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A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …
Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …
Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …
RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced …
Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with …
Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause premature reverse transcription termination and deletions (referred to as crosslink-induced mutation …
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous …
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 …
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 …
Ythdf m6A readers compensate each other in a context dependent manner [eCLIP]
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor. (2025)
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. (2025)
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)
Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex. (2025)
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. (2024)
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. (2024)
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
ePRINT: exonuclease assisted mapping of protein-RNA interactions. (2024)
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)