Reverse transcription of retroviral genomic RNA yields double-stranded DNA that is integrated into the host genome to form a provirus. Transcription of proviral DNA recreates the full-length viral RNA genome, and subgenomic-sized RNA molecules are generated by RNA processing. All RNA products serve as templates for the production of viral proteins.

The formation of the provirus is a unique strategy among animal viruses and places retroviruses among the classes of mobile elements known as retrotransposons. In the DNA intermediate stage, the virus mimics a cellular gene and relies almost entirely on the host-cell machinery for gene expression. Although this strategy accommodates a viral genome that encodes a limited number of protein products, it necessitates that the genome also contain a large array of cis-acting elements that direct the host-cell machinery to function in viral gene expression. Most of these elements lie in the long terminal repeats (LTRs) of the proviral DNA (Fig. 1). The provirus is significantly longer than the viral genomic RNA in both the 5′ and 3′ directions. The U3 region that is found upstream of the transcription start site contains the majority of cis-acting control elements that regulate transcriptional initiation by cellular RNA polymerase II. The U3, R, and U5 regions of the 3′ LTR contain the cis-acting control elements involved in posttranscriptional processing of the 3′ end of the RNA product.

Figure 1

Overview of retroviral transcription and RNA processing: Typical proviral structure (A) with identical 5′ and 3′ LTRs. Genes illustrated above the line are shared by all replication-competent retroviruses. The horizontal arrow marks the (more...)

Retroviruses employ a wide spectrum of host-cell transcription factors, including proteins that are ubiquitous, constitutively expressed activators and those that are tissue-specific or ligand-dependent activators. The repertoire of transcription factors used by a particular retrovirus reflects the unique characteristics of its own replication mechanism. For example, retroviruses that infect lymphoid cells depend on the activity of lymphoid-specific transcription factors. The complex retroviruses encode their own transcriptional activators, such as the Tat and Tax proteins of human immunodeficiency virus (HIV) and human T-cell leukemia virus (HTLV), respectively, which act in concert with host factors to provide the virus with additional control over gene expression. This results in the establishment of feedback circuits that further enhance transcription during a single viral replicative cycle. The virally encoded regulatory proteins may also have effects on host-cell biology; for example, the HTLV Tax protein affects cellular genes involved in growth regulation, apparently contributing to oncogenesis.

Following transcription, the viral RNA products are modified by cellular RNA processing machinery. Each viral transcript acquires a cap addition at the 5′ end and is polyadenylated at the 3′ end (Fig. 1). Most retroviruses rely on a single transcription start site, and this places unusual demands on the posttranscriptional steps in the regulation of gene expression. During retroviral replication, full-length viral RNA transcripts are packaged into virions as genomic RNA. However, a typical 8–10-kb retroviral genome contains open reading frames for up to 12 different viral protein products. In some cases, multiple protein products are synthesized from a single RNA species by frameshifting and processing of polyproteins by proteolysis (see Chapter 7. In all cases, subgenomic-sized messenger RNA molecules are generated from viral genomic RNA by alternative RNA splicing. Both genomic- and subgenomic-sized RNAs function as mRNA. The virus requires cis-acting signals to define the structure of the alternative spliced products and to recruit host-cell splicing machinery.

Retroviruses face the critical task of regulating the relative amounts of unspliced and spliced RNAs that reach the cytoplasm. Unlike the products of most cellular genes, a significant fraction of viral RNA must reach the cytoplasm unspliced. Complex retroviruses, which direct the synthesis of both singly and multiply spliced mRNAs, encode viral proteins, Rex and Rev, which affect the fate of unspliced and singly spliced RNAs. Like the viral transcriptional regulators, Rex and Rev interact with host-cell RNA processing pathways to promote control over the progression of viral infection. Simple retroviruses appear to have evolved other mechanisms to regulate the ratio of unspliced to spliced mRNA either by use of variably efficient splice sites or by the incorporation into their genome of cis-acting sequences that regulate export of unspliced RNAs from the nucleus.

Proviral DNA is assembled into chromatin in a manner similar to that of host-cell DNA. Although the mechanism(s) by which chromatin structure influences gene expression is not understood, it is clear that expression of a provirus can be affected by the chromatin structure of contiguous cellular sequences. Expression of the provirus also can affect the expression state of the flanking cellular sequences. This effect is dramatically exemplified by the insertional activation of cellular proto-oncogenes during the induction of tumors by nonacutely transforming retroviruses. In these cases, the transcriptional control elements located in the LTRs of a provirus become the dominant control elements for the aberrant expression of cellular genes. Proviruses also can act as mutagens by disrupting the expression of cellular genes.

Although different retroviruses share many essential features of gene regulation, each retrovirus has evolved unique solutions to replicate in specific cell types. This chapter presents an overview of the mechanisms employed by retroviruses for transcriptional and posttranscriptional regulation of gene expression. Special emphasis is placed on the transcriptional controls that mediate viral pathogenesis and the virally encoded regulatory proteins of human retroviruses. The dissection of these viral regulatory strategies has provided new insights into potential targets for control of human viral infections as well as a better understanding of transcriptional and posttranscriptional regulatory mechanisms employed by vertebrate cells.