scholarly journals Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

2016 ◽  
Vol 13 (6) ◽  
pp. 508-514 ◽  
Author(s):  
Eric L Van Nostrand ◽  
Gabriel A Pratt ◽  
Alexander A Shishkin ◽  
Chelsea Gelboin-Burkhart ◽  
Mark Y Fang ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Protein Binding Sites

scholarly journals Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

2011 ◽  
Vol 286 (43) ◽  
pp. 37063-37066 ◽  
Author(s):  
Philip J. Uren ◽  
Suzanne C. Burns ◽  
Jianhua Ruan ◽  
Kusum K. Singh ◽  
Andrew D. Smith ◽  
...  
Keyword(s):  
Complex Network ◽  
Binding Sites ◽  
Target Genes ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Genomic Analyses ◽  
Hu Antigen R

scholarly journals Investigating the Roles of RNA Binding Protein Combinations in Neuronal Function and Organismal Behavior

2019 ◽  
Vol 4 (Spring 2019) ◽  
Author(s):  
Alexa Vandenburg
Keyword(s):  
Binding Sites ◽  
Neuronal Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Wild Type ◽  
C Elegans ◽  
Neuronal Gene ◽  
Touch Response

The Norris lab recently identified two RNA binding proteins required for proper neuron-specific splicing. The lab conducted touch- response behavioral assays to assess the function of these proteins in touch-sensing neurons. After isolating C. elegans worms with specific phenotypes, the lab used automated computer tracking and video analysis to record the worms’ behavior. The behavior of mutant worms differed from that of wild-type worms. The Norris lab also discovered two possible RNA binding protein sites in SAD-1, a neuronal gene implicated in the neuronal development of C. elegans1. These two binding sites may control the splicing of SAD-1. The lab transferred mutated DNA into the genome of wild-type worms by injecting a mutated plasmid. The newly transformed worms fluoresced green, indicating that the two binding sites control SAD-1 splicing.

scholarly journals Synthetic 5′ UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding

Cell Systems ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 93-106.e8 ◽  
Author(s):  
Noa Katz ◽  
Roni Cohen ◽  
Oz Solomon ◽  
Beate Kaufmann ◽  
Orna Atar ◽  
...  
Keyword(s):  
Protein Binding ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals Helical Defects in MicroRNA Influence Protein Binding by TAR RNA Binding Protein

PLoS ONE ◽  
2015 ◽  
Vol 10 (1) ◽  
pp. e0116749 ◽  
Author(s):  
Roderico Acevedo ◽  
Nichole Orench-Rivera ◽  
Kaycee A. Quarles ◽  
Scott A. Showalter
Keyword(s):  
Protein Binding ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Tar Rna

scholarly journals HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif

Aging ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 2430-2446 ◽  
Author(s):  
Yingcheng Wu ◽  
Hao Chen ◽  
Yuyan Chen ◽  
Lishuai Qu ◽  
Erhao Zhang ◽  
...  
Keyword(s):  
Protein Binding ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Binding Motif

scholarly journals Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits and Diseases

2019 ◽  
Author(s):  
Lei Li ◽  
Yipeng Gao ◽  
Fanglue Peng ◽  
Eric J. Wagner ◽  
Wei Li
Keyword(s):  
Genetic Variants ◽  
Binding Sites ◽  
Genetic Basis ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Alternative Polyadenylation ◽  
Molecular Phenotype ◽  
Protein Binding Sites ◽  
Coding Variants

SUMMARYGenome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants remains a major challenge. Here, we describe the first atlas of human 3’-UTR alternative polyadenylation (APA) Quantitative Trait Loci (3’QTLs), i.e. ∼0.4 million genetic variants associated with APA of target genes across 46 Genotype-Tissue Expression (GTEx) tissues from 467 individuals. APA occurs in approximately 70% of human genes and substantively impacts cellular proliferation, differentiation and tumorigenesis. Mechanistically, 3’QTLs could alter polyA motifs and RNA-binding protein binding sites, leading to thousands of APA changes. Importantly, 3’QTLs can be used to interpret ∼16.1% of trait-associated variants and are largely distinct from other QTLs such as eQTLs. The genetic basis of APA (3’QTLs) thus represent a novel molecular phenotype to explain a large fraction of non-coding variants and to provide new insights into complex traits and disease etiologies.HighlightsThe first atlas of human 3’QTLs: ∼0.4 million genetic variants associated with alternative polyadenylation of target genes across 46 tissues from 467 individuals3’QTLs could alter polyA motifs and RNA-binding protein binding sites3’QTLs can be used to interpret ∼16.1% of trait-associated variantsMany disease-associated 3’QTLs contribute to phenotype independent of gene expression

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