Chapter 16
Biolayer Interferometry: Protein–RNA Interactions
Stephen R. Martin, Andres Ramos, and Laura Masino
Abstract
RNA-binding proteins often contain multiple RNA-binding domains connected by short flexible linkers.
This domain arrangement allows the protein to bind the RNA with greater affinity and specificity than
would be possible with individual domains and sometimes to remodel its structure. It is therefore important
to understand how multiple modules interact with RNA because it is the modular nature of these proteins
which specifies their biological function. This chapter is concerned with the use of biolayer interferometry
to study protein–RNA interactions.
Key words Biolayer interferometry, RNA, Kinetics
1 Introduction
1.1 Protein–RNA
Interactions
Posttranscriptional gene regulation consists of a ubiquitous and
essential network of protein–RNA-based cellular processes that
expands genomic diversity, and it is essential in the development
and function of complex organisms. Not surprisingly, misfunction
of the different RNA regulation steps has been associated with a
range of pathologies, including different cancers, neurodevelopmental and neurodegenerative diseases, immunopathologies, and
viral infection [1, 2].
RNA regulation is mediated by between 1000 and 2000
RNA-binding proteins, a few hundred of which have been validated
functionally [3]. In contrast, a human cell typically contains 10 to
20,000 different mRNAs [4], each binding many different
RNA-binding proteins. Most RNA-binding proteins recognize
large and diverse sets of RNA targets, including both mRNAs and
noncoding RNAs. An accurate recognition of these targets is essential not only to define the set of genes regulated by a protein but
also to define gene expression programs in different cellular locations at specific times [1, 2]. Understanding, at a mechanistic level,
how RNA-binding proteins recognize the RNA targets is one of the
main challenges in gene regulation.
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5_16, © Springer Science+Business Media, LLC, part of Springer Nature 2021
351
Biolayer Interferometry: Protein–RNA Interactions
Stephen R. Martin, Andres Ramos, and Laura Masino
Abstract
RNA-binding proteins often contain multiple RNA-binding domains connected by short flexible linkers.
This domain arrangement allows the protein to bind the RNA with greater affinity and specificity than
would be possible with individual domains and sometimes to remodel its structure. It is therefore important
to understand how multiple modules interact with RNA because it is the modular nature of these proteins
which specifies their biological function. This chapter is concerned with the use of biolayer interferometry
to study protein–RNA interactions.
Key words Biolayer interferometry, RNA, Kinetics
1 Introduction
1.1 Protein–RNA
Interactions
Posttranscriptional gene regulation consists of a ubiquitous and
essential network of protein–RNA-based cellular processes that
expands genomic diversity, and it is essential in the development
and function of complex organisms. Not surprisingly, misfunction
of the different RNA regulation steps has been associated with a
range of pathologies, including different cancers, neurodevelopmental and neurodegenerative diseases, immunopathologies, and
viral infection [1, 2].
RNA regulation is mediated by between 1000 and 2000
RNA-binding proteins, a few hundred of which have been validated
functionally [3]. In contrast, a human cell typically contains 10 to
20,000 different mRNAs [4], each binding many different
RNA-binding proteins. Most RNA-binding proteins recognize
large and diverse sets of RNA targets, including both mRNAs and
noncoding RNAs. An accurate recognition of these targets is essential not only to define the set of genes regulated by a protein but
also to define gene expression programs in different cellular locations at specific times [1, 2]. Understanding, at a mechanistic level,
how RNA-binding proteins recognize the RNA targets is one of the
main challenges in gene regulation.
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5_16, © Springer Science+Business Media, LLC, part of Springer Nature 2021
351