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N -Methyladenosine, an abundant chemical modification in mRNA, plays crucial roles in regulating gene expression and biological processes. Research on mA and its functions has progressed rapidly in the past few years, aided substantially by advances in high-throughput sequencing-based methods to profile mA along the transcriptome. We present here a protocol for mA crosslinking immunoprecipitation sequencing (mA-CLIP-seq), which profiles mA on mRNA at high resolution from as little as 1 μg of poly(A)-selected mRNA.
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http://dx.doi.org/10.1007/978-1-4939-8808-2_5 | DOI Listing |
Am J Hum Genet
September 2025
Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, Rotterdam 3000 CA, the Netherlands.
Microtubule-actin cross-linking factor 1 (MACF1) is a large protein of the spectraplakin family, which is essential for brain development. MACF1 interacts with microtubules through the growth arrest-specific 2 (Gas2)-related (GAR) domain. Heterozygous MACF1 missense variants affecting the zinc-binding residues in this domain result in a distinctive cortical and brain stem malformation.
View Article and Find Full Text PDFMol Cell Proteomics
September 2025
Institute of Biotechnology, HiLIFE, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Electronic address:
Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based approaches, including cross-linking MS (XL-MS), hydrogen-deuterium exchange MS (HDX-MS), and limited proteolysis MS (LiP-MS), now enable unprecedented insights into protein topology, conformational dynamics, and protein-protein interactions. These methods, complemented by affinity purification (AP), co-immunoprecipitation (co-IP), proximity labeling (PL), and spatial proteomics techniques, have expanded our ability to characterize the structural proteome at a systems-wide scale.
View Article and Find Full Text PDFNeurosci Bull
September 2025
State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by neurotoxic amyloid beta (Aβ) deposition in the brain. Neurons can internalize and exocytose Aβ; however, the molecular pathways governing Aβ release remain poorly understood. To identify key regulators of Aβ42 transport, we applied formaldehyde cross-linking of protein complexes combined with co-immunoprecipitation and mass spectrometry analysis to identify TMED10 as a novel Aβ42-interacting protein.
View Article and Find Full Text PDFRNA
September 2025
Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy;
Heat shock proteins have been increasingly identified in RNA-interactomes, suggesting potential roles beyond their canonical functions. Among those, the cancer-linked chaperone TRAP1 has been mainly characterized for its regulatory role on respiratory complex activity and protein synthesis, while its specific function as an RNA-binding protein (RBP) remains unclear. In this study, we confirmed the RNA-binding activity of TRAP1 in living cells using both protein- and RNA-centric approaches and demonstrated that multiple TRAP1 regions cooperate in such binding.
View Article and Find Full Text PDFbioRxiv
August 2025
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies.
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