Matthew Cockman

Quantitative profiling of JMJD6-catalysed lysine hydroxylation reveals residue-dependent oxygen sensitivity

Preprint

Authors (7)

Pallavi Kesavan
Sophie Stuermer
Katrin Räbel
Oliver Popp
Philipp Mertins
Matthew Cockman
Yoichiro Sugimoto

bioRxiv

Published 8 June 2026

Crick labs/ facilities

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Inactivation of the PHD3-FOXO3 axis blunts the type I interferon response in microglia and ameliorates Alzheimer's disease progression

Authors (19)

Manuel A Sanchez-Garcia
Nieves Lara-Ureña
Rosana March-Diaz
Clara Ortega-de San Luis
Silvia Quiñones-Cañete
Bella Mora-Romero
[...]
Ana M Muñoz-Cabello
Ana B Muñoz-Manchado
Matthew Cockman
Alicia E Rosales-Nieves
Alberto Pascual

Science advances

Published 30 May 2025

Crick labs

Peter Ratcliffe

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Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6

Authors (10)

Matthew Cockman
Yoichiro Sugimoto
Hamish Pegg
Norma Masson
Eidarus Salah
Anthony Tumber
Helen R Flynn
Joanna Kirkpatrick
Christopher J Schofield
Peter Ratcliffe

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

Published 9 August 2022

Crick labs/ facilities

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Factor inhibiting HIF can catalyse two asparaginyl hydroxylations in VNVN motifs of ankyrin fold proteins

Authors (16)

Thomas M Leissing
Adam P Hardy
Hokfung Chan
Yihua Wang
Anthony Tumber
Rasheduzzaman Chowdhury
[...]
Roman Fischer
Benedikt M Kessler
Peter Ratcliffe
Xin Lu
Christopher J Schofield

Journal of Biological Chemistry

Published 1 June 2022

Crick labs

Peter Ratcliffe

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Ogfod1 deletion increases cardiac beta-alanine levels and protects mice against ischaemia-reperfusion injury

Authors (11)

Michael Harris
Junhui Sun
Karen Keeran
Angel Aponte
Komudi Singh
Danielle Springer
Marjan Gucek
Mehdi Pirooznia
Matthew Cockman
Elizabeth Murphy
Leslie M Kennedy

Cardiovascular Research

Published 1 September 2022

Crick labs

Peter Ratcliffe

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Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates

Authors (11)

Matthew Cockman
Kerstin Lippl
Ya-Min Tian
Hamish Pegg
William D Figg
Martine I Abboud
Raphael Heilig
Roman Fischer
Johanna Myllyharju
Christopher J Schofield
Peter Ratcliffe

eLife

Published 10 September 2019

Crick labs/ facilities

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Inherent DNA-binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin

Authors (11)

James A Smythies
Min Sun
Norma Masson
Rafik Salama
Peter D Simpson
Elizabeth Murray
Viviana Neumann
Matthew Cockman
Hani Choudhry
Peter Ratcliffe
David R Mole

EMBO Reports

Published 1 January 2019

Crick labs

Peter Ratcliffe

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The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases

Authors (23)

Suzana Markolovic
Qinqin Zhuang
Sarah E Wilkins
Charlotte D Eaton
Martine I Abboud
Maximiliano J Katz
[...]
Roman Fischer
Pablo Wappner
Rasheduzzaman Chowdhury
Mathew L Coleman
Christopher J Schofield

Nature Chemical Biology

Published 18 June 2018

Crick labs

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A ribosomopathy reveals decoding defective ribosomes driving human dysmorphism

Authors (20)

Nahuel A Paolini
Martin Attwood
Samuel B Sondalle
Carolina Marques Dos Santos Vieira
Anita M van Adrichem
Franca M di Summa
[...]
Taco W Kuijpers
Jonathan D Dinman
Susan J Baserga
Matthew Cockman
Alyson W MacInnes

American Journal of Human Genetics

Published 2 March 2017

Crick labs

Peter Ratcliffe

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Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

Authors (12)

Christoph Loenarz
Rok Sekirnik
Armin Thalhammer
Wei Ge
Ekaterina Spivakovsky
Mukram M Mackeen
[...]
Matthew Cockman
Benedikt M Kessler
Peter Ratcliffe
Alexander Wolf
Christopher J Schofield

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

Published 18 March 2014

Crick labs

Peter Ratcliffe

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OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation

Authors (19)

Rachelle S Singleton
Phebee Liu-Yi
Fabio Formenti
Wei Ge
Rok Sekirnik
Roman Fischer
[...]
Benedikt M Kessler
Pablo Wappner
Christopher J Schofield
Peter Ratcliffe
Matthew Cockman

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

Published 18 March 2014

Crick labs

Peter Ratcliffe

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Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth

Authors (17)

Maximiliano J Katz
Julieta M Acevedo
Christoph Loenarz
Diego Galagovsky
Phebee Liu-Yi
Marcelo Pérez-Pepe
[...]
Graciela L Boccaccio
Christopher J Schofield
Matthew Cockman
Peter Ratcliffe
Pablo Wappner

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

Published 18 March 2014

Crick labs

Peter Ratcliffe

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Optimal translational termination requires C4 lysyl hydroxylation of eRF1

Authors (22)

Tianshu Feng
Atsushi Yamamoto
Sarah E Wilkins
Elizaveta Sokolova
Luke A Yates
Martin Münzel
[...]
Ludmila Y Frolova
Elena Alkalaeva
Peter Ratcliffe
Christopher J Schofield
Mathew L Coleman

Molecular Cell

Published 20 February 2014

Crick labs

Peter Ratcliffe

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Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans

Authors (32)

Wei Ge
Alexander Wolf
Tianshu Feng
Chia-hua Ho
Rok Sekirnik
Adam Zayer
[...]
Benedikt M Kessler
Peter Ratcliffe
Gail M Preston
Mathew L Coleman
Christopher J Schofield

Nature Chemical Biology

Published 1 December 2012

Crick labs

Peter Ratcliffe

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ModLS: post-translational modification localization scoring with automatic specificity expansion

Authors (5)

David C Trudgian
Rachelle Singleton
Matthew Cockman
Peter Ratcliffe
Benedikt M Kessler

Journal of Proteomics & Bioinformatics

Published 1 January 2012

Crick labs

Peter Ratcliffe

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Quantitative profiling of JMJD6-catalysed lysine hydroxylation reveals residue-dependent oxygen sensitivity

Inactivation of the PHD3-FOXO3 axis blunts the type I interferon response in microglia and ameliorates Alzheimer's disease progression

Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6

Factor inhibiting HIF can catalyse two asparaginyl hydroxylations in VNVN motifs of ankyrin fold proteins

Ogfod1 deletion increases cardiac beta-alanine levels and protects mice against ischaemia-reperfusion injury

Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates

Inherent DNA-binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin

The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases

A ribosomopathy reveals decoding defective ribosomes driving human dysmorphism

Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation

Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth

Optimal translational termination requires C4 lysyl hydroxylation of eRF1

Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans

ModLS: post-translational modification localization scoring with automatic specificity expansion

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