New York Attorney General Andrew Cuomo has issued a subpoena to former Merrill Lynch CEO John Thain as part of an investigation into billions of dollars in bonuses paid to Merrill Lynch employees before the company's Jan. 1 takeover by Bank of America (BAC) - Get Report

BofA chief administrative officer J. Steele Alphin has also been subpoenaed. According to reports, the

Securities and Exchange Commission

is also investigating BofA regarding the Merrill bonuses.

Thain and BofA

have reportedly been scuffling over whether Thain insisted on going forward with the bonus payments even after it became apparent Merrill would report a fourth-quarter loss in excess of $15 billion.

Thain also has been defending his $1.2 million office-renovation project in late 2007. In a memo to Merrill employees, he said he called the project, which had been done at Merrill's expense, a mistake and said he would personally reimburse the company.

Shares of Bank of America were lately up 7.5% at $6.45 in midday trading.