RNA-binding proteins: modular design for efficient function

By B. M. Lunde, C. Moore, Gabriele Varani. Nature reviews. Molecular cell biology, 2007

1,302 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6bbf36d4374a33e7dff2e998181815f386b5b325

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Citations in the corpus

Transcription factors interact with RNA to regulate genes (2022, background): “TFs do not contain sequence motifs that resemble those of structured RNA-binding domains (Corley et al., 2020; Lunde et al., 2007) (Figure S3), so we searched for local amino acid features that might be common to TFs.”
Comprehensive Identification of RNA-Binding Domains in Human Cells (2016, background): “To evaluate the capacity of RBDmap to identify bona fide RBDs, we focused on RBPs that harbor at least one classical RBD (as listed in Lunde et al., 2007).”
A census of human RNA-binding proteins (2014, background): “, 2007) zf-CCHC Zinc knuckle, C-x2-C-x4-H-x4-C, ssRNA-binding (Krishna et al., 2003; Lunde et al., 2007) zf-RanBP RNA-binding Ran-binding-protein-like zinc finger (Krishna et al.”
Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein (2013, background): “…containing an RRM have multiple copies of this domain (Maris et al. 2005; Clery et al. 2008), with the spatial arrangement of the domains, their sequence variation, and the presence of auxiliary domains dictating the affinity, specificity, and function of these proteins (Lunde et al. 2007).”
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “In addition to SR proteins, these include the heterogeneous ribonucleoprotein (hnRNP) family of proteins as well as RBPs containing RRM, K homology domain (KH), zinc-finger, or other domains (Lunde et al., 2007).”
N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein (2017, background): “This modular domain structure can contribute to RNA binding affinity or specificity, define the spacing between binding sites, organize RNA topology, or allow a single protein to simultaneously interact with multiple RNA molecules (51).”
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (2012, neutral): “…properties of these putative mRNAbindingWD domains differ fromWDdomains of proteins that are not present in the HeLa mRNA interactome, being enriched for most of the amino acids typically found at protein-RNA interfaces (especially basic amino acids) (Lunde et al., 2007) (Figure S5E).”
Learning the sequence determinants of alternative splicing from millions of random sequences. (2015, background): “Furthermore, most known RNA binding proteins (RBPs) are reported to bind sequences between 4–8 nt (Lunde et al., 2007).”
RNA-Binding Proteins in Cancer: Old Players and New Actors. (2017, background): “Many RBPs bind to sequence-specificmotifs or RNA secondary structures, or a combination of both, through unique modular arrangements of individual RNA-binding domains (RBDs, Figure 1) [8].”
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP (2010, background): “Several hundred RBPs are encoded in the human genome, many of them containing combinations of RNA-binding domains which are drawn from a relatively small repertoire, resulting in diverse structural arrangements and different specificities of target RNA recognition (Lunde et al., 2007).”
Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis (2019, background): “Some RBPs, such as TDP-43, are also implicated in neurodegenerative diseases which therefore hints of disturbances in the RNA metabolism as a causative factor (Maris et al., 2005; Lunde et al., 2007; Clery et al., 2008).”
Protein Phase Separation: A New Phase in Cell Biology (2018, background): “RNA-binding proteins (RBPs) are known to have a multivalent modular domain architecture [43], which seems to be a critical factor in phase separation (Box 2).”