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TransPennine Express has lost its contract to run its service following customer complaints of poor service and cancelled trains.
The government has announced it will now run the rail service which covers the North of England and parts of Scotland.
There had been calls for its contract to be removed after poor levels of service over the past year.
Around one in six of its services were cancelled in March.
This was the highest rate in the UK.
The Department for Transport said that TransPennine's contract would not be renewed on 28 May.
It will now be run by an "Operator of Last Resort" which means a business will step in on behalf of the government to take over the management of the service.
Transport Secretary Mark Harper said: "After months of commuters and Northern businesses bearing the brunt of continuous cancellations, I've made the decision to bring Transpennine Express into Operator of Last Resort."
Transpennine has stood out for the number of trains it has cancelled the night before they are due to run, because of staff shortages.
The company has said a recovery plan was bringing the numbers down.
It has previously blamed high staff sickness, a backlog of driver training and the lack of an overtime working agreement with the drivers' union Aslef.
Mr Harper said taking the TransPennine Express under state control was "not a silver bullet and will not instantaneously fix a number of challenges being faced".
He blamed strikes by Aslef for hampering a full service being offered on TransPennine Express routes.