# Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (_SLC34A1_/Pfn3)
## 1 Introduction  
Natural antisense transcripts (NATs) are long noncoding RNAs that are partly complementary to their protein coding sense counterparts. They are fully processed, i.e., spliced,polyadenylated and capped. NATs are predominantly expressed in testis, but also in somatic tissues, mostly together with the sense transcript and at low levels [1; 2; 3]. Bi-directionally transcribed genomic loci that encode complementary transcripts were discovered in the 1980s, though the scale of antisense transcription in all kingdoms, particularly in animals, only became apparent with the breakthrough in parallel sequencing strategies. Early pipelines to mine for NATs used bioinformatic tools to identify complementary sequences within comprehensive datasets or repositories [4]. To minimize the detection of false positive calls from reverse transcription artefacts, the input data were carefully parsed using hallmarks of RNA processing such as capping, splicing and polyadenylation. As a result, these early collections of NATs included predominantly fully processed mRNA-like transcripts. NATs are depleted from the X chromosome in humans and mice, suggesting a selection against complementarity exons [5; 6; 7]. Interestingly, the bias is not evident for transcripts from bi-directionally transcribed loci that hybridize as primary transcripts but not as processed RNAs, i.e., only display intron-exon complementarity. This observation suggests that at some point during the life cycle of NATs, formation of double-stranded RNA (dsRNA) occurs. The number of bi-directionally transcribed loci detected in mammalian genomes crucially depends on specific experimental conditions and ranges between 40% and 70% [8]. Phylogenetic conservation for NATs is not clearly apparent and applies to indicators of bi-directional transcription per se, rather than primary sequence similarity [9; 10]. Nevertheless, the prevalence of NATs and their intricate relation with protein coding genes have sparked countless efforts to decipher the regulatory potential of NATs. The relative stability of NATs allows for both transcriptional and post-transcriptional modes of action, and in both cases, stimulatory as well as inhibitory effects have been reported [8]. The topic has been reviewed extensively and will only briefly be touched here [2; 11; 12; 13]. Activity on any of the DNA strands of a bi-directionally transcribed locus will lead to transcriptional interference, meaning that transcription on one strand influences the processivity on the opposite strand. Competition for transcription factors or transcription-dependent alteration of epigenetic marks generally leads to divergent expression levels of sense and antisense transcripts [13]. Conversely, if transcription on one strand facilitates access to enhancers/promoters on the other strand, a convergent sense/antisense relation may be observed. A scenario where two polymerase complexes are on collision course and 'crash' into each other is conceivable in yeast and bacterial model systems but unlikely to be of relevance in mammals [13]. NATs are fully processed mRNAs that can act as lncRNA either in the nucleus or the cytoplasm. NATs that serve as a platform for chromatin-modifying enzymes are widely documented [14]. Moreover, NATs often overlap with the 3'-UTR of the sense transcript and affect miRNA-mediated regulation of the sense transcript by masking binding sites or acting as a miRNA sponge [15]. Processed sense and antisense transcripts can also hybridize and form dsRNA [16], though the RNA hybrids come with a note of caution: Long stretches of dsRNA are reminiscent of viral structures that trigger an innate immune response and potential apoptosis [17]. Mammalian cells display a number of proteins that recognize dsRNA with different modalities and downstream effects, including ADAR (Adenosine Deaminase Rating on RNA), MDA-5 (Melanoma Differentiation Associated protein 5), Dicer and PKR (Protein Kinase R) [18].