteins
10.8K
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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K