Dark Matter RNA: Existence, Function, and Controversy

Abstract

The mysteries surrounding the ∼97-98% of the human genome that does not encode proteins have long captivated imagination of scientists. Does the protein-coding, 2-3% of the genome carry the 97-98% as a mere passenger and neutral "cargo" on the evolutionary path, or does the latter have biological function? On one side of the debate, many commentaries have referred to the non-coding portion of the genome as "selfish" or "junk" DNA (Orgel and Crick, 1980), while on the other side, authors have argued that it contains the real blueprint for organismal development (Penman, 1995; Mattick, 2003), and the mechanisms of developmental complexity. Thus, this question could be referred to without much exaggeration as the most important issue in genetics today.

Keywords: dark matter RNA; gene; genomics; intronic RNA; linc; non-coding; transcriptome; vlinc.

Figure 1

Types of RNA molecules derived from annotated and unannotated loci that constitute “dark matter” RNAs.

Figure 2

Coverage of the genome by “dark matter” RNAs. (A) Information currently available about the regions of dark matter transcription and the actual RNA molecules made from these region comes from various types of experiments and databases. There is relatively little overlap between these different databases suggesting that the actual extend of dark matter transcription is far greater than any one database suggests. (B) A theoretical curve showing expected results of the fraction of the genome that is transcribed as a function of the number of biological sources whose RNA is profiled. The coverage of transcribed genome by protein coding genes including their introns is 42% and lincRNAs bring it up to 58%. However, the full extent of the transcribed genome is expected to be much greater than that.