Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay Bronwyn A. Lucasa,b, Eitan Lavic, Lily Shiued, Hana Choa,b, Sol Katzmane, Keita Miyoshia,b, Mikiko C. Siomif, Liran Carmelc, Manuel Ares Jr.d,1, and Lynne E. Maquata,b,1 aDepartment of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642; bCenter for RNA Biology, University of Rochester, Rochester, NY 14642; cDepartment of Genetics, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel; dCenter for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064; eCenter for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064; and fGraduate School of Science, University of Tokyo, Tokyo 113-0032, Japan Edited by Marlene Belfort, University at Albany, Albany, NY, and approved December 11, 2017 (received for review September 1, 2017) Primate-specific Alu short interspersed elements (SINEs) as well as from 7SL RNA, whereas B2 elements were derived from tRNA, rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated B4 elements from the fusion of a tRNAAla-derived ID element at decay (SMD) when present in mRNA 3′-untranslated regions (3′-UTRs). the 5′-end and a B1 element at the 3′-end, and ID elements from The transposable nature of SINEs, their presence in long noncoding tRNAAla or a neuronally expressed brain cytoplasmic (BC1) RNAs, their interactions with Staufen, and their rapid divergence in RNA (1, 15–17). Alu and B or ID (B/ID) SINE families emerged different evolutionary lineages suggest they could have generated after primates and rodents diverged ∼90 million years ago substantial modification of posttranscriptional gene-control networks (MYA), and have continuously amplified independently in the during mammalian evolution. Some of the variation in SMD regula- two mammalian lineages (1, 18, 19) (Fig. 1A). tion produced by SINE insertion might have had a similar regulatory Despite integrating independently in their respective genomes, effect in separate mammalian lineages, leading to parallel evolution the positions of extant Alu and B/ID elements correlate over of the Staufen network by independent expansion of lineage-specific large genomic regions (15), are predominately found in introns SINEs. To explore this possibility, we searched for orthologous gene (20), and are enriched in upstream and intronic sequences of ′ pairs, each carrying a species-specific 3 -UTR SINE and each regulated groups of genes with similar functions (21). Additionally, retro- BIOCHEMISTRY by SMD, by measuring changes in mRNA abundance after individual transposons, including SINEs, are overrepresented in the 3′- depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both UTRs of both human and mouse and correlate with decreased human and mouse myoblasts. We identified and confirmed ortholo- expression of their encoded transcripts (22). The large number, gous gene pairs with 3′-UTR SINEs that independently function in similar positioning in the human and mouse genomes, and the SMD control of myoblast metabolism.Expandingtootherspecies, analogous function of Alu and B/ID SINEs in SMD led us we demonstrated that SINE-directed SMD likely emerged in both pri- to speculate that alterations to posttranscriptional regulation mate and rodent lineages >20–25 million years ago. Our work reveals resulting from lineage-specific 3′-UTR SINE insertion may a mechanism for the convergent evolution of posttranscriptional gene have resulted in parallel alterations to gene expression in regulatory networks in mammals by species-specific SINE transposi- the two lineages. tion and SMD. Significance Staufen1 | UPF1 | Staufen-mediated mRNA decay | SINEs | convergent evolution Short interspersed elements (SINEs) are retrotransposons that have accumulated in genomes through a “copy-and-paste” hort interspersed elements (SINEs) are retrotransposable mechanism. Once inserted, these sequences have the potential SDNA sequences of ∼100–600 base pairs (bp). Lineage- to gain novel functions, including regulating gene expression. specific SINEs have expanded to now account for ∼8% of Here, we demonstrate the unexpected finding that independently mouse and ∼13% of human genomic sequences (1, 2). SINEs evolved SINEs have accumulated in the 3′-untranslated regions of that have integrated into RNA polymerase (Pol) II transcription orthologous human and mouse genes. We demonstrate that, in units have adopted an array of roles that include generating pre- some cases, this has resulted in their regulating gene expression by mRNA splice sites or polyadenylation sites, and regulating Staufen-mediated mRNA decay (SMD) in human and mouse mRNA localization or mRNA translation (3). myoblasts. Thus, SINE-directed SMD has convergently evolved to The large number of SINEs in mRNAs provides the oppor- regulate myoblast metabolism. This represents an example of the tunity for intermolecular base pairing to form a partially com- convergent evolution of posttranscriptional gene regulation plementary duplex between SINEs in, e.g., a long noncoding using SINEs. RNA (lncRNA) or another mRNA. Such duplexes can contain binding sites for the double-stranded (ds) RNA-binding pro- Author contributions: B.A.L., E.L., L.C., M.A., and L.E.M. designed research; B.A.L., E.L., teins(RBPs)Staufen(STAU)1and/orSTAU2(4–6), which, H.C., K.M., and L.C. performed research; K.M. and M.C.S. contributed new reagents/ana- when present in an mRNA 3′-UTR, can trigger STAU-mediated lytic tools; B.A.L., E.L., L.S., S.K., L.C., M.A., and L.E.M. analyzed data; and B.A.L., E.L., L.C., M.A., and L.E.M. wrote the paper. mRNA decay (SMD), a process that additionally requires the ATP-dependent RNA helicase UPF1 (4, 5, 7–9). SMD has been The authors declare no conflict of interest. implicated in the regulation of myogenesis (10, 11), adipogenesis This article is a PNAS Direct Submission. (12), cell mobility and invasion (4, 5), and stress-induced Published under the PNAS license. apoptosis (13). Data deposition: The data reported in this paper have been deposited in the Gene Ex- In primates, SMD can be triggered by base pairing between pression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE89588). Perl scripts used in this text are available on Figshare https://figshare.com under Alu elements (4, 5). Alu elements emerged from a dimer of 7SL doi:10.6084/m9.figshare.4765015. ∼ RNA and expanded in the primate lineage to 1.4 million copies 1To whom correspondence may be addressed. Email: [email protected] or lynne_maquat@ per human genome (2, 14). In rodents, which lack Alu elements, urmc.rochester.edu. homoduplexes can form between B1, B2, B4, or identifier (ID) This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. elements (11). Like Alu elements, B1 elements were derived 1073/pnas.1715531115/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1715531115 PNAS Early Edition | 1of6 Downloaded by guest on September 26, 2021 Ancestral gene found 1,192 (7.4%), wherein both orthologs are 3′-UTR SINE- A B 3' UTR SINE representation in 16,064 orthologous gene pairs containing (Fig. 1B). Similarly, 1,109 (7.0%) of the 15,736 90 MYA human Alu: 1:1 orthopairs generated by the mouse ENCODE project (24) 2,833 (17.6%) are likewise 3′-UTR SINE-containing (SI Appendix, Table S1). Mouse Human both (overlap) This overlap represents a statistically significant approximately Alu B/ID neither 10,689 1,192 (7.4%) twofold enrichment relative to a random insertion model (SI (67.9%) mouse B/ID: Appendix, Table S1). One possible source of this enrichment SMD ? SMD 3,538 (22.0%) might be parallel evolution of SMD control; however, several Number of genes upregulated upon C 106 D ′ AllAll orthologs knockdown of each protein in human correlated features of mouse and human 3 -UTRs with the po- 3'3' UTR UTR SINE-containing SINE-containing orthologs and mouse myoblasts tential to lead to biased SINE insertion also contribute to this 105 STAU1 UPF1 STAU1 UPF1 enrichment (discussed below). To search for the existence of 3′-UTR SINE-containing 104 1138 1275781 672 1077 1247 orthopairs where both orthologs are under SMD control, we sought a common biological context within which a large number 103 r=0.6266 of orthopairs would be similarly expressed, including a minimum n=9201 ′ 102 r=0.8453 of distinct mRNA isoforms with widely variable 3 -UTRs that Mouse ortholog expression n=770 599 895182 often typify different cell types and differentiation states (25). A 101 common context is also expected to depend on SMD in similar 102 103 104 105 106 human mouse Human ortholog expression ways, as the efficiency of SMD can vary among different cell types Orthologous genes subject to SMD – E F and can change during the process of differentiation (10 12). We 3' UTR SINE representation in 182 chose human hSkMc skeletal muscle myoblasts (hMBs) and 2 orthologous gene pairs subject to SMD SLC7A2 r=0.3699 mouse C2C12 skeletal muscle myoblasts (mMBs), knowing that in myoblasts 1.5 n=21 SMD targets in: PDK1 GPR155 Both species SMD is efficient in mMBs (4, 10, 11), and expecting it would also human Alu: 1 Human only be efficient in hMBs. Triplicate cultures of MBs from each species 46 (25.3%) DCUN1D22 SNX27 Mouse only Neither were treated with control or SMD factor-targeting siRNA, either neither 0.5 PHLPP2 + both (overlap): ZNRF3 Not tested 108 STAU1 siRNA or UPF1 siRNA, and poly(A) RNA from each 24 (13.2%) (59.1%) ortholog expression 0 AAK1ING5 condition was sequenced and analyzed (see below) using DESeq Log2-fold change in mouse 0.0 0.5 1.0 1.5 2.0 2.5 3.0 mouse B/ID: (26).