title: SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells.
abstract: Despite recent efforts in discovering novel long non-coding RNAs (lncRNAs) and unveiling their functions in a wide range of biological processes their applications as biotechnological or therapeutic tools are still at their infancy. We have recently shown that AS Uchl1, a natural lncRNA antisense to the Parkinson's disease-associated gene Ubiquitin carboxyl-terminal esterase L1 (Uchl1), is able to increase UchL1 protein synthesis at post-transcriptional level. Its activity requires two RNA elements: an embedded inverted SINEB2 sequence to increase translation and the overlapping region to target its sense mRNA. This functional organization is shared with several mouse lncRNAs antisense to protein coding genes. The potential use of AS Uchl1-derived lncRNAs as enhancers of target mRNA translation remains unexplored. Here we define AS Uchl1 as the representative member of a new functional class of natural and synthetic antisense lncRNAs that activate translation. We named this class of RNAs SINEUPs for their requirement of the inverted SINEB2 sequence to UP-regulate translation in a gene-specific manner. The overlapping region is indicated as the Binding Doman (BD) while the embedded inverted SINEB2 element is the Effector Domain (ED). By swapping BD, synthetic SINEUPs are designed targeting mRNAs of interest. SINEUPs function in an array of cell lines and can be efficiently directed toward N-terminally tagged proteins. Their biological activity is retained in a miniaturized version within the range of small RNAs length. Its modular structure was exploited to successfully design synthetic SINEUPs targeting endogenous Parkinson's disease-associated DJ-1 and proved to be active in different neuronal cell lines. In summary, SINEUPs represent the first scalable tool to increase synthesis of proteins of interest. We propose SINEUPs as reagents for molecular biology experiments, in protein manufacturing as well as in therapy of haploinsufficiencies.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy ; Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Zucchelli
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Fasolo
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Russo
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Cimatti
authors.affiliation: Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Patrucco
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan.
authors.forename: Hazuki
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Cell Guidance Systems Cambridge, UK.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Jones
authors.affiliation: Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Santoro
authors.affiliation: Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Sblattero
authors.affiliation: Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Cotella
authors.affiliation: Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Persichetti
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan.
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience Trieste, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
keywords: SINEUP; antisense; cell lines; long non-coding RNA; protein expression