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90 results for “RNA-Binding”
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Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.
Advances in experimental medicine and biology · 2016 · 907: 61-88
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …
PMID 27256382 DOI ↗
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RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology · 2016 · 23(12): 1101-1110
Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …
PMID 27775709 DOI ↗
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SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.
Molecular cell · 2016 · 64(2): 282-293
RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down …
PMID 27720645 DOI ↗
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Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.
Nature communications · 2016 · 7: 12143
The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs …
PMID 27378374 DOI ↗
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Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Nature methods · 2016 · 13(6): 508-14
As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically …
PMID 27018577 DOI ↗
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Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes.
Cell reports · 2016 · 15(10): 2200-2213
Alternative splicing (AS) defects that adversely affect gene expression and function have been identified in diabetic hearts; however, the mechanisms responsible are largely unknown. Here, we show that the RNA-binding protein RBFOX2 contributes to transcriptome changes under diabetic conditions. RBFOX2 …
PMID 27239029 DOI ↗
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Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.
Nature · 2016 · 532(7600): 508-511
Umbilical cord blood-derived haematopoietic stem cells (HSCs) are essential for many life-saving regenerative therapies. However, despite their advantages for transplantation, their clinical use is restricted because HSCs in cord blood are found only in small numbers. Small molecules that enhance …
PMID 27121842 DOI ↗
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Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Cell reports · 2016 · 15(3): 666-679
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad …
PMID 27068461 DOI ↗
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Applications of Cas9 as an RNA-programmed RNA-binding protein.
BioEssays : news and reviews in molecular, cellular and developmental biology · 2015 · 37(7): 732-9
The Streptococcus pyogenes CRISPR-Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can …
PMID 25880497 DOI ↗
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RNA-binding proteins in neurodegeneration: Seq and you shall receive.
Trends in neurosciences · 2015 · 38(4): 226-36
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, …
PMID 25765321 DOI ↗
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ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP.
Nature communications · 2015 · 6: 6171
The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS), is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their …
PMID 25625564 DOI ↗
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Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nature structural & molecular biology · 2013 · 20(12): 1434-42
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …
PMID 24213538 DOI ↗
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Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry · 2013 · 288(49): 35372-86
Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …
PMID 24151077 DOI ↗
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LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 DOI ↗
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Misregulated RNA processing in amyotrophic lateral sclerosis.
Brain research · 2012 · 1462: 3-15
Amyotrophic lateral sclerosis (ALS) research is undergoing an era of unprecedented discoveries with the identification of new genes as major genetic causes of this disease. These discoveries reinforce the genetic, clinical and pathological overlap between ALS and frontotemporal lobar degeneration …
PMID 22444279 DOI ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
RBP Footprint Grand Challenge: An evaluation of novel computational approaches to RNA-binding protein target prediction from structural data
Homo sapiens · GPL20301
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]
Homo sapiens · Illumina
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE)
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]
GPL20301, GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
GPL24676
An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia
Homo sapiens · GPL16791
Proteomic discovery of chemical probes that perturb protein complexes in human cells
Homo sapiens · GPL24676
Proteomic discovery of chemical probes that perturb protein complexes in human cells II
Homo sapiens · GPL18573
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Homo sapiens · GPL15520
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL24676
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
Showing first 25 dataset results.
Analyses 25+
GSE244832 · 9 steps · scRNA-seq · geo_data_processing
RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis. (2026)
GSE290248 · 1 step · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290281 · 1 step · eCLIP · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290282 · 3 steps · RNA-seq · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE299099 · 3 steps · RNA-Seq · code_examples
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)
GSE315347 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315406 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315407 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE145805 · 7 steps · SHAPE-seq · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE227455 · 7 steps · eCLIP · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE262542 · 4 steps · RNA-Seq · code_examples
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE104949 · 9 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE114820 · 4 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE143437 · 7 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE145480 · 11 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE147127 · 5 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE193134 · 18 steps · RIP-Seq · code_examples
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. (2024)
GSE210263 · 10 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE230717 · 9 steps · RIP-Seq · code_examples
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
GSE232597 · 5 steps · RIP-Seq · code_examples
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
GSE232598 · 6 steps · RNA-Seq · code_examples
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
GSE232599 · 5 steps · GSE · code_examples
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
GSE237099 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE243675 · 9 steps · RIP-Seq · code_examples
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. (2024)
GSE273092 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
Showing first 25 analysis results.