UPDATED: Bryan Singer, the director of “Bohemian Rhapsody,” has responded to new allegations published in the Atlantic on Wednesday that he engaged in sexual misconduct with underage boys.

In the report, four men allege that Singer had sexual encounters with them when they were teenagers in the late 1990s. One of the men, Victor Valdovinos, says he was a 13-year-old extra on the set of “Apt Pupil” when Singer fondled his genitals.

The three other accusers are identified in the story by pseudonyms. One, identified in the story as Andy, says that he had sex with Singer when he was 15. Another man, identified as Eric, says he was 17 when he began having sex with the director. Singer would have been 31 at the time. The third man, Ben, alleges that he and Singer had oral sex when he was 17 or 18.

“He would stick his hands down your pants without consent,” the man told the Atlantic. “He was predatory in that he would ply people with alcohol and drugs and then have sex with them.”

Singer’s attorney, Andrew Brettler, denied to the magazine that Singer had ever had sex with underage boys, and disputed various details of the accusers’ accounts.

Singer also responded to the story on Wednesday, calling it a “homophobic smear piece.”

“The last time I posted about this subject, Esquire magazine was preparing to publish an article written by a homophobic journalist who has a bizarre obsession with me dating back to 1997,” Singer said in a statement. “After careful fact-checking and, in consideration of the lack of credible sources, Esquire chose not to publish this piece of vendetta journalism. That didn’t stop this writer from selling it to The Atlantic. It’s sad that The Atlantic would stoop to this low standard of journalistic integrity. Again, I am forced to reiterate that this story rehashes claims from bogus lawsuits filed by a disreputable cast of individuals willing to lie for money or attention. And it is no surprise that, with ‘Bohemian Rhapsody’ being an award-winning hit, this homophobic smear piece has been conveniently timed to take advantage of its success.”

Singer was fired two weeks before the end of production on “Bohemian Rhapsody” in December 2017. The film received five Academy Award nominations on Tuesday, including best picture and best actor for Rami Malek as Freddie Mercury. Singer remains the credited director, but was not nominated. He is next scheduled to direct “Red Sonja” for Millennium Films.

The authors of the Atlantic article, Alex French and Maximillian Potter, spoke to 50 sources over the course of a 12-month investigation. French and Potter are both affiliated with Esquire, French as a writer at large and Potter as the editor at large. In their own statement on Wednesday, the writers said that Hearst Communications, which owns Esquire, had killed the piece.

“We have been asked why a story reported and written by two Esquire writers is being published in the Atlantic,” they said. “This story began with our editors at Esquire. After months of reporting, the story went through Esquire’s editorial process, which included fact-checking and vetting by a Hearst attorney, and the story was approved for publication. The story was then killed by Hearst executives. We do not know why. We feel fortunate that the Atlantic decided to work with us, and we are grateful that the piece has gone through the Atlantic’s thoughtful editorial process, which included another rigorous fact-check and robust legal vetting. We are most grateful that the alleged victims now have a chance to be heard and we hope the substance of their allegations remains the focus.”

The investigation first came into public view on Oct. 15, when Singer posted on Instagram that Esquire was looking to write a negative article about him.

“In today’s climate where people’s careers are being harmed by mere accusations, what Esquire is attempting to do is a reckless disregard for the truth, making assumptions that are fictional and irresponsible,” Singer wrote at the time.

In April 2014, Michael Egan sued Singer, alleging that the director had raped him several times in Hawaii in 1999, when Egan was 17. That case was dropped several months later, after discrepancies emerged in Egan’s story.

Cesar Sanchez-Guzman sued Singer in December 2017, claiming that Singer raped him on a yacht in 2003. Singer has denied the allegation, and the case is still pending.

“The industry will brush things under the rug and pretend nothing happened,” Sanchez-Guzman told the magazine. “Most people don’t see the truth.”