Transcriptome-wide Binding Sites
Transcriptome-wide Binding Sites - Related Videos
12:24
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Cited by 267 •
2010
RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.
01:49
Conserved Binding Sites
0 Views •
2020
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...
01:49
Conserved Binding Sites
0 Views •
2023
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...
02:40
Ligand Binding Sites
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2020
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands. Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
02:40
Ligand Binding Sites
0 Views •
2023
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands. Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
FAQs
Crosslinking first creates recoverable protein-RNA complexes, allowing the selected interacting molecule and its associated RNA fragments to be handled together. After isolation, sequencing identifies the fragment sequences, and alignment to the transcriptome places them at particular transcript regions. Enrichment across those regions produces a map of interaction sites rather than merely a list of expressed RNAs.
The molecule chosen for isolation determines which RNA interactions the experiment recovers. Selecting a particular RNA-binding protein focuses the map on transcripts associated with that protein, whereas selecting a regulatory RNA focuses attention on its interacting transcript regions. This choice connects the resulting enrichment pattern to a specific post-transcriptional regulatory system.
Binding-site maps can connect molecular interactions with several post-transcriptional outcomes, including changes in splicing, mRNA stability, localization, and translation. Examining where interactions occur across transcripts helps researchers relate binding patterns to these regulatory processes. The approach therefore links the physical location of an interaction with potential consequences for gene-expression control.
A typical workflow crosslinks protein-RNA complexes, isolates a selected protein or RNA together with associated RNA fragments, and sequences those fragments. Researchers then locate the sequences within the transcriptome and identify regions showing enrichment. This progression converts molecular interaction material into a transcriptome-wide map that can be examined for regulatory elements.
Enriched transcript regions identify locations where the selected protein or regulatory RNA is represented among the recovered RNA fragments. Researchers can use these locations to identify regulatory elements and relate them to processes such as splicing, mRNA stability, localization, or translation. The map thus provides spatial information about interactions across many cellular RNA transcripts.
Transcriptome-wide binding-site analysis is useful when researchers need to connect RNA interactions with broader gene-expression regulation. In biology, it supports studies of development and disease mechanisms by showing where regulatory interactions occur across transcripts. The same information can also help identify interactions or regulatory elements that may be relevant to therapeutic targets.