The Tug1 lncRNA locus is essential for male fertility

Jordan P Lewandowski,Gabrijela Dumbović,Abigail F Groff,Hopi E Hoekstra,Martin Sauvageau,Chiara Gerhardinger,Kyle M Turner,Nimrod D Rubinstein,Taeyoung Hwang,Christian Much,Emily Jacobs-Palmer,Christopher Kirby,Audrey R Watson,Steve C Liapis,Nydia Chang,John G Clohessy,Pier Paolo Pandolfi,John L Rinn,Assaf Bester

doi:10.1186/s13059-020-02081-5

Abstract

BackgroundSeveral long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA function has been a challenge due to their diverse biological roles and because lncRNA loci can contain multiple molecular modes that may exert function.ResultsWe previously generated and characterized a cohort of 20 lncRNA loci knockout mice. Here, we extend this initial study and provide a more detailed analysis of the highly conserved lncRNA locus, taurine-upregulated gene 1 (Tug1). We report that Tug1-knockout male mice are sterile with underlying defects including a low number of sperm and abnormal sperm morphology. Because lncRNA loci can contain multiple modes of action, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region have any activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors two distinct noncoding regulatory activities, as a cis-DNA repressor that regulates neighboring genes and as a lncRNA that can regulate genes by a trans-based function. We also show that Tug1 contains an evolutionary conserved open reading frame that when overexpressed produces a stable protein which impacts mitochondrial membrane potential, suggesting a potential third coding function.ConclusionsOur results reveal an essential role for the Tug1 locus in male fertility and uncover evidence for distinct molecular modes in the Tug1 locus, thus highlighting the complexity present at lncRNA loci.

Highlights

Several long noncoding RNAs have been shown to function as components of molecular machines that play fundamental roles in biology
The taurine-upregulated gene 1 (Tug1) long noncoding RNAs (lncRNAs) locus is widely expressed and highly conserved The murine Tug1 lncRNA locus is located on chromosome 11 and has three annotated transcripts (Fig. 1a)
The Tug1 locus is enriched with hallmarks of active transcription, such as RNA polymerase II (Pol II) and histone H3 lysine 4trimethylation (H3K4me3) at its promoter, H3K36me3 across its gene body, and abundant transcription as shown by RNA-seq (Fig. 1a)

Summary

Introduction

Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. LncRNAs have been found to possess open reading frames (ORFs) [13, 14], and an increasing number have been found to encode proteins with biological roles [15,16,17,18,19]. With this in mind, it is likely that more regulatory DNA, RNA, and hidden protein activities will be uncovered at lncRNA loci. Identifying the molecular activities present at lncRNA loci is important for further functional dissection of phenotypes attributed to lncRNA loci

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Discussion

Conclusion