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Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop CR-mediated inkage of barcoded dapters o nucleic acid lements for uencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.
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http://dx.doi.org/10.1073/pnas.1918068117 | DOI Listing |
ESC Heart Fail
September 2025
Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', Naples, Italy.
Aims: The current therapeutic approach to ischaemic (IsHF) and non-ischaemic (NIsHF) heart failure (HF) mainly overlooks the underlying aetiology owing to a lack knowledge of the differential molecular pathways that contribute to HF with reduced ejection fraction (HFrEF). Alterations in myocardial DNA methylation levels have been identified as potential biomarkers for HF irrespective of its aetiology. Due to the limited availability of cardiac tissues in clinics, our goal is to determine if DNA methylation changes in circulating CD4 T lymphocytes, which are strongly involved in left ventricle remodelling, can help in differentiating IsHF and NIsHF causes among patients with HFrEF and if DNA methylation levels associate with key clinical features.
View Article and Find Full Text PDFOsteoarthritis Cartilage
August 2025
Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA; Institute for Biomechanics, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI, USA; Departmen
Objective: Chronic synovitis is associated with osteoarthritis (OA) pain, but the molecular underpinnings remain unclear. Our objective was to characterize the transcriptional phenotype of OA synovium with a focus on signaling relevant to pain.
Design: Eight publicly-available microarray and RNA-sequencing GEO datasets from human non-OA and OA subjects underwent quality control and re-analysis for differentially-expressed genes (DEGs).
Protein J
August 2025
Yenepoya University, Mangalore, India.
Ataxin-2 (ATXN2), a key RNA-binding protein, regulates RNA metabolism, stress granule formation, and neuronal homeostasis, with dysregulated phosphorylation contributing to Spinocerebellar Ataxia type 2 (SCA2), amyotrophic lateral sclerosis (ALS), and cancer. This review integrates structural biology, phosphoproteomics, and interactome analyses to map six critical phosphosites (S772, T741, S624, S684, S784, S889) within ATXN2's intrinsically disordered regions. Modulated by kinases GSK3β and CDK13 and phosphatases like INPP5F, these sites orchestrate interactions with RNA-binding partners (e.
View Article and Find Full Text PDFMol Cancer Res
August 2025
University of Puerto Rico Comprehensive Cancer Center, San Juan, PR, United States.
FOXA1 is a pioneer transcription factor essential for chromatin accessibility and transcriptional regulation in hormone-driven cancers. In breast cancer, FOXA1 plays a central role in facilitating nuclear receptor binding, reprogramming enhancer landscapes, and promoting transcriptional changes associated with therapy resistance. While FOXA1's function has been primarily studied in the context of estrogen receptor-α (ER), its broader protein interaction network remains incompletely defined.
View Article and Find Full Text PDFmBio
August 2025
Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA.
, a widespread human parasite, persists in hosts through complex molecular interactions. Protein-protein interactions (PPIs) underpin essential biological processes, including parasite-host interactions and cellular invasion. Herein, we utilized advanced crosslinking mass spectrometry (XL-MS) techniques to map a tachyzoite cytosolic extract interactome.
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