Resolving RNA complexity to decipher regulatory rules governing biological networks

By Donny D. Licatalosi, R. Darnell. Nature reviews genetics, 2010

705 citations recorded by the source corpus.

In recent years views of eukaryotic gene expression have been transformed by the finding that enormous diversity can be generated at the RNA level. Advances in technologies for characterizing RNA populations are revealing increasingly complete descriptions of RNA regulation and complexity; for example, through alternative splicing, alternative polyadenylation and RNA editing. New biochemical strategies to map protein–RNA interactions in vivo are yielding transcriptome-wide insights into mechanisms of RNA processing. These advances, combined with bioinformatics and genetic validation, are leading to the generation of functional RNA maps that reveal the rules underlying RNA regulation and networks of biologically coherent transcripts. Together these are providing new insights into molecular cell biology and disease.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/03784afedefa99507249d32c42ffafc61ce74032

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

MicroRNA regulation by RNA-binding proteins and its implications for cancer (2011, background): “Novel high-throughput techniques to measure RNA–RNA and RNA–protein interactions (reviewed in Ref”
Mechanisms and Regulation of Alternative Pre-mRNA Splicing (2015, background): “Average number of unique exons per gene (median) 33 (26) 22 (15) 7.”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, background): “In addition, we intend to integrate other CLIP-Seq data from other RNA binding proteins (51), such as PUM2 (22), Nova (52), FOX2 (53) and PTB (54), into starBase to improve our understanding of the eukaryotic regulatory networks.”
RBPDB: a database of RNA-binding specificities (2010, background): “RNA-binding proteins (RBPs) have a fundamental role in a wide variety of cellular processes including transcription, RNA splicing and processing, localization, stability and translation (1–6).”
Predicting RNA-Protein Interactions Using Only Sequence Information (2011, background): “Regulation of gene expression at the post-transcriptional level is often mediated by interactions between RNA binding proteins and mRNAs or ncRNAs [5,11,40].”
Anti-apoptosis and cell survival: a review. (2011, background): “This serves to indicate that the repertoire of pro- and anti-apoptotic proteins will also require a complex understanding of the entire transcriptome and proteome [332,333].”
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation (2010, background): “Alternative splicing (AS) of pre-mRNAs is a key step in the regulation and diversification of gene function (Blencowe, 2006; Hallegger et al., 2010; Licatalosi and Darnell, 2010).”
Functional consequences of developmentally regulated alternative splicing (2011, background): “Alternative splicing is the most prominent of several mechanisms generating mRNA structural complexity ; others include alternative transcription initiation, RNA editing and alternative poly(A) site selectio”
Revealing protein–lncRNA interaction (2015, neutral): “splicing, polyadenylation, transport, stability and translation [1–4].”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, methodology): “…(CLIP) (Wang et al., 2009b) and its variations, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) (Licatalosi and Darnell, 2010) and photoactivatable-ribonucleoside-enhanced CLIP (Hafner et al., 2010a) have been used to identify targets of RBPs…”
A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, background): “…type- and developmentally-regulated AS events are coordinately controlled by individual RBPs, and that these events are significantly enriched in genes that operate in common biological processes and pathways (Calarco et al., 2011; Irimia and Blencowe, 2012; Licatalosi and Darnell, 2010).”
Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA (2016, background): “Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 30-end cleavage and polyadenylation [1,2,3,4].”