Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms

Abstract

Many genomic loci contain transcription units on both strands, therefore two oppositely oriented transcripts can overlap. Often, one strand codes for a protein, whereas the transcript from the other strand is non-encoding. Such natural antisense transcripts (NATs) can negatively regulate the conjugated sense transcript. NATs are highly prevalent in a wide range of species--for example, around 15% of human protein-encoding genes have an associated NAT. The regulatory mechanisms by which NATs act are diverse, as are the means to control their expression. Here, we review the current understanding of NAT function and its mechanistic basis, which has been gathered from both individual gene cases and genome-wide studies. In parallel, we survey findings about the regulation of NAT transcription. Finally, we hypothesize that the regulation of antisense transcription might be tailored to its mode of action. According to this model, the observed relationship between the expression patterns of NATs and their targets might indicate the regulatory mechanism that is in action.

Figure 1

Relative orientation of cis-natural antisense transcript pairs. (A) Headto-head (5′ to 5′) overlap involving 5′-untranslated regions and coding exons. (B) Tail-to-tail (3′ to 3′) overlap. (C) Fully overlapping (one gene included entirely within the region of the other). Coloured boxes represent exons, grey boxes represent untranslated regions.

Figure 2

The main mechanisms by which natural antisense transcripts regulate gene expression. Each mechanism is accompanied by what it requires from, or imposes on, the relationship between the levels of sense and antisense transcripts. (A) Transcriptional interference. Two bulky RNA polymerase II complexes on opposite DNA strands might collide with and stall one another. The interference occurs mostly in the elongation step, resulting in either transcription arrest or transcription in one direction (sense or antisense) only. Such a mechanism might occur in cases in which inverse expression is observed. (B) RNA masking. A specific case is shown in which the antisense masks a splice site on the sense pre-mRNA sequence. This prevents a given splice variant from being formed and shifts the balance towards splice variants that do not require splicing of the masked region. Such a mechanism could be observed by correlated expression of the antisense and favoured splice variant and an inverse relationship with the repressed variant. (C) Double-stranded RNA-dependent mechanisms such as RNA editing and RNA interference require the simultaneous presence of sense and antisense transcripts for duplex formation, and might therefore account for the observed co-expression of numerous sense–antisense pairs. A delay in expression of sense compared with antisense (or vice versa) is also possible as long as there is a period in which both transcripts are present (see Fig 3). (D) Chromatin remodelling. Transcription of non-encoding antisense transcripts is involved in monoallelic gene expression, including genomic imprinting, X-inactivation and clonal expression of lymphocyte genes. In these processes, antisense transcripts have been suggested to silence the expression of nearby gene clusters by chromatin remodelling, most likely through the recruitment of histone-modifying enzymes. If such mechanisms are in action, an inverse expression profile of the antisense compared with all genes in the silenced cluster would be expected.

Figure 3

Differences in activation times of the sense compared with the antisense transcript. Such differences might be easily encoded in differential affinities to a shared transcription factor, assuming that this transcription factor is an activator and that it accumulates with time. (A) A higher affinity of the transcription factor to the sense transcript might result in a delayed shutdown, whereby the transcription factor initially activates transcription of the sense messenger RNA up to a certain level and only then is triggered by antisense transcription. The delayed antisense transcription prevents the sense transcript from exceeding the level it has reached when antisense transcription is switched on. (B) A higher affinity of the transcription factor to the antisense transcript. In this case, antisense transcription precedes sense transcription and acts as a buffer for the sense transcript. When the transcription factor accumulates, transcription of sense mRNA begins, but only sense transcripts exceeding the threshold set by the antisense level can be effectively translated. This generates a step-like function in the concentration of the sense transcript. Fluctuations in the amount of sense transcript below the threshold are dampened.

Michal Lapidot

Yitzhak Pilpel