Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.

Autor: Street LA; Department of Biological Sciences, Columbia University, New York, NY, USA., Rothamel KL; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA., Brannan KW; Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA; Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA., Jin W; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Bokor BJ; Department of Biological Sciences, Columbia University, New York, NY, USA., Dong K; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Rhine K; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Madrigal A; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Al-Azzam N; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Kim JK; Department of Biological Sciences, Columbia University, New York, NY, USA., Ma Y; Department of Biological Sciences, Columbia University, New York, NY, USA., Gorhe D; Department of Biological Sciences, Columbia University, New York, NY, USA., Abdou A; Department of Biological Sciences, Columbia University, New York, NY, USA., Wolin E; Department of Biological Sciences, Columbia University, New York, NY, USA., Mizrahi O; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA., Ahdout J; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Mujumdar M; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Doron-Mandel E; Department of Biological Sciences, Columbia University, New York, NY, USA., Jovanovic M; Department of Biological Sciences, Columbia University, New York, NY, USA. Electronic address: mj2794@columbia.edu., Yeo GW; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA; Sanford Stem Cell Institute, Innovation Center, San Diego, CA, USA. Electronic address: geneyeo@ucsd.edu.

Publikováno v: Molecular cell [Mol Cell] 2024 Oct 03; Vol. 84 (19), pp. 3790-3809.e8. Date of Electronic Publication: 2024 Sep 19.

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

Autor: Her H; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA., Rothamel KL; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA., Nguyen GG; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA., Boyle EA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA., Yeo GW; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: geneyeo@ucsd.edu.

Publikováno v: Cell genomics [Cell Genom] 2024 Jul 10; Vol. 4 (7), pp. 100603. Date of Electronic Publication: 2024 Jul 01.

A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.

Autor: Antal CE; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.; Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA.; Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA., Oh TG; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.; Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73117, USA., Aigner S; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Luo EC; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Yee BA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Campos T; The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK., Tiriac H; Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA.; Department of Surgery, Division of Surgical Oncology, University of California San Diego, La Jolla, CA, 92037, USA., Rothamel KL; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Cheng Z; Center for Epigenomics, University of California San Diego, La Jolla, CA, 92037, USA., Jiao H; Center for Epigenomics, University of California San Diego, La Jolla, CA, 92037, USA., Wang A; Center for Epigenomics, University of California San Diego, La Jolla, CA, 92037, USA., Hah N; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Lenkiewicz E; Mayo Clinic in Arizona, Scottsdale, AZ, 85259, USA., Lumibao JC; Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Truitt ML; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Estepa G; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Banayo E; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Bashi S; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Esparza E; Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA.; Department of Surgery, Division of Surgical Oncology, University of California San Diego, La Jolla, CA, 92037, USA., Munoz RM; Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA., Diedrich JK; Mass Spectrometry Core for Proteomics and Metabolomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Sodir NM; The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.; Genentech, Department of Translational Oncology, 1 DNA Way, South San Francisco, CA, 94080, USA., Mueller JR; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Fraser CR; HonorHealth Research Institute, Scottsdale, AZ, 85258, USA.; Scottsdale Pathology Associates, Scottsdale, AZ, 85260, USA., Borazanci E; Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.; HonorHealth Research Institute, Scottsdale, AZ, 85258, USA., Propper D; Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, USA., Von Hoff DD; Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.; HonorHealth Research Institute, Scottsdale, AZ, 85258, USA., Liddle C; Storr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead Hospital, Westmead, NSW, 2145, Australia., Yu RT; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Atkins AR; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Han H; Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA., Lowy AM; The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.; Department of Surgery, Division of Surgical Oncology, University of California San Diego, La Jolla, CA, 92037, USA., Barrett MT; Molecular Medicine Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA., Engle DD; Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA., Evan GI; The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK., Yeo GW; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.; Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, 92037, USA., Downes M; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. downes@salk.edu., Evans RM; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. evans@salk.edu.

Publikováno v: Nature communications [Nat Commun] 2023 Sep 06; Vol. 14 (1), pp. 5195. Date of Electronic Publication: 2023 Sep 06.