Minireview: global regulation and dynamics of ribonucleic Acid

Abstract

Gene expression starts with transcription and is followed by multiple posttranscriptional processes that carry out the splicing, capping, polyadenylation, and export of each mRNA. Interest in posttranscriptional regulation has increased recently with explosive discoveries of large numbers of noncoding RNAs such as microRNAs, yet posttranscriptional processes depend largely on the functions of RNA-binding proteins as well. Glucocorticoid nuclear receptors are classical examples of environmentally reactive activators and repressors of transcription, but there has also been a significant increase in studies of the role of posttranscriptional regulation in endocrine responses, including insulin and insulin receptors, and parathyroid hormone as well as other hormonal responses, at the levels of RNA stability and translation. On the global level, the transcriptome is defined as the total RNA complement of the genome, and thereby, represents the accumulated levels of all expressed RNAs, because they are each being produced and eventually degraded in either the nucleus or the cytoplasm. In addition to RNA turnover, the many underlying posttranscriptional layers noted above that follow from the transcriptome function within a dynamic ribonucleoprotein (RNP) environment of global RNA-protein and RNA-RNA interactions. With the exception of the spliceosome and the ribosome, thousands of heterodispersed RNP complexes wherein RNAs are dynamically processed, trafficked, and exchanged are heterogeneous in size and composition, thus providing significant challenges to their investigation. Among the diverse RNPs that show dynamic features in the cytoplasm are processing bodies and stress granules as well as a large number of smaller heterogeneous RNPs distributed throughout the cell. Although the localization of functionally related RNAs within these RNPs are responsive to developmental and environmental signals, recent studies have begun to elucidate the global RNA components of RNPs that are dynamically coordinated in response to these signals. Among the factors that have been found to affect coordinated RNA regulation are developmental signals and treatments with small molecule drugs, hormones, and toxins, but this field is just beginning to understand the role of RNA dynamics in these responses.

Figure 1

Pathway of gene expression in eukaryotic cells showing intervening steps of mRNA processing (red) that are coupled together with RBPs coordinating multiple mRNAs from transcription to translation. These processes are dynamic with multiple copies of each mRNA changing within and among heterogeneous RNPs in time and space (inset). The approach of using microarrays or deep sequencing to identify RNP-associated subsets of functionally related RNAs (RIP-chip or RIP-seq) is depicted, as is the use of nuclear run-on array measurements to assess nascent transcripts before RNA processing. [Adapted with permission from J. D. Keene: Proc Natl Acad Sci USA 98:7018–7024, 2001 (2). ©National Academy of Sciences.]

Figure 2

The complexity of transcriptomics can be reduced by probing its underlying layers. Transcriptomics has generated data with overwhelming complexity. Polysome-arrays and decay arrays dissect layers of gene expression and can also reveal coordinated posttranscriptional events. mRNAs identified using RIP-chip are functionally related as coordinated and dynamic RNP modules (posttranscriptional RNA operons and regulons). There are procedures used to globally quantify RNAs at the levels of RNA stability or translation that are not otherwise evident from complex transcriptomic analysis. Depiction of a microarray (middle) that displays transcriptomic data representing the accumulated levels of each mRNA depending upon both its rate of synthesis and its rate of degradation. Methods such as RIP-chip (and RIP-seq), RNA decay-array analysis, and polysome gradient-array analysis have been devised in recent years to assess these “under layers” of the transcriptome. RNA turnover due to differences in RNA stability among the RNAs is depicted as up and down arrows below the array.

Figure 3

Multiple copies allow multiple combinations of mRNAs. Illustration of the multiple lives of each mRNA based on the posttranscriptional RNA operon/regulon model (16). Functionally related mRNAs are “clustered” in time and space such that the proteins encoded by them can be coordinately produced in concert. Each of the four mRNAs has the potential to be a member of more than one subset because the protein it encodes serves multiple functional roles in different cellular processes. The colored circles represent different RBPs or different posttranslationally modified isoforms of a given RBP that bind to the colored bars in the 3′ or 5′ UTRs. Noncoding RNAs that bind in combination with RBPs to sequences in these mRNAs can affect posttranscriptional outcomes such as RNA stability and translation. Posttranscriptional RNA Operons (PTRos) are coordinated subsets of functionally related mRNAs in association with regulatory RBPs and noncoding RNAs that are spliced, transported, stabilized, localized, or translated in a coherent manner. Multiple PTRos can share certain mRNAs to form overlapping posttranscriptional regulons that coordinate the production of several related subsets of functionally related proteins.