U1 Snrnp Regulates Chromatin Retention of Noncoding Rnas

Article U1 snRNP regulates chromatin retention of noncoding RNAs https://doi.org/10.1038/s41586-020-2105-3 Yafei Yin1 ✉, J. Yuyang Lu1, Xuechun Zhang1, Wen Shao1, Yanhui Xu1, Pan Li1,2, Yantao Hong1, Li Cui1, Ge Shan3, Bin Tian4, Qiangfeng Cliff Zhang1,2 & Xiaohua Shen1 ✉ Received: 26 November 2018 Accepted: 9 January 2020 Long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable Published online: xx xx xxxx transcripts locate preferentially to chromatin, where some regulate chromatin structure, Check for updates transcription and RNA processing1–13. Although several RNA sequences responsible for nuclear localization have been identifed—such as repeats in the lncRNA Xist and Alu-like elements in long RNAs14–16—how lncRNAs as a class are enriched at chromatin remains unknown. Here we describe a random, mutagenesis-coupled, high-throughput method that we name ‘RNA elements for subcellular localization by sequencing’ (mutREL-seq). Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucleoprotein (snRNP) and is essential for the localization of reporter RNAs to chromatin. Across the genome, chromatin-bound lncRNAs are enriched with 5′ splice sites and depleted of 3′ splice sites, and exhibit high levels of U1 snRNA binding compared with cytoplasm-localized messenger RNAs. Acute depletion of U1 snRNA or of the U1 snRNP protein component SNRNP70 markedly reduces the chromatin association of hundreds of lncRNAs and unstable transcripts, without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear and genome-wide localization of the lncRNA Malat1. Moreover, U1 snRNP interacts with transcriptionally engaged RNA polymerase II. These results show that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a transcription-dependent manner. Our fndings have uncovered a previously unknown role of U1 snRNP beyond the processing of precursor mRNA, and provide molecular insight into how lncRNAs are recruited to regulatory sites to carry out chromatin-associated functions. To identify cis elements that contribute to the localization of RNA to Data Fig. 1g–j and Supplementary Note 2). The majority of enChrs over- chromatin, we developed and performed REL-seq screens with satu- lap with predicted U1-recognition sites and/or exhibit strong binding rated fragment coverage of nine representative lncRNA and mRNA signals of U1 snRNA, as shown by RNA affinity purification followed transcripts in mouse and human cells (Extended Data Fig. 1a–f and by RNA sequencing (RAP–RNA-seq)17, except for repeat-associated Supplementary Note 1). The strategy involves expressing a randomly enChrs in Xist (Extended Data Figs. 1k, 2, Supplementary Table 2 and fragmented RNA sequence alone or fusing it with a minigene encod- Supplementary Discussion 1). ing green fluorescent protein (GFP), and then analysing its subcellular U1 snRNP defines the 5′ splice sites of pre-mRNAs and initiates location through sequencing. We detected a total of 26 chromatin- spliceosome assembly at introns—a process that involves sequential enriched RNA fragments (enChrs; P < 0.05), mainly 50–500 nucleotides recruitments of U1, U2 and then U4/U6–U5 tri-snRNPs18. It has been in length, in the sense orientation of the host chromatin-associated reported that the 5′ splice site regulates the nuclear retention of a hand- RNAs but not in cytoplasm-located mRNAs (Extended Data Fig. 2 and ful of mRNAs19,20. To test a role of U1 recognition in RNA–chromatin Supplementary Tables 1, 2). To uncover key residues that contribute retention, we constructed GFP reporters that harbour U1 motifs but to RNA localization, we chose a 162-nucleotide NXF1-enChr, identi- lack the 3′ splice site, in vectors containing either a polyadenylation fied from an isoform of NXF1 in which the introns are retained in the signal (PAS) or a Malat1 3′-end sequence (Extended Data Fig. 3a, b). final mRNA, for random mutagenesis followed by REL-seq (mutREL- The Malat1 3′-end sequence stabilizes GFP RNA through a triple-helix seq; Extended Data Figs. 1b, 2g). Out of 23 mutations with impaired RNA structure21,22, thus bypassing the inhibitory effect of U1 snRNP chromatin binding, 19 are located in a loop region (positions 39–45) on polyadenylation and RNA stability23. The wild-type but not mutant containing 7 nucleotides, which, together with 2 upstream nucleo- U1-targeting sequences promoted the chromatin association of GFP in tides, comprise a U1-recognition site that base pairs perfectly with the both the PAS and the 3′ Malat1 reporters (Extended Data Fig. 3c–g and 9-nucleotide 5′ targeting sequence of U1 snRNA (Fig. 1a, b, Extended Supplementary Note 3). In addition, NXF1-enChr RNA captured core 1Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China. 2Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. 3School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, China. 4Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, USA. ✉e-mail: [email protected]; [email protected] Nature | www.nature.com | 1 Article a mutREL-seq c Strong U1 site (exon) d Chromatin localization –64 4. 5 39–45{ 15 P = 4.1 × 10 P = 0 P = 2.9 10–14 s × A T C G – l P = 0 5 20 3. 5 1.5 12 U1 site 0.51 0.63 4 73G>C 1.0 0.40 2. 5 0.29 3 edicted site per kilobase 0.5 2 1.20 1.98 Pr omatin per cel 0.57 1 0.28 1. 5 0.0 Chr 0 3′ss (gene body) Cytosol/chromatin ratio (normalized to wild type) U1 RAP-RNA –165 51G>C P = 6.3 10 –96 0. 5 15 × P = 3.2 × 10 31 36 41 46 51 56 61 66 71 76 s ) P = 3.8 × 10–22 Position (nucleotide) 5 P = 2.1 × 10–161 3 40 b 3′ 20 1.58 ···· NXF1-enChr 01 2 1.40 1.27 10 G 37 (partial) 1.16 edicted site U per kilobase A C 1 3.77 5.24 A G Pr 3.05 C G 34 G G G ··· 5 39 CG U C C 5′ 1.81 C G CC 0 U 42 G GG A G G U A U ··· 3′ 0 RNA RAP per input (exonic A 45 G A c Cyto===>>>Chr 5 · U A lncRNA mRNA ln mRNA ′ Ψ Ψ C A G G U A capcap 5′ mRNA U1 snRNA Sense Reverse- lncRNA(97) complementary (2262 each) Fig. 1 | MutREL-seq identifies a U1-recognition site that contributes to (bottom) of lncRNAs (U1 site: n = 3,385; 3′ss: n = 7,661) and mRNAs (U1 site: RNA–chromatin tethering. a, MutREL-seq identifies a seven-nucleotide n = 47,298; 3′ss: n = 78,227) in mice. Genes with transcript length (for U1 sites) or region (dashed box) that contributes to chromatin retention of NXF1-enChr. genomic length (for 3′ss) of more than 1 kilobase (kb) were analysed. The y axis shows the fold change of cytoplasmic versus chromatin signals, d, Enrichment in chromatin localization (top) and U1 RAP–RNA signals normalized to that in wild-type cells. Grey dots indicate deletions. b, Predicted (bottom) in mRNAs (n = 2,262 genes in each group) and lncRNAs (n = 97; secondary structure of NXF1-enChr and its interaction with U1 snRNA. Ψ:G fragments per kilobase per million mapped reads (FPKM) of more than 1; no wobble base-pairing is indicated by dots. The scale bar shows the probability of overlap with mRNA) that are ranked from low to high levels of chromatin base-pairing (or lack of pairing). c, Densities of predicted strong U1- association (left to right). For c and d, box plots show 5th, 25th, 50th, 75th and recognition sites in exons (top) and 3′ splice sites (3′ss) in the gene body 95th percentiles, with median values labelled. P-values, two-sided t-tests. components of U1 snRNP, whose knockdown impaired the chromatin had a minor effect on the expression of the lncRNAs analysed, and did not binding of reporter RNA (Extended Data Fig. 3h–m, Supplementary elicit apoptosis (Extended Data Fig. 5g–k). Consistently, total RNA-seq of Table 3 and Supplementary Note 4). To test a role of the 3′ splice site auxin-treated SNRNP70AID mESCs revealed 346 chromatin-downregulated in RNA localization, we inserted an ACTB intron into a GFP reporter. lncRNAs (27%; P < 0.05), which substantially overlap with those affected Mutation of the 3′ splice site dramatically increased chromatin-bound by U1 AMOs and show increased signals in the cytoplasm and/or nucleo- GFP RNA, in a manner dependent on an intact 5′ U1 site (Extended Data plasm fractions (Fig. 2, Extended Data Figs. 5f, l, m, 6 and Supplementary Fig. 3n). These results demonstrate that U1 snRNP promotes the chro- Table 5). The sets of chromatin-downregulated lncRNAs following U1 matin association of a reporter RNA that harbours a 5′ U1-recognition AMO and/or SNRNP70AID treatment exhibit stronger U1 snRNA binding site but lacks the 3′ splice sequence. activities and higher expression levels compared with lncRNAs that are not Although U1 motifs tend to be depleted in gene exons, lncRNA tran- downregulated, providing evidence that U1 snRNP promotes chromatin scripts exhibit substantially higher densities of the U1-recogntion motif association of its target lncRNAs (Extended Data Fig. 5n). in exons, yet lower densities of 3′ splice sites in the gene body, com- We then investigated whether the U1 mechanism regulates the locali- pared with mRNA (Fig.

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