An increasing number of eukaryotic genes are being found to have naturally occurring antisense transcripts. Here we study the extent of antisense transcription in the human genome by analyzing the public databases of expressed sequences using a set of computational tools designed to identify sense-antisense transcriptional units on opposite DNA strands of the same genomic locus. The resulting data set of 2,667 sense-antisense pairs was evaluated by microarrays containing strand-specific oligonucleotide probes derived from the region of overlap. Verification of specific cases by northern blot analysis with strand-specific riboprobes proved transcription from both DNA strands. We conclude that > or =60% of this data set, or approximately 1,600 predicted sense-antisense transcriptional units, are transcribed from both DNA strands. This indicates that the occurrence of antisense transcription, usually regarded as infrequent, is a very common phenomenon in the human genome. Therefore, antisense modulation of gene expression in human cells may be a common regulatory mechanism.

Transcription of a gene usually ends at a regulated termination point, preventing the RNA-polymerase from reading through the next gene. However, sporadic reports suggest that chimeric transcripts, formed by transcription of two consecutive genes into one RNA, can occur in human. The splicing and translation of such RNAs can lead to a new, fused protein, having domains from both original proteins. Here, we systematically identified over 200 cases of intergenic splicing in the human genome (involving 421 genes), and experimentally demonstrated that at least half of these fusions exist in human tissues. We showed that unique splicing patterns dominate the functional and regulatory nature of the resulting transcripts, and found intergenic distance bias in fused compared with nonfused genes. We demonstrate that the hundreds of fused genes we identified are only a subset of the actual number of fused genes in human. We describe a novel evolutionary mechanism where transcription-induced chimerism followed by retroposition results in a new, active fused gene. Finally, we provide evidence that transcription-induced chimerism can be a mechanism contributing to the evolution of protein complexes.[Supplemental material is available online at www.genome.org.]Eukaryotic genes are generally well defined on the genome. Transcription usually begins from a transcription start site, which is guided by the promoter, and ends at a regulated termination point (Zhao et al. 1999;Proudfoot et al. 2002). Consecutive genes are usually separated from each other by intergenic, nonexpressed regions (Lander et al. 2001). In recent years, however, evidence for the existence of mammalian transcripts that span two adjacent, independent genes, have emerged. Typically, such chimeric transcripts begin at the promoter of the upstream gene and end at the termination point of the downstream gene. The intergenic region is spliced out of the transcript as an intron, so that the resulting fused transcripts possess exons from the two different genes (Fig. 1). This phenomenon was coined intergenic splicing or cotranscription and considered extremely rare. In human, only a handful of such transcription-induced chimeras (TICs; see also the accompanying paper by Parra et al. 2006 in this issue) were so far reported (Table 1).Fused RNAs were shown to be regulated and to have unique expression patterns. For example, the HHLA1-OC90 fusion transcript is restricted to teratocarcinoma cell lines while absent from normal cells (Kowalski et al. 1999). In the case of LY75-CD302 (CD205-DCL1) fusion, the chimera is predominant in Hodgkin and Reed-Strenberg cell lines (Kato et al. 2003). The fusion can change the properties of the participating proteins, or change their localization, such as in the case of Kua-UBE2Vl fusion, where the fused protein is localized to the cytoplasm, while UBE2Vl is a nuclear protein (Thomson et al. 2000). The most characterized human fusion transcript is of two members of the TNF ligand family, TNFSF12 (previously known as TWEAK) and TNFSF1...

Summary• Anisohydric plants are thought to be more drought tolerant than isohydric plants. However, the molecular mechanism determining whether the plant water potential during the day remains constant or not regardless of the evaporative demand (isohydric vs anisohydric plant) is not known.• Here, it was hypothesized that aquaporins take part in this molecular mechanism determining the plant isohydric threshold. Using computational mining a key tonoplast aquaporin, tonoplast intrinsic protein 2;2 (SlTIP2;2), was selected within the large multifunctional gene family of tomato (Solanum lycopersicum) aquaporins based on its induction in response to abiotic stresses. SlTIP2;2-transformed plants (TOM-SlTIP2;2) were compared with controls in physiological assays at cellular and whole-plant levels.• Constitutive expression of SlTIP2;2 increased the osmotic water permeability of the cell and whole-plant transpiration. Under drought, these plants transpired more and for longer periods than control plants, reaching a lower relative water content, a behavior characterizing anisohydric plants. In 3-yr consecutive commercial glasshouse trials, TOM-SlTIP2;2 showed significant increases in fruit yield, harvest index and plant mass relative to the control under both normal and water-stress conditions.• In conclusion, it is proposed that the regulation mechanism controlling tonoplast water permeability might have a role in determining the whole-plant ishohydric threshold, and thus its abiotic stress tolerance.

The sweet melon fruit is characterized by a metabolic transition during its development that leads to extensive accumulation of the disaccharide sucrose in the mature fruit. While the biochemistry of the sugar metabolism pathway of the cucurbits has been well studied, a comprehensive analysis of the pathway at the transcriptional level allows for a global genomic view of sugar metabolism during fruit sink development. We identified 42 genes encoding the enzymatic reactions of the sugar metabolism pathway in melon. The expression pattern of the 42 genes during fruit development of the sweet melon cv Dulce was determined from a deep sequencing analysis performed by 454 pyrosequencing technology, comprising over 350,000 transcripts from four stages of developing melon fruit flesh, allowing for digital expression of the complete metabolic pathway. The results shed light on the transcriptional control of sugar metabolism in the developing sweet melon fruit, particularly the metabolic transition to sucrose accumulation, and point to a concerted metabolic transition that occurs during fruit development.

Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron–specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron–specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a-/-) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.DOI: http://dx.doi.org/10.7554/eLife.08638.001