The district administration has blocked internet services in Aligarh since midnight in view of the protests.
Sharjeel Usmani, the son of Assistant Professor Tariq Usmani of the AMU's Department of Geography, was picked by the Uttar Pradesh's anti-terrorist squad (ATS) sleuths from his uncle's house in Azamgarh on Wednesday and was subsequently produced in a court in Aligarh which remanded him in judicial custody, they said.
The protesters raised slogans and demanded that police leave the JNU campus.
The Aligarh Muslim University Teachers' Association on Thursday urged political parties "not to play politics over the dead bodies" of the victims of the communal clashes in Muzaffarnagar.
One of the men held earlier for the crime is an alleged sex offender who targeted children in recent years.