<iframe width="560" height="315" src="//www.youtube.com/embed/UPk1B1bxUPg" frameborder="0" allowfullscreen></iframe>

<iframe width="560" height="315" src="//www.youtube.com/embed/UPk1B1bxUPg/?wmode=transparent" frameborder="0" allowfullscreen></iframe>

$str = '<iframe width="560" height="315" src="//www.youtube.com/embed/UPk1B1bxUPg" frameborder="0" allowfullscreen></iframe>';

$dom = new DOMDocument();
$dom->loadHTML($str);
foreach($dom->getElementsByTagName('iframe') as $iframe) {
    $src = $iframe->getAttribute('src');
    $src .= '?wmode=transparent'; // use a regex for better results
    $iframe->setAttribute('src', $src);
}

echo $dom->saveHTML();

<?php
$videoEmbedCode = '<iframe width="560" height="315" src="//www.youtube.com/embed/UPk1B1bxUPg" frameborder="0" allowfullscreen></iframe>';
$appendString = '/?wmode=transparent';

/* Youtube video sticky menu overlap fix */
$searchStartLen = strpos($videoEmbedCode, 'youtube');
$searchEndLen = strpos($videoEmbedCode, '"', $searchStartLen);
$newVideoEmbedCode = substr_replace($videoEmbedCode, $appendString, $searchEndLen, 0);

print $newVideoEmbedCode;
?>

$doc = new DOMDocument();
$doc->loadHTML($your_html);

foreach($doc->getElementsByTagName('iframe') as $iframe)
{
$iframe->setAttribute("src",$iframe->getAttribute('src').'?wmode=transparent');
}

echo $doc->saveHTML();