Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci

Abstract

The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organization, transcription, various post-transcriptional processes, and translation. In this study, the Transcriptional Interference Network (TIN) hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighboring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronized cascade of gene expression in functionally linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses. The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular organisms too.

Keywords: Hox genes; antisense RNA; genomic organization; herpesvirus; polycistronic RNAs; pseudorabies virus; tandem genes; transcriptional interference.

FIGURE 1

The structural organization of the pseudorabies virus genome. The genome of PRV is atypical among alpha-herpesviruses because it does not have inverted repeat sequences around the Ul region. Color code: light grey, immediate early gene (i.e., 180 gene); black, early genes; dark grey, E/L genes; white, L genes.

FIGURE 2

The structural organization of the Hox clusters. Drosophila has a single set of Hox genes termed the Homeotic complex, which is made up of two clusters, the Antennapedia and the Bithorax complexes. Vertebrates have four sets of Hox clusters generated by two rounds of polyploidization events that occurred prior to the divergence of jawless and jawed vertebrates.

FIGURE 3

Possible overlaps producing antiparallel transcripts. (A) Tandem (parallel, head-to-tail, 5′–3′) overlap. Transcription of the upstream genes of a tandem gene cluster often fails to stop at their poly(A) signal, thereby producing long polycistronic RNA molecules. (B) Convergent (antiparallel) overlaps. (B1) Head-to-head (5′–5′) overlap between two divergently positioned genes. (B2) Tail-to-tail (3′–3′) overlap between convergently oriented genes. Two opposing genes can overlap at their 3′-UTR regions (a) or can exhibit a 3′-UTR–ORF (b), or ORF–ORF overlap. (B3) Transcriptional read-through overlap occurs when the major poly(A) signal occasionally fails to terminate by the advancing RNAP (a). The use of alternative polyadenylation provides a mechanism similar to that of transcriptional read-through for the spatiotemporal control of gene expression (b).

FIGURE 4

Antisense transcripts regulating the two key transcriptional activators of pseudorabies virus. The immediate early 180 (IE180) and early protein 0 (EP0) proteins are the major regulators of global gene expression of PRV. The latency-associated transcript (LAT), the antisense transcript (AST) and the long latency transcripts (LLT) are RNA molecules transcribed from the complementary DNA strands of these genes from their own promoters. The antisense transcripts are driven by LAP (latency-associated transcript promoter) and ASP (antisense promoter).

FIGURE 5

Inverse expression pattern between the sense and antisense transcripts of pseudorabies virus. The transcription rates (R_Δ values) of sense (mRNAs) and antisense RNAs exhibit reciprocal relationships [67]. That is, high transcriptional activity of mRNAs results in a decrease in the transcription rate of the antisense transcripts, and vice versa.

FIGURE 6

A prototypical genetic module of the herpesviruses. The PRV genome exhibits a modular design composed of tandemly overlapping genes, as opposed to another tandem gene cluster in the prototypical Genetic Modules. Many tandem genes are assumed to be transcriptionally overlapping in a parallel fashion (e.g., ul42, ul43, and ul44); however, no reports have been published on this to date.

FIGURE 7

Alternative polyadenylation leads to TIN between opposing genes. The Mest and Copg2 genes are positioned in a convergent orientation relative to each other on the mouse DNA. Transcription of the Mest gene is terminated “normally,” without overlapping with the Copg2 gene in embryonic liver cells (A), whereas Mest transcription is continued within the Copg2 gene in neurons, thereby reducing the expression of this gene (B).