Article

Hif-2α programs oxygen chemosensitivity in chromaffin cells.
Prange-Barczynska, M., Jones, H.A., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Cheng, X., Lima, J.D. ORCID: https://orcid.org/0000-0001-6804-8666, Ratnayaka, I., Douglas, G. ORCID: https://orcid.org/0000-0002-9090-5326, Buckler, K.J. ORCID: https://orcid.org/0000-0002-4870-1311, Ratcliffe, P.J. ORCID: https://orcid.org/0000-0002-2853-806X, Keeley, T.P. and Bishop, T.
Journal of Clinical Investigation 134 (18): e174661. 6 August 2024

Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679 and Ratcliffe, P.J.
Nature Structural & Molecular Biology 29 (9): 871–880. September 2022

Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.
Cockman, M.E. ORCID: https://orcid.org/0000-0002-3310-4821, Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Pegg, H.B. ORCID: https://orcid.org/0000-0003-0810-3349, Masson, N. ORCID: https://orcid.org/0000-0002-9714-905X, Salah, E. ORCID: https://orcid.org/0000-0001-7552-4966, Tumber, A., Flynn, H.R. ORCID: https://orcid.org/0000-0001-7002-9130, Kirkpatrick, J.M. ORCID: https://orcid.org/0000-0001-9291-7294, Schofield, C.J. ORCID: https://orcid.org/0000-0002-0290-6565 and Ratcliffe, P.J. ORCID: https://orcid.org/0000-0002-2853-806X
Proceedings of the National Academy of Sciences of the United States of America 119 (32): e2201483119. 9 August 2022

USP25 promotes pathological HIF-1-driven metabolic reprogramming and is a potential therapeutic target in pancreatic cancer.
Nelson, J.K., Thin, M.Z. ORCID: https://orcid.org/0000-0003-0036-2776, Evan, T., Howell, S., Wu, M. ORCID: https://orcid.org/0000-0002-2074-6171, Almeida, B. ORCID: https://orcid.org/0000-0002-0578-5690, Legrave, N., Koenis, D. S., Koifman, G., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Llorian Sopena, M., MacRae, J. ORCID: https://orcid.org/0000-0002-1464-8583, Nye, E., Howell, M. ORCID: https://orcid.org/0000-0003-0912-0079, Snijders, A.P. ORCID: https://orcid.org/0000-0002-5416-8592, Prachalias, A., Zen, Y., Sarker, D. ORCID: https://orcid.org/0000-0003-4814-8429 and Behrens, A. ORCID: https://orcid.org/0000-0002-1557-1143
Nature Communications 13 (1): 2070. 19 April 2022

A retained intron in the 3'-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites.
Sharangdhar, T., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Heraud-Farlow, J., Fernández-Moya, S.M., Ehses, J., Ruiz de Los Mozos, I. ORCID: https://orcid.org/0000-0003-4097-6422, Ule, J. ORCID: https://orcid.org/0000-0002-2452-4277 and Kiebler, M.A. ORCID: https://orcid.org/0000-0002-8850-6297
EMBO Reports 18 (10): 1762-1774. 1 October 2017

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Chakrabarti, A.M., Luscombe, N.M. and Ule, J.
Nature Protocols 12 (3): 611-637. March 2017

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, 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

Structure of the large ribosomal subunit from human mitochondria.
Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Edwards, P.C., Murshudov, G., Scheres, S.H.W. and Ramakrishnan, V.
Science 346 (6210): 718-722. 7 November 2014

iCLIP: protein-RNA interactions at nucleotide resolution.
Huppertz, I., Attig, J., D'Ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Tajnik, M., König, J. and Ule, J.
Methods 65 (3): 274-87. February 2014

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. ORCID: https://orcid.org/0000-0003-1646-7679, Paramor, M., Gleeson, J.G., Odom, D.T., Ule, J. and Frye, M.
Cell Reports 4 (2): 255-261. 25 July 2013

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. ORCID: https://orcid.org/0000-0003-1646-7679, Modic, M., Haberman, N., Tollervey, J., Fujii, R., Takumi, T., Shaw, C.E. and Ule, J.
Scientific Reports 2 : 603. 28 August 2012

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, König, J., Hussain, S., Zupan, B., Curk, T., Frye, M. and Ule, J.
Genome Biology 13 (8): R67. 3 August 2012

Poly(ethylene glycol)-lipid-conjugated antibodies enhance dendritic cell phagocytosis of apoptotic cancer cells.
Tomita, U., Yamaguchi, S., Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Takamori, S. and Nagamune, T.
Pharmaceuticals 5 (5): 405-416. 26 April 2012

Preprint

Developmental changes in the carotid body transcriptome accompanying the maturation of chemosensitivity.
Hodson, Emma J. ORCID: https://orcid.org/0000-0003-3646-9348, Sugimoto, Yoichiro ORCID: https://orcid.org/0000-0003-1646-7679, Manamperige, Rahul S., Ford, Sage G., Botting-Lawford, Kimberley J., Niu, Youguo, Nathan, James A. ORCID: https://orcid.org/0000-0002-0248-1632, Giussani, Dino A. and Ratcliffe, Peter J.
bioRxiv : 2025.08.21.671502. 25 August 2025