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Brauchli will become a consultant to News Corp., the company announced after a meeting between the members of a special committee designed to protect the editorial integrity of the newspaper.
Dow Jones, the parent of the Journal and now a unit of Murdoch's conglomerate, said it will begin a search for Brauchli's replacement immediately.
"Marcus is a brilliant journalist who has played a key role in the growth of The Wall Street Journal over the past 20 years," said Dow Jones Chief Executive Les Hinton.
"He deftly guided the Journal's coverage of every major news event of the past decade and is leaving the paper in a position of great strength."
In his new role, Brauchli "will provide guidance to senior management in a wide range of areas, from advising The Wall Street Journal to exploring the possibility of a business news channel for STAR-TV in Asia," according to a Dow Jones statement.
Brauchli (46), became the Journal's managing editor last May, overseeing the print and online operations in the US and abroad.
Murdoch, who agreed to guarantee editorial independence when he acquired the daily, is nonetheless making changes in management and in strategy as he seeks to take on competition such as the New York Times.
A top newspaper union leader said employees view Brauchli's departure as damaging to the newspaper's editorial independence.
"It was reassuring that he was there because he was not a News Corp. guy," Steve Yount, president of the Independent Association of Publishers Employees, was quoted as saying by Editor and Publisher.
"They had hopes he was maintaining the editorial independence."
A separate report in the Journal said News Corp. was near a deal to acquire the suburban New York daily Newsday for around $580-million.
AFP