Search publications
6 results for “eCLIP-seq”
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The YTHDF proteins modulate Alzheimer's disease-associated brain gene signatures.
Molecular neurodegeneration · 2026 · 21(1)
Gene signatures of Alzheimer's disease (AD) brains reflect the output of a complex interplay of genetic, epigenetic, epi-transcriptomic, and post-transcriptional regulations. To nominate candidate factors modulating these signatures, we developed a machine learning model to integrate cellular and molecular features …
PMID 42811341 DOI ↗
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Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.
bioRxiv : the preprint server for biology · 2025
The <i>AUTS2</i> gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2's chromatin-and RNA-related functions are recognized, its direct binding to RNA in human neural progenitors has not been …
PMID 41278797 DOI ↗
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Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery.
Nucleic acids research · 2023 · 51(19): 10768-10781
Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). …
PMID 37739431 DOI ↗
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Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.
Nucleic acids research · 2023 · 51(12): 6461-6478
In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome …
PMID 37224531 DOI ↗
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …
PMID 32848060 DOI ↗
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Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Nature communications · 2019 · 10(1): 1338
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 …
PMID 30902979 DOI ↗
Datasets 25+
The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
6239 · GPL13657
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
Homo sapiens · GPL24676
SerRS mediates translational readthrough of through engagement of the selenocysteine incorporation machinery
Homo sapiens · GPL30173
Enhanced CLIP (eCLIP) identified differential UPF1 binding sites in mouse neural progenitor cells (NPCs) samples
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]
Mus musculus · GPL24676
Mitochondrial double-stranded RNA triggers chronic stress in aged neurons
Homo sapiens · GPL24676, GPL30173
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]
Homo sapiens · GPL16791
Mapping cell structure across scales by fusing protein images and interactions
Homo sapiens · GPL20301
RBM17 Mediates Evasion of Pro-Leukemic Factors from Splicing-coupled NMD to Enforce Leukemic Stem Cell Maintenance
Homo sapiens · GPL20301
Global Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Homo sapiens · GPL18573
SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.
Homo sapiens · GPL20301
LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function
Homo sapiens · GPL20301
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]
Homo sapiens · GPL16791
Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9
Homo sapiens · GPL18573
Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [miR130aKD_Kasumi]
Homo sapiens · GPL16791
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]
Homo sapiens · GPL24676
Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor mutant neoplasms
Homo sapiens · GPL20301
The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]
Homo sapiens · GPL20301
Widespread RNA editing dysregulation in Autism Spectrum Disorders [eCLIP-seq]
Homo sapiens · GPL20301
Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [RNA-Seq]
Homo sapiens · GPL11154
The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism
Thermus thermophilus HB27 · GPL27012
Best practices for eCLIP experiments and analysis [poor quality]
Homo sapiens · GPL20301
Showing first 25 dataset results.
Analyses 7
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE232597 · 5 steps · RIP-Seq · code_examples
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
GSE240521 · 9 steps · RIP-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE180686 · 20 steps · RIP-Seq · code_examples
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. (2022)
GSE107895 · 32 steps · RIP-Seq · code_examples
Widespread RNA editing dysregulation in brains from autistic individuals. (2019)
GSE125809 · 6 steps · RIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE78507 · 33 steps · OTHER · code_examples
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. (2016)