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The control of gene expression in all cells involves an elaborate and dynamic interplay among what might best be described as regulatory molecules. These molecules include RNA polymerases, myriad transcription factors, the DNA template, the RNA produced by transcription, and the protein produced by translation with its attendant processing. To interfere with or in some way modify any of these critical elements is to potentially cause a profound change in the phenotypic manifestation of one or more genes or gene relays. It is clear that transcription is a consequence of a series of well-orchestrated, ordered events. Contemporary methods that examine this aspect of gene expression have revealed the dynamic nature of this biochemical process.

Transcription is the intermediary process that copies a DNA-encoded gene into a form which is either functional in its own right (stable RNAs, such as ribosomal or transfer RNAs) or can be decoded by the translational machinery into a functional protein. Transcripts destined for translation are called messenger RNAs (mRNAs), since they act as go-betweens from DNA to protein. Although RNAs are transcribed as single-stranded molecules, most can assume complicated secondary and tertiary structures that are critical for proper functioning. As a result, each mRNA contains not only the sequence information required to synthesize a protein, but also structural components that can regulate mRNA localization, stability, and translation efficiency. Thus the initiation of transcription occupies a preeminent place in the regulation of gene expression.

Alternative splicing (AS) is widely accepted to play an important role in the regulation of gene expression in higher organisms and to be responsible for the protein diversity necessary to maintain the complexity of life. The unexpected observation that the number of human genes was not in the hundreds of thousands, but in the range of . 25,000, created an apparent discrepancy between gene numbers and organismal complexity. It was difficult to explain how such a simple worm like could have almost 20,000 genes compared to the relatively low number in highly complex humans. Although there are other mechanisms that generate protein diversity, AS is the most important () because it can modulate transcript expression levels by marking transcripts for degradation nonsensemediated decay (NMD), and modify the structure of gene products by inserting or deleting protein domains (). Even though, in most cases, a direct link between AS and its function in regulating a specific pathway or process is not known, it is clear that AS is essential for guaranteeing the complexity of an organism and for insuring proper organ functioning, as well. A global analysis of human genes indicates that the majority of AS is involved in transmission, reception and response to cellular signals, with prevalence seen in immune and nervous systems which are involved in processing a large amount of information ().

Posttranscriptional control is important in the overall regulation of gene expression in plants. Such control may be manifested through numerous mechanisms such as RNA turnover, transport and/or sequestration, and differential translation. Many of these processes involve, in some manner, the 3′-untranslated region (or UTR) and polyadenylation signal of the gene. It follows that the nature of the 3′-UTR, and choice of polyadenylation site in genes with multiple sites, may play a role in the expression of a gene, with important physiological consequences. Consequently, the processes involved in alternative and regulated RNA polyadenylation, as well as generating 3′-UTR and 3′-end heterogeneity, are of considerable importance in terms of defining the expression profile of the plant genome.

For a long time, it was thought that RNA molecules were essential molecules only for carrying the genetic information from the nucleus to the cytoplasm and helping in the protein synthesis process. Current studies have shown that most RNAs do not encode proteins. The role and diversity of these numerous non-coding RNAs is yet to be understood. Recent discoveries have indicated that RNAs are more than inactive molecules. For example, a class of small (≈ 21 nucleotides [nt]) RNA molecules is involved in many of the cell’s controls, from defense mechanisms (against pathogens and other mobile genetic elements such as transposons) to regulation of the expression of their own genes during development. Among these 21 nt RNAs, microRNAs (miRNAs) and short interfering RNAs (siRNAs), are the two major types. Both diverged from their origin (miRNAs are endogenous small RNAs while siRNAs derive from exogenous dsRNA) but not from their function (). The finding of such small RNAs adds a “twist” to the general models of gene regulation and has opened an active field of research.

Newly synthesized mRNA is neither naked nor static. Transcription is coupled to the assembly of mRNPs (messenger ribonucleoprotein particles) so that RNA-binding factors which are recruited to active transcription sites are available for immediate construction of the mRNP complex. These factors specify the processing, export, subcellular location, and stability of the mRNA. Assembly of the mRNP proceeds in an orderly fashion beginning with the association of the cap-binding protein complex. This step is followed by the splicing-dependent assembly of proteins at the exon junctions of intron-containing genes and the addition of adaptor proteins to facilitate RNA export. In this way it can be said that transcription is physically and functionally coupled to the pre-mRNA processing events that lead to the final, export-competent mRNP. The relationships among these processes are summarized in Figure 6.1.