Coupling genetics and post-genomic approaches to decipher the cellular splicing code at a systems-wide level

2010 ◽  
Vol 38 (1) ◽  
pp. 237-241 ◽  
Author(s):  
Yilei Liu ◽  
David J. Elliott
Keyword(s):  
Rna Processing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Eukaryotic Gene Expression ◽  
Nuclear Rna ◽  
Processing Pathways ◽  
Eukaryotic Gene ◽  
Alternatively Spliced ◽  
Nuclear Rna Processing

Nuclear RNA processing is a critical stage in eukaryotic gene expression, and is controlled in part by the expression and concentration of nuclear RNA-binding proteins. Different nuclear RNA-binding proteins are differentially expressed in different cells, helping the spliceosome to decode pre-mRNAs into alternatively spliced mRNAs. Recent post-genomic technology has exposed the complexity of nuclear RNA processing, and is starting to reveal the mechanisms and rules through which networks of RNA-binding proteins can regulate multiple parallel pathways. Identification of multiple parallel processing pathways regulated by nuclear RNA-binding proteins is leading to a systems-wide understanding of the rules and consequences of alternative nuclear RNA processing.

RNA-Binding Proteins Required for Chloroplast RNA Processing

2010 ◽  
pp. 177-203 ◽  
Author(s):  
Reimo Zoschke ◽  
Christiane Kupsch ◽  
Christian Schmitz-Linneweber
Keyword(s):  
Rna Processing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Chloroplast Rna

scholarly journals RNA-Binding Proteins in Amyotrophic Lateral Sclerosis and Neurodegeneration

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Scott E. Ugras ◽  
James Shorter
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Neurodegenerative Disease ◽  
Rna Processing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Future Studies ◽  
Inclusion Formation ◽  
Als Patients ◽  
Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is an adult onset neurodegenerative disease, which is universally fatal. While the causes of this devastating disease are poorly understood, recent advances have implicated RNA-binding proteins (RBPs) that contain predicted prion domains as a major culprit. Specifically, mutations in the RBPs TDP-43 and FUS can cause ALS. Cytoplasmic mislocalization and inclusion formation are common pathological features of TDP-43 and FUS proteinopathies. Though these RBPs share striking pathological and structural similarities, considerable evidence suggests that the ALS-linked mutations in TDP-43 and FUS can cause disease by disparate mechanisms. In a recent study, Couthouis et al. screened for protein candidates that were also involved in RNA processing, contained a predicted prion domain, shared other phenotypic similarities with TDP-43 and FUS, and identified TAF15 as a putative ALS gene. Subsequent sequencing of ALS patients successfully identified ALS-linked mutations in TAF15 that were largely absent in control populations. This study underscores the important role that perturbations in RNA metabolism might play in neurodegeneration, and it raises the possibility that future studies will identify other RBPs with critical roles in neurodegenerative disease.

scholarly journals Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1

2020 ◽  
Vol 21 (3) ◽  
pp. 1166 ◽  
Author(s):  
Marian Scherer ◽  
Michal Levin ◽  
Falk Butter ◽  
Marion Scheibe
Keyword(s):  
Quantitative Proteomics ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Full Length ◽  
Interacting Proteins ◽  
Non Coding Rna ◽  
Nuclear Rna ◽  
Long Non Coding Rna ◽  
Shed Light

The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.

scholarly journals Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Eric L. Van Nostrand ◽  
Gabriel A. Pratt ◽  
Brian A. Yee ◽  
Emily C. Wheeler ◽  
Steven M. Blue ◽  
...  
Keyword(s):  
Rna Processing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins

The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved

Gene ◽  
1990 ◽  
Vol 90 (2) ◽  
pp. 299-302 ◽  
Author(s):  
Carol S. Surowy ◽  
George Hoganson ◽  
John Gosink ◽  
Kathleen Strunk ◽  
Richard A. Spritz
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Nuclear Rna

scholarly journals Scaffold proteins ITSN1 and ITSN2 interact with nuclear RNA-binding proteins

2019 ◽  
Vol 35 (2) ◽  
pp. 81-90 ◽  
Author(s):  
S. V. Pankivskyi ◽  
N. V. Senchenko ◽  
P. B. Busko ◽  
A. V. Rynditch
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Scaffold Proteins ◽  
Nuclear Rna

scholarly journals Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Laura Arribas-Hernández ◽  
Sarah Rennie ◽  
Tino Köster ◽  
Carlotta Porcelli ◽  
Martin Lewinski ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Activity ◽  
Sequence Motifs ◽  
Intrinsically Disordered ◽  
Eukaryotic Gene ◽  
Yth Domain ◽  
Nucleotide Resolution ◽  
Mrna Targeting

Specific recognition of N6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH-domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A binding activity. Here, we apply iCLIP (individual-nucleotide resolution cross-linking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2, and analyze the patterns of enriched sequence motifs around ECT2 crosslink sites. Our analyses show that ECT2 does in fact bind to RR(m6A)CH. Pyrimidine-rich motifs are enriched around, but not at m6A-sites, reflecting a preference for N6-adenosine methylation of RRACH/GGAU islands in pyrimidine-rich regions. Such motifs, particularly oligo-U and UNUNU upstream of m6A sites, are also implicated in ECT2 binding via its intrinsically disordered region (IDR). Finally, URUAY-type motifs are enriched at ECT2 crosslink sites, but their distinct properties suggest function as sites of competition between binding of ECT2 and as yet unidentified RNA-binding proteins. Our study provides coherence between genetic and molecular studies of m6A-YTH function in plants, and reveals new insight into the mode of RNA recognition by YTH-domain-containing proteins.

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