SAN FRANCISCO (MarketWatch) -- The office of New York Attorney General Andrew Cuomo said Tuesday it issued subpoenas to former Merrill Lynch Chief Executive Officer John Thain and Bank of America Chief Administrative Officer J. Steele Alphin. The subpoenas were issued as part of its ongoing inquiry into billions of dollars in bonuses paid by Merrill Lynch just days before Merrill was taken over by Bank of America BAC, -1.32% . "The fact that Merrill Lynch appears to have moved up the timetable to pay bonuses before its merger with Bank of America is troubling to say the least and warrants further investigation," Cuomo said in a statement. Cuomo also said his office launched a probe into executive compensation practices at other TARP funded institutions in coordination with the TARP Special Inspector General Neil Barofsky.