(CNN) The U.S. Justice Department is investigating whether Chicago police have made a habit of violating the law or the U.S. Constitution in their policing, Attorney General Loretta Lynch said Monday.

The "pattern-and-practice" probe, as it's known, will focus on use of force, deadly force, accountability and how the Chicago Police Department "tracks and treats" those incidents, she said.

Mayor Rahm Emanuel said he welcomes the investigation and promised the city's total cooperation in achieving the "mutual goal" of keeping Chicago safe while respecting citizens' rights.

"Nothing is more important to me than the safety and well-being of our residents and ensuring that the men and women of our Police Department have the tools, resources and training they need to be effective crime fighters, stay safe and build community trust," Emanuel said in a statement.

He later told reporters that the city will be made better because of the investigation.

"We accept it, and we need it," he said, describing the current moment as an inflection point.

"None of the measures we have taken have ever measured up to the seriousness, the scope, the scale of the challenge in front of us as a city," Emanuel said.

City, department under fire

Word of the federal probe comes about two weeks after police released the October 2014 video of Officer Jason Van Dyke fatally shooting Laquan McDonald on a Chicago street, and it comes after reports released by the city over the weekend indicate that accounts from police on the scene appear to contradict what the footage shows

The video of McDonald's fatal shooting outraged many Chicagoans, who took to the streets to protest what they felt was an excessive use of force and dishonesty by the city and Van Dyke's fellow officers, who initially accused McDonald of threatening officers. The demonstrators also questioned why it took more than 400 days to release the video, despite the city paying McDonald's mother $5 million in April.

The spotlight on the case shone bright enough to illuminate another case -- that of Ronald Johnson, who was killed by police eight days before McDonald's death. Video from that incident was shown to reporters Monday, as Emanuel promised last week. Cook County State's Attorney Anita Alvarez said Monday that there will be no charges against the officer responsible for Johnson's death.

The federal investigation -- which places the Chicago Police Department in the company of forces in other cities such as Cleveland; Ferguson, Missouri; and Albuquerque, New Mexico -- is necessary, Lynch said, because failing to hold police accountable for misconduct creates "profound consequences" for communities.

"When suspicion and hostility is allowed to fester it can erupt into unrest," she said, adding that the investigation will not home in on individuals but will aim to "improve systems."

Leadership changes in Chicago

Calls for a federal probe intensified after Chicago police on November 24 released the video of McDonald being shot 16 times last year. Political upheaval came quickly on the heels of Chicago's demonstrations, with Emanuel asking for (and getting) Police Superintendent Garry McCarthy's resignation.

On Sunday, the mayor announced that Scott Ando, head of the authority that investigates police shooting incidents such as the McDonald and Johnson cases, had stepped down.

Sharon Fairley will be the new chief administrator for the city's Independent Police Review Authority, replacing Ando, a veteran Drug Enforcement Administration agent who joined the IPRA in 2011 and took its reins last year. Fairley was general counsel to the city's Office of the Inspector General and previously served as an assistant U.S. attorney where she prosecuted national security, financial and government fraud cases.

"Sharon brings the experience and independence to ensure that when an officer breaks the rules, they will be held accountable," the mayor said in a statement, adding that "new leadership is required as we rededicate ourselves to dramatically improving our system of police accountability and rebuilding trust."

This follows a series of initiatives taken by Emanuel's office in the past two weeks, including expanding the body camera program and establishing a task force to review police discipline procedures, according to the statement.

The City Council formed the IPRA in 2007 "in response to concerns about how allegations of police misconduct were being investigated," according to its website . It is staffed by civilian investigators charged with independently reviewing allegations against police.

Latest in federal police probes

Federal police probes like the one undertaken in Chicago are nothing new to President Barack Obama's administration. Many cities have fallen under the federal microscope during his administration. A few examples:

-- In Ferguson, federal authorities determined after the fatal shooting of Michael Brown that the police department had engaged in discriminatory and unconstitutional practices.

-- A federal probe that began in Cleveland in 2013 documents several instances of unnecessary force after two unarmed civilians were shot more than 20 times after a high-speed police chase.

-- In East Haven, Connecticut, federal investigators determined Latinos were subjected to more traffic stops, harsher treatment and more retaliation over discrimination complaints, a 2011 Justice Department report said. The following year, four officers were arrested and charged with targeting Latinos.

-- The Justice Department and Missoula, County, Montana, officials reached an agreement last year after a federal probe highlighted allegations of gender bias against victims of sexual assault. The agreement to approve policies, training, communication and data sharing, among other measures, ended a lawsuit in which the county attorney accused the feds of bullying and defaming prosecutors.

-- A 2011 report on New Orleans found minorities were subjected to excessive force, illegal stops and pat-down searches. It also found that more African-American residents were arrested, compared with white residents, and that police targeted transgender people for arrest on prostitution charges.

-- The Justice Department accused the Albuquerque, New Mexico, police department of engaging in "a pattern" of using excessive force after a two-year investigation. In some instances, the department alleged, officers failed to turn on their cameras and recorders before such encounters.

Following the announcement of the Ferguson probe in September 2014, CNN senior legal analyst Jeffrey Toobin explained -- much as the attorney general did Monday -- that these types of investigations focus more on reform than punishing individuals for past misconduct.

Still, Toobin said, "it's very serious because it can lead to a virtual federal takeover of the police."