Transcription is common at active mammalian enhancers sometimes giving rise to stable and unidirectionally transcribed enhancer-associated long intergenic noncoding RNAs (elincRNAs). ElincRNA expression is associated with changes in neighboring gene product abundance and local chromosomal topology, suggesting that transcription at these loci contributes to gene expression regulation in cis. Despite the lack of evidence supporting sequence-dependent functions for most elincRNAs, splicing of these transcripts is unexpectedly common. Whether elincRNA splicing is a mere consequence of their cognate enhancer activity or if it directly impacts enhancer-associated cis-regulation remains unanswered.Here we show that elincRNAs are efficiently and rapidly spliced and that their processing rate is strongly associated with their cognate enhancer activity. Our results highlight an unexpected contribution of elincRNA splicing to enhancer function.

To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes.How an effective stoichiometry of this many constituent subunits is co-ordinated posttranscriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation (OXPHOS) and, with miR-488-3p, represent novel targets for the modulation of complex I activity.

1Pervasive enhancer transcription is at the origin of more than half of all long 2 noncoding RNAs in humans. Transcription of enhancer-associated long 3 noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and 4 gene expression regulation in cis. Recently, splicing of elncRNAs was shown 5 to be associated with elevated enhancer activity. However, whether splicing of 6 elncRNA transcripts is a mere consequence of accessibility at highly active 7 enhancers or if elncRNA splicing directly impacts enhancer function, remains 8 unanswered. 9We analysed genetically driven changes in elncRNA expression, in humans, to 10 address this outstanding question. We showed that splicing related motifs 11 within multi-exonic elncRNAs evolved under selective constraints during human 12 evolution, suggesting the processing of these transcripts is unlikely to have 13 resulted from transcription across spurious splice sites. Using a genome-wide 14 and unbiased approach, we used nucleotide variants as independent genetic 15 factors to directly assess the causal relationship that underpin elncRNA splicing 16and their cognate enhancer activity. We found that the splicing of most 17 elncRNAs is associated with changes in chromatin signatures at cognate 18 enhancers and target mRNA expression. 19We conclude that efficient and conserved processing of enhancer-associated 20 elncRNAs contributes to enhancer activity. 21 22

Quorum sensing (QS) is a regulatory process achieved via cell-to-cell communication that involves release and detection of autoinducers (AIs), and which occurs in a wide range of bacteria. To date, QS has been associated with events of pathogenesis, biofilm formation, and antibiotic resistance in clinical, industrial, and agricultural contexts. The main objective of this study was to characterise the role of N-Acyl homoserine lactone (AHL) type QS in Hafnia alvei FB1, a bacterial strain isolated from frozen vacuum-packed fish paste meatballs, via identification of QS core genes using a genomic approach, followed by comparative transcriptomic profiling between QS-deficient mutants and wild-type strains. H. alvei FB1 is known to produce two types of AHLs, namely, N-(3-oxohexanoyl) homoserine lactone (3OC6-HSL) and N-(3-oxooctanoyl) homoserine lactone (3OC8-HSL). The complete genome sequence of strain FB1 was obtained and a single gene for AHL synthase (halI) and its cognate receptor (halR) were identified. QS-deficient mutants of FB1 were constructed via the λ-Red recombineering method. Removal of the QS genes in strain FB1 affected mainly mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment.Impact statement: Members of the genus Hafnia are known as opportunistic pathogens in both nosocomial and community-acquired infections. However, the involvement and mechanism of pathogenesis of Hafnia in infectious diseases remains uncertain. We investigatd the role of the signalling molecule group, N-acyl homoserine lactones (AHLs), in a Hafnia alvei strain, since AHLs play important roles in pathogenicity, survival or adaptation in other pathogens. The comparative transcriptomic study revealed that AHLs are involved in mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment. These findings provide insight into possible strategies to combat this opportunistic pathogen.