Related Experiment Video
Updated: Dec 31, 2025
10:34
Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture
Published on: July 22, 2016
24.3K
Human protein-RNA interaction network is highly stable across mammals
Aarthi Ramakrishnan1, Sarath Chandra Janga2,3,4
1Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, 46202, USA.
BMC Genomics
|January 1, 2020
Summary
RNA-binding protein (RBP) binding sites are highly conserved across primates, with conserved RBP-RNA interactions suggesting importance in vertebrate evolution. RBP expression and target number influence binding site conservation, particularly in 3' gene regions.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- RNA-binding proteins (RBPs) regulate RNA metabolism and RBP-RNA interactions in eukaryotes.
- Previous studies on RBP target conservation focused on lower eukaryotes, leaving mammalian conservation less understood.
Purpose of the Study:
- To investigate the conservation of RNA-binding protein (RBP) binding sites across mammalian species.
- To identify factors influencing the conservation patterns of RBP binding sites.
Main Methods:
- Utilized CLIP-seq datasets for 60 human RBPs.
- Performed comparative analysis of RBP binding site conservation across vertebrate species.
- Conducted multivariate analysis to identify contributing factors to conservation differences.
- Examined binding site locations at the gene level (e.g., 3' regions).
- Performed gene set enrichment analysis for phenotype associations.
Main Results:
- Most binding sites for a third of studied RBPs are conserved in at least 50% of vertebrate species.
- RBP binding sites show median conservation of 58%, significantly higher than random genomic locations.
- Binding sites are highly conserved in primates, with weaker conservation in birds and fishes.
- RBP expression level and number of post-transcriptional targets are key factors in conservation extent.
- Binding sites in 3' gene regions are highly conserved (90% of RBPs show higher conservation here than in 5' regions).
- Enrichment for developmental abnormalities was found when analyzing conserved binding sites.
Conclusions:
- Human RBP binding sites are highly conserved in primates, with weaker conservation in lower vertebrates.
- Phylogenetic relationships do not explain RBP binding site conservation patterns.
- RBP expression and target number significantly impact binding site conservation.
- 3' gene regions represent the most conserved locations for RBP binding sites.
- Conserved binding sites highlight the role of developmental events in post-transcriptional regulatory network evolution.
Related Concept Videos
01:53RNA Stability
35.5K
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...
35.5K
02:28Leaky Scanning
5.6K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.6K
02:51mRNA Stability and Gene Expression
3.3K
3.3K
02:51mRNA Stability and Gene Expression
6.4K
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
Cis-acting Elements involved in mRNA stability
6.4K
02:51Multi-species Conserved Sequences
4.6K
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...
4.6K
02:26Protein Networks
4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K