Consider the DNA to be the basic hardware of life ... there has to be software layers that control how, when, where and how much information is to be decoded from the DNA. One layer of abstraction is epigenetics - DNA strands being modified by various (ex. methyl) groups, that regulate how the information is copied. Depending on where these methyl groups are on the gene, copying of DNA will greatly vary.
To add another layer of abstraction, scientists are discovering the importance of RNAs .. in particular small or micro RNAs in regulating how, when, where information is decoded from the DNA. These tiny RNA molecules travel and impact regions of the DNA that was previously considered barren wastelands or vestiges of our evolutionary past.
To study them, it is a very tough undertaking. They are easily degraded and also, they are expressed at various time points. So imagine, you try to collect all RNA from cells during the day .. but what about the ones that are expressed at night that regulate the circadien clock? Or what if you collect it at a time when cells are undergoing division and you miss on the RNAs that are responsible for suppressing cell division ..
Furthermore, how much of an RNA present in the cell, adds additional complications. How do you quantify how much at what time ... (for science geeks: qRT and northern is a good estimate :)
Furthermore x2, an RNA that can be positively regulating one region in the DNA (aka gene :) .. might be negatively regulating another region.
Hopefully with the current research, it would be much easier to get a very detailed catalog of all RNA molecules and over time, build a comprehensive tool kit to better treat genetic diseases.