Browse by Research Team

Cell Reports

NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs.
Hussain, S., Sajini, A.A., Blanco, S., Dietmann, S., Lombard, P., Sugimoto, Y., Paramor, M., Gleeson, J.G., Odom, D.T., Ule, J. and Frye, M.
Cell Reports 4 (2): 255-261. 25 July 2013

EMBO Reports

A retained intron in the 3'-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites.
Sharangdhar, T., Sugimoto, Y., Heraud-Farlow, J., Fernández-Moya, S.M., Ehses, J., Ruiz de Los Mozos, I., Ule, J. and Kiebler, M.A.
EMBO Reports 18 (10): 1762-1774. 1 October 2017

Genome Biology

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M. and Ule, J.
Genome Biology 13 (8): R67. 3 August 2012

Journal of Clinical Investigation

Hif-2α programs oxygen chemosensitivity in chromaffin cells.
Prange-Barczynska, M., Jones, H.A., Sugimoto, Y., Cheng, X., Lima, J.D., Ratnayaka, I., Douglas, G., Buckler, K.J., Ratcliffe, P.J., Keeley, T.P. and Bishop, T.
Journal of Clinical Investigation 134 (18): e174661. 6 August 2024

Methods

iCLIP: protein-RNA interactions at nucleotide resolution.
Huppertz, I., Attig, J., D'Ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y., Tajnik, M., König, J. and Ule, J.
Methods 65 (3): 274-87. February 2014

Nature

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
Sugimoto, Y., Vigilante, A., Darbo, E., Zirra, A., Militti, C., D'Ambrogio, A., Luscombe, N.M. and Ule, J.
Nature 519 (7544): 491-494. 26 March 2015

Nature Communications

USP25 promotes pathological HIF-1-driven metabolic reprogramming and is a potential therapeutic target in pancreatic cancer.
Nelson, J.K., Thin, M.Z., Evan, T., Howell, S., Wu, M., Almeida, B., Legrave, N., Koenis, D. S., Koifman, G., Sugimoto, Y., Llorian Sopena, M., MacRae, J., Nye, E., Howell, M., Snijders, A.P., Prachalias, A., Zen, Y., Sarker, D. and Behrens, A.
Nature Communications 13 (1): 2070. 19 April 2022

Nature Protocols

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
Sugimoto, Y., Chakrabarti, A.M., Luscombe, N.M. and Ule, J.
Nature Protocols 12 (3): 611-637. March 2017

Nature Structural & Molecular Biology

Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer.
Sugimoto, Y. and Ratcliffe, P.J.
Nature Structural & Molecular Biology 29 (9): 871–880. September 2022

Pharmaceuticals

Poly(ethylene glycol)-lipid-conjugated antibodies enhance dendritic cell phagocytosis of apoptotic cancer cells.
Tomita, U., Yamaguchi, S., Sugimoto, Y., Takamori, S. and Nagamune, T.
Pharmaceuticals 5 (5): 405-416. 26 April 2012

Proceedings of the National Academy of Sciences of the United States of America

Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.
Cockman, M.E., Sugimoto, Y., Pegg, H.B., Masson, N., Salah, E., Tumber, A., Flynn, H.R., Kirkpatrick, J.M., Schofield, C.J. and Ratcliffe, P.J.
Proceedings of the National Academy of Sciences of the United States of America 119 (32): e2201483119. 9 August 2022

Science

Structure of the large ribosomal subunit from human mitochondria.
Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y., Edwards, P.C., Murshudov, G., Scheres, S.H.W. and Ramakrishnan, V.
Science 346 (6210): 718-722. 7 November 2014

Scientific Reports

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain.
Rogelj, B., Easton, L.E., Bogu, G.K., Stanton, L.W., Rot, G., Curk, T., Zupan, B., Sugimoto, Y., Modic, M., Haberman, N., Tollervey, J., Fujii, R., Takumi, T., Shaw, C.E. and Ule, J.
Scientific Reports 2 : 603. 28 August 2012