Here is a statement by the "Chemical & Engineering News" that is about as specific as the "experts" ever get on this issue these days:

 

QUOTE:  What are trans fatty acids?

Unsaturated fats, found in such foods as avocados and olive and corn oils are heart healthy, but in the air they can go rancid by absorbing oxygen and then decompose, C&EN explains. Manufacturers can stop this process by bubbling hydrogen (hydrogenation) through the fat at a high temperature in the presence of a catalyst like nickel and in the absence of oxygen.

The process raises a fat's melting point, turning liquid vegetable oil into products ranging from soft margarine to solid shortening, according to the newsmagazine. When the healthful unsaturated fats are partially hydrogenated, the double bonds are rearranged, converting some to the trans configuration and shifting the double bonds along the chain. Unfortunately, this newly created trans fatty acid is an artery-clogger...  UNQUOTE.

Note that these claims are mostly based upon terribly flawed statistical correlation ("epidemiological") studies.  The most likely explanation is that who are generally least healthy eat the most "trans fat" and so have more heart attacks and that most "trans fat" sources have less antioxidants than unsaturated oils that have not undergone partial hydrogenation.  But the claim in the above passage is that the trans configuration is to blame for clogging arteries.  How can this possibly be the case?  How can the double bond be so different in a cis configuration than a trans configuration, in terms of one causing "heart disease" and the other "protecting" against it?  This is an extraordinary claim, and the evidence needs to at least meet the standards of the scientific method, one would think.  The idea that polyunsaturated fatty acids are "protective" against heart disease is ludicrous in terms of what is now known on the molecular level (which I've cited on this site in other places), but let us assume that they are unaware of this evidence.  Where is the experiment that has shown how a trans fatty acid molecule creates atherosclerotic plaque, and where is the experiment that has shown how a polyunsaturated fatty acid prevents plaque buildup?  The best they have to offer are exeperiments in animals that are terribly flawed, and don't show exactly how the molecules supposedly cause the damage.  In any case, as I ask people, why don't they just do an experiment on rats or dogs or a species of monkey that doesn't live more than about 15 years, control for all relevant factors (including dietary antioxidants and the amount of oxidized cholesterol in the diet), and see which diet results in the best longevity?

Source of the quoted passage:  http://www.sciencedaily.com/releases/2003/09/030924055334.htm