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James Harding has quit as editor of The Times and will leave the newspaper at the end of the month.
He handed in his resignation this morning to the national independent directors of The Times. He had been at the helm of the newspaper for five years.
Rupert Murdoch, chairman and chief executive officer of News Corporation, which owns The Times, said he hopes he will one day work with Harding again.
He said: "James has been a distinguished editor for The Times, attracting talented staff to the paper and leading it through difficult times.
"I have great respect for him as a colleague and friend, and truly hope we can work together again."
Harding said: "For any journalist, it is an extraordinary privilege and a point of pride to see your work appear beneath the masthead of The Times, the greatest name in newspapers in the world.
"I feel hugely honoured to have been given the opportunity to edit the paper and deeply grateful for the experience of working among the finest journalists in the world. This paper has an unrivalled history and, I am extremely confident, a long and impressive future ahead of it."
Harding was educated at Cambridge and he began his career at the Financial Times, where he opened their Shanghai Bureau. He joined The Times as business editor in 2006.
His replacement has not yet been announced. Harding said he was leaving because it had been made clear News Corporation want to appoint a new editor.
Many colleagues said his leaving speech was tearful. In it, he said: "I hope you will, like me, look back with a sense of achievement at the work we have done.
"I am proud of the campaigns we have run on family courts, adoption and cycling, as well as the investigations we have done, among other things, into tax avoidance and child sex grooming."
Addressing members of staff: It is also something else; a wonderful place to work, full of smart, warm, extraordinary people. I will miss it, but most of all you."
Following the announcement, Kat Brown, commercial projects editor of The Times, said: "Shock and some tears at the news James Harding is standing down as our editor. We have been lucky to have him at The Times.
"As well as being a great editor, JH was a passionate advocate of The Times Spelling Bee - one of my favourite projects here. All very sad."
Patrick Kidd, journalist at The Times, said: "A stunned Times newsroom has just been told James Harding is leaving as editor. Given lengthy applause by staff. One of Fleet St's good guys.
"Feel immensely saddened by James Harding's enforced resignation, like when Andrew Strauss went. Universally admired, a real positive force."
John Gapper, Financial Times columnist, said: "Farewell, or probably just au revoir, to James Harding, a fine editor of The Times and fun former FT colleague."
Daily Telegraph Square up to Cameron's Government
Meanwhile, the Daily Telegraph has clashed with the government over another MPs expenses scandal.
The newspaper published a report about culture secretary Maria Miller claiming £90,000 for a second home where her parents live. However, it has emerged that the Telegraph was warned to consider the minister's role in implementing new press regulations before publishing.
In response, the newspaper has decided to disclose private conversations between minister advisers and reporters "amid widespread concern about the potential dangers of politicians being given a role in overseeing the regulation of the press".
"In the wake of the disclosures of the threats made by Mrs Miller's adviser, other senior media figures have expressed alarm over the references being made to the Leveson inquiry in the context of journalistic inquiries."
According to the newspaper, Miller is now facing calls to step down from her role in the development of press regulations.
The newspaper went on to reveal a phone call to the Telegraph editor Tony Gallagher by Craig Oliver, David Cameron's director of communications, who said that the articles may be poorly timed as "she [Maria Miller] is looking at Leveson at the moment."
The adviser then telephoned a public affairs executive at Telegraph Media Group who has no role in editorial decisions at the newspaper.
The Downing Street communications director said that the Cabinet Minister, who is currently overseeing negotiations over a new system of press regulation, was considering making a complaint to the Press Complaints Commission.
Downing Street aides have insisted that the adviser was raising "legitimate concerns" despite the references to the Leveson Inquiry - which were irrelevant to the article.