Regulation of gene expression by non-protein-coding RNAs

Abstract: The human genome sequencing projects revealed that the human genome contains over 3 billion DNA base pairs, but only 20,000 25,000 protein-coding genes. In fact, only about 1.2% of the genome codes for proteins. Surprisingly, the number of human genes seems to be almost equal to lower mammals like rodents, and less than a factor of two greater than that of many much simpler organisms, such as the roundworm and the fruit fly. On the other hand, recent studies have revealed that eukaryotic genomes are almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs). Thus there may be a vast reservoir of biologically meaningful ncRNAs that greatly exceed the 1.2% of the genome that corresponds to conventional protein coding genes. Several classes of functional ncRNAs have been identified in recent years. One prominent and complex class of ncRNAs is natural antisense transcripts (NATs). NATs are RNA molecules transcribed from the opposite strand of conventional genes often overlapping in part with mature sense mRNA. Indeed a large fraction of NATs is expressed in specific regions of the brain, supporting involvement of these ncRNAs in sophisticated regulatory brain functions as well as in complex neurological disorders. Recent research on NATs, including several large-scale expression-profiling studies, has conclusively established the existence of NATs in eukaryotic genomes. In fact, the consensus opinion is that natural antisense transcripts, most of which represent ncRNAs, occur abundantly in the mammalian genome. However, there are many unanswered questions that still exist concerning NATs biological functions and their heterogeneous mode of actions in various cells. For instance, what fraction of NATs may have functional significance, and how many different regulatory mechanisms may exist for these RNA molecules? NATs appear to be utilizing various cellular pathways, but it is still not clear which intrinsic properties of natural antisense RNA molecules or extrinsic features, such as protein interactions, cellular and developmental context are decisive for any given pathway. How is the expression of these ncRNAs regulated in various cells, and what are the extrinsic factors that affect the regulatory output of antisense RNA transcripts? Based on what we know about the broad expression of NATs in different tissues and cell types, and their varied proposed functions, NATs appear to be a heterogeneous group of regulatory RNAs with a wide variety of biological roles. During the course of my studies, I initially tried to uncover some general aspects of NAT-mediated regulation of gene expression. Thereafter I have investigated, in further detail, the functional significance of a number of these regulatory RNA elements. I have also reviewed all the reported cases of NATs and summarized them in the introduction section of my thesis. In conclusion, I found that there are widespread occurrences of NATs in mammalian genomes and that many of these regulatory elements are indeed functionally relevant in controlling conventional (sense) gene expression. Considering tissue- and cell type-specific expression patterns of NATs and their heterogeneous proposed functions, it seems that we have, so far, only touched parts of an elephant in the dark. The big picture, in the light of future studies, probably will include these parts, but it could be dissimilar to our current understanding. My work, like any other scientific project, has generated many more questions than answers. Several other Ph.D. assignments are needed to address these questions and to generate more questions for future projects and this is the nature of growing sciences.