Root has been appointed as executive vice-president and general manager of the Discovery Channel in the US and is to leave the BBC in mid May. Her position as BBC Two controller is to be advertised immediately.
The moves comes as a coup for Discovery, which has been trying to poach Root for some time. She is understood to have visited the broadcaster's Washington headquarters a number of times recently.
BBC director of television Jana Bennett said: "I don't feel that this is really a departure. Although she won't be with us in the UK, her presence in Washington will strengthen the thriving partnership between the BBC and Discovery in the US."
The BBC and Discovery have a co-production deal, which was last year extended to give the Discovery Channel access to content from BBC News.
Root is a well-respected figure in the industry. She joined the channel in 1999 and since then has been voted as one of the most influential women in the UK by Good Housekeeping magazine. Under her reign BBC Two was awarded channel of the year at the Guardian International Media Festival last year. She was previously head of the Independent Commissioning Group.
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