- Research article
- Open Access
Species-specific alternative splicing leads to unique expression of sno-lncRNAs
- Xiao-Ou Zhang†1,
- Qing-Fei Yin†2,
- Hai-Bin Wang3,
- Yang Zhang2,
- Tian Chen2,
- Ping Zheng4,
- Xuhua Lu3,
- Ling-Ling Chen2Email author and
- Li Yang1Email author
© Zhang et al.; licensee BioMed Central Ltd. 2014
- Received: 19 September 2013
- Accepted: 3 April 2014
- Published: 16 April 2014
Intron-derived long noncoding RNAs with snoRNA ends (sno-lncRNAs) are highly expressed from the imprinted Prader-Willi syndrome (PWS) region on human chromosome 15. However, sno-lncRNAs from other regions of the human genome or from other genomes have not yet been documented.
By exploring non-polyadenylated transcriptomes from human, rhesus and mouse, we have systematically annotated sno-lncRNAs expressed in all three species. In total, using available data from a limited set of cell lines, 19 sno-lncRNAs have been identified with tissue- and species-specific expression patterns. Although primary sequence analysis revealed that snoRNAs themselves are conserved from human to mouse, sno-lncRNAs are not. PWS region sno-lncRNAs are highly expressed in human and rhesus monkey, but are undetectable in mouse. Importantly, the absence of PWS region sno-lncRNAs in mouse suggested a possible reason why current mouse models fail to fully recapitulate pathological features of human PWS. In addition, a RPL13A region sno-lncRNA was specifically revealed in mouse embryonic stem cells, and its snoRNA ends were reported to influence lipid metabolism. Interestingly, the RPL13A region sno-lncRNA is barely detectable in human. We further demonstrated that the formation of sno-lncRNAs is often associated with alternative splicing of exons within their parent genes, and species-specific alternative splicing leads to unique expression pattern of sno-lncRNAs in different animals.
Comparative transcriptomes of non-polyadenylated RNAs among human, rhesus and mouse revealed that the expression of sno-lncRNAs is species-specific and that their processing is closely linked to alternative splicing of their parent genes. This study thus further demonstrates a complex regulatory network of coding and noncoding parts of the mammalian genome.
- Alternative splicing
Although only about 2% of the human genome encodes protein sequences [1, 2], recent advances in genomewide analyses have revealed that the majority of the human genome is transcribed [3, 4], largely from noncoding segments that used to be considered as “junk sequences” or “dark matter” [5, 6]. Besides well-characterized housekeeping noncoding RNAs (such as tRNA, rRNA, snRNA and snoRNA) and small regulatory ncRNAs [7, 8], the transcriptome has become even more complex with pervasively transcribed long noncoding RNAs (lncRNAs, at least 200 nt long) [4, 9, 10]. Using systematic and integrative strategies and by considering multiple biological features, thousands of lncRNAs were identified from intergenic regions (long intergenic noncoding RNAs, lincRNAs) in mouse , zebrafish  and human  genomes. Importantly, the strategy of lincRNA discovery has served as a road map for the systematic annotation of other lncRNAs.
In addition to intergenic regions, introns account for over 20% of noncoding sequences in the human genome and provide yet another source to generate lncRNAs. By removal of redundant rRNAs and poly(A)+ RNAs, a relatively pure population of non-polyadenylated and non-ribosomal (poly(A)-/ribo-) RNAs was obtained and subjected to high-throughput deep sequencing . This type of poly(A)- RNA-seq of the human cell transcriptomes surprisingly revealed previously-ignored RNA signals in exons and introns [14–16]. Interestingly, nuclear fractionation also indicated the presence of stable transcripts from intronic sequences in X. tropicalis . What mechanism(s) can protect these excised introns from rapid degradation after splicing? Further analyses revealed a class of intron-derived lncRNAs that depend on the snoRNA machinery at both ends for their processing (sno-lncRNAs) . This finding shed new light on lncRNA characterization from “junk” intronic sequences.
Strikingly, five sno-lncRNAs derived from introns of the Prader-Willi syndrome (PWS) region (15q11-q13) were highly expressed in human embryonic stem cells and strongly associated with Fox family splicing regulators to alter patterns of splicing . The PWS 15q11-q13 region is imprinted, leading to the expression of the SNURF-SNRPN gene and downstream noncoding region from the paternal chromosome. All paternal transcripts downstream of the SNRPN gene are noncoding and have been considered primarily as precursors for small RNAs, including the SNORD116 cluster of 29 similar snoRNAs [18, 19]. Importantly, SNORD116 deficiency has been recognized as the primary cause of PWS in recent disease model [20–22]. Although the function of SNORD116s remained elusive, the recently identification of PWS region sno-lncRNAs and their association with Fox family splicing regulators offers a functional connection of sno-lncRNAs in the molecular pathogenesis of PWS . However, it was not clear how many other sno-lncRNAs may exist in the genome. Given that the vast majority of snoRNAs are encoded in introns of protein-coding genes , it was of interest to annotate sno-lncRNAs in a genomewide manner. Moreover, signals of poly(A)- transcripts from intronic regions have been widely detected in a variety of cultured cells , which has provided a rich data source to explore sno-lncRNAs from different cell lines.
Here, we applied computational pipelines to identify sno-lncRNAs genome-widely from poly(A)-/ribo- transcriptomes of human, rhesus and mouse. In total, 19 sno-lncRNAs have been identified with tissue- and species-specific expression patterns from available species/cell lines. PWS region sno-lncRNAs are highly expressed in human, somewhat in rhesus, and none in mouse. In contrast, a RPL13A region sno-lncRNA is highly expressed in mouse, but almost absent in human. We further demonstrated that the formation of sno-lncRNAs often requires alternative splicing, indicating a complex regulatory network of coding and noncoding parts of the genome.
Genomewide identification of sno-lncRNAsacross species
Summary of sno-lncRNAs identified from human, rhesus and mouse ESCs
Expression level (RPKM)
Validated by NB
Additional file 1
Additional file 2
ENCODE Cell Lines
human sno-IncRNA3 homologue
human sno-IncRNA4 homologue
RPL13A region sno-IncRNA homologue
RPL13A region sno-IncRNA
To further explore sno-lncRNA candidates, we developed a custom computational pipeline to predict sno-lncRNAs by integrating snoRNA annotations with poly(A)-/ribo- RNA-seq datasets from human , rhesus and mouse (GEO:GSE53942) (Figure 1B, Methods). By applying this pipeline to multiple poly(A)-/ribo- RNA-seq datasets, 19 sno-lncRNAs were identified from different species and/or different cell lines (Table 1). Two additional sno-lncRNAs were predicted in H9 cells and, importantly, both could be validated by Northern blots in human H9, HeLa-J and PA1 cells (Additional file 1). Three more sno-lncRNAs were further predicted from ENCODE cell lines (Table 1), suggesting that more sno-lncRNAs could be identified when this prediction pipeline is applied to other trancriptomes. Furthermore, it is expected that more sno-lncRNAs will be identified after improvements in snoRNA annotation. Interestingly, only one sno-lncRNA could be predicted from the entire mouse ESC transcriptomes used in this study (Table 1). This mouse sno-lncRNA could be validated by Northern blots from different murine cell lines, as indicated below, but its homolog expression was much lower in rhesus and undetectable in human.
Low conservation of sno-lncRNAswith highly conserved snoRNA ends
PWS region sno-lncRNAsare highly expressed in human, but undetectable in mouse
The genomic context of the PWS region is complex and the characterization of this region across species is still lacking comprehensive analysis. We first examined the genomic context of PWS region sno-lncRNAs by comparing their genomic sequences from different species. Given that sno-lncRNA formation depends on snoRNA sequences at both ends within a single intron, the highly conserved PWS region SNORD116 snoRNAs suggested the likelihood of the formation of PWS region sno-lncRNAs in other species. Compared to five in human (Figure 4A and Additional file 3), interrogation of poly(A)-/ribo- RNA-seq datasets revealed only two PWS region sno-lncRNAs from alternative spliced introns in rhesus ESC cells (Figure 4B and Additional file 4), but none in mouse cells (Figure 4C and Additional file 5). In addition, no clear evidence for PWS region sno-lncRNAs could be found in mouse brain/hippocampus in which the SNURF-SNRPN transcript and its downstream noncoding region are highly transcribed (Additional file 5), further indicating the absence of PWS region sno-lncRNAs in mouse.
SNORD116 snoRNAs are highly conserved from human and rhesus to mouse (Figure 3C and Additional file 3); however, obvious differences in their genomic locations were observed in the PWS region. In human/rhesus genomes, SNORD116s are located in introns of the parent SNURF-SNRPN transcript and some of them form snoRNA pairs in one alternative spliced intron, which results in the formation of sno-lncRNAs (Figures 4A and B). In the mouse genome, SNORD116s are located in introns of a series of spliced ESTs, which are located at least 50 kb away from the SNURF-SNRPN locus (Figure 4C and Additional file 5). Although there are expressed signals of spliced ESTs in the mouse hippocampus transcriptome (Additional file 5), no SNORD116 snoRNA pairs were found between these spliced ESTs, thus no sno-lncRNAs could be generated from this region in mouse. Taken together, although snoRNA ends are essential for the formation of sno-lncRNAs, the existence of highly-conserved snoRNAs alone is not sufficient for their formation.
The genomic region encoding 15q11-13 sno-lncRNAs is specifically deleted in human PWS. PWS is a multiple system disorder with a minimal paternal deletion in chr15 . The deficiency of SNORD116 snoRNAs within the minimal deletion has been thought to play an important role in the pathogenesis of PWS [20–22]. However, mouse models with SNORD116 deletions can only partially mimic PWS phenotypes, including metabolism and growth deficiency, but not obesity [28, 29]. Although the mechanism of PWS pathogenesis still remains mysterious, the recent finding of sno-lncRNAs in the PWS region in human and their regulatory function in splicing has offered an additional functional layer of gene regulation underlying PWS pathogenesis . The finding of no expression of PWS region sno-lncRNAs in mouse indicates a possible limitation of the use of mouse models to study human PWS.
Characterization of PWS region sno-lncRNAs in rhesus revealed that they sequester Fox proteins like human sno-lncRNAs
Sequence alignment of SNORD116 snoRNAs and their parent SNURF-SNRPN exons revealed that two PWS region sno-lncRNAs in rhesus are similar to human PWS region sno-lncRNA3 and sno-lncRNA4, respectively. Although predicted rhesus SNORD116 snoRNAs are scattered among individual introns (Figure 5A), de novo assembly with rhesus poly(A)+ RNA-seq revealed a variety of alternatively spliced SNURF-SNRPN transcripts in rhesus, thus leading to the formation of sno-lncRNAs in rhesus SNURF-SNRPN region (Figure 4B, transcripts from de novo assembly shown in thick black lines).
Human PWS region sno-lncRNAs could function as molecular sponges by associating with Fox family splicing regulators and altering patterns of splicing . Due to the high similarity of rhesus PWS region sno-lncRNAs with human in the genomic context, we reasoned that they might function similarly as well. We thus scanned the rhesus sno-lncRNA sequence for Fox binding motifs, and identified an enrichment of Fox binding sites (Figure 5B), further indicating that rhesus PWS region sno-lncRNAs might also interact with Fox family splicing regulators and play a similar role in splicing regulation. On the other hand, the absence of PWS region sno-lncRNAs in mouse indicated that a similar regulation mechanism is absent in mouse.
In sum, PWS region sno-lncRNAs are highly expressed in human and rhesus, but are absent in mouse. The absence of PWS region sno-lncRNAs in mouse also suggests one possible reason to explain the failure of current mouse deletion models to fully recapitulate pathological features of human PWS [27–29]. However, we cannot exclude other regulatory pathways or mechanisms during PWS pathogenesis.
A non-human sno-lncRNAand its possible association with the regulation of lipid toxicity
SnoRNAs within RPL13A introns are critical mediators of lipotoxic cell death in both hamster and mouse . Lipotoxic stress strongly induces expression of these snoRNAs, but has no effect on the steady state levels of the parent RPL13A gene . While it is unclear whether RPL13A region sno-lncRNA is also involved in lipotoxicity like its snoRNA ends, our finding offers another possible regulation for gene expression in this region and it will be of interest to study the function of this RPL13A region sno-lncRNA.
Species-specific alternative splicing leads to the formation of the RPL13A region sno-lncRNAin the mouse
The analyses of PWS region sno-lncRNAs and the mouse RPL13A region sno-lncRNA strongly indicated that sno-lncRNAs are expressed in a species-specific manner. To determine whether there are differences in the biogenesis process of sno-lncRNAs in different species, we individually transfected expression vectors for mouse sno-lncRNA into human cells or expression vectors for human sno-lncRNA into mouse cells. Interestingly, both species-specific sno-lncRNAs could be recapitulated in cultured cells from other species (Additional file 9), suggesting that species-specificity of sno-lncRNAs is mainly derived from their genomic context instead of from the underlying biogenesis machinery.
Very interestingly, further analyses revealed that the specific RPL13A alternative splicing event that leads to the production of sno-lncRNA could also generate a protein of altered amino acid sequence in both mouse (Figure 7D) and rhesus (data not shown), although the change of protein sequence and its consequence need to be further experimentally confirmed. As a 60S ribosomal subunit protein, RPL13A is highly conserved across species and plays an essential role in protein synthesis. Therefore, the finding of alternative splicing of RPL13A has implicated a possible role in the regulation of 60S ribosome assembly or function in a species-specific manner. Since a large diversification of splicing exists between tissues and species [31, 32] and sno-lncRNAs are expressed with tissue- and species-specific patterns, it quite likely that more such RNAs will be uncovered when additional tissues and species samples are examined. Taken together, alternative splicing not only increases the diversity of coding mRNAs/proteins, but also expands transcriptome complexity by promoting the formation of noncoding RNAs from untranslated intron sequences.
We explored non-polyadenylated transcriptomes (poly(A)-/ribo-) from human, rhesus and mouse, and systematically annotated sno-lncRNAs across species. Although primary sequence analysis revealed that snoRNA ends of such molecules are highly conserved, PWS region sno-lncRNAs are highly expressed in human and rhesus, but absent in mouse. The absence of PWS region sno-lncRNAs in mouse suggested a possible reason for the failure of the current mouse model to fully recapitulate pathological features of human PWS. Only one mouse sno-lncRNA was identified from the limited available mouse datasets in RPL13A region, and snoRNAs themselves in this region have been suggested to be involved in lipotoxicity in mouse. Our results also demonstrated that the formation of sno-lncRNAs often requires alternative splicing within their parent genes, indicating a complex regulatory network of coding and noncoding parts of the genome.
Annotation of snoRNAs across species
Annotated human snoRNAs derived from snoRNABase  (https://www-snorna.biotoul.fr/) were downloaded from UCSC Genome Bioinformatics database (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz, updated on 2010/10/3). 132 mouse snoRNA annotations were downloaded from RefSeq database (http://www.ncbi.nlm.nih.gov/refseq/, downloaded on 2013/3/4). 375 putative rhesus snoRNAs were transposed from human and mouse snoRNA annotations using liftOver (http://genome.ucsc.edu/cgi-bin/hgLiftOver) with minMatch = 0.95 and combined together to be used as rhesus snoRNA annotations. All these snoRNA annotations were overlapped respectively with relevant gene annotations according to their species-derivation (Human: UCSC Genes, updated on 2012/2/5; Rhesus: RefSeq Genes, updated on 2013/3/24; Mouse: UCSC Genes, updated on 2011/5/30) to find snoRNA pairs (at least two snoRNAs in one intron) in introns, as indicated in Figure 1A. SnoRNA pairs in the same introns were further examined from poly(A)-/ribo- RNA-seq datasets to identify putative sno-lncRNAs.
Sequencing read alignment and transcript de novoassembly
The poly(A)+ or poly(A)-/ribo- RNA-seq reads were uniquely aligned to relevant genomes (Human: hg19, GRCh37; Rhesus: rheMac3, BGI CR_1.0; Mouse: mm9, NCBI37) using TopHat 2.0.8  (parameters: -g 1 -a 6 -i 50 --microexon-search --coverage-search -m 2) with existing annotations (Human: UCSC Genes, updated on 2012/2/5; Rhesus: RefSeq Genes, updated on 2013/3/24; Mouse: UCSC Genes, updated on 2011/5/30), respectively. To facilitate the identification of potential sno-lncRNAs, Bowtie 0.12.9  (parameters: -v 3 -k 1 -m 1) was also employed to map poly(A)-/ribo- RNA-seq reads to annotated genome references. Expression level (RPKM) of annotated genes (including snoRNAs) was obtained with customized pipeline (Zhu et al., in preparation). Cufflinks v2.0.2  (parameters: -F 0) was employed to assemble poly(A)+ RNA-seq mapping results to obtain de novo RNA transcripts. All mapping results were normalized and uploaded to the UCSC Genome Browser (http://genome.ucsc.edu/) for visualization.
Computational pipeline to identify sno-lncRNAsfrom poly(A)-/ribo- RNA-seq datasets
To systematically identify sno-lncRNAs independently from known gene annotation, we developed a custom sno-lncRNA identification pipeline (termed as SNOLNCfinder), as indicated in Figure 1B. Briefly, for each two adjacent snoRNAs (distance < 10 kb), RPKMs of snoRNA regions and their internal regions were calculated with a customized pipeline (Zhu et al., in preparation) from Bowtie mapped poly(A)-/ribo- RNA-seq reads. A putative sno-lncRNA was selected with 1) both snoRNA pairs are expressed with RPKM ≥ 1; 2) at least 80% of the internal region between snoRNA pairs have poly(A)-/ribo- RNA-seq signals by sliding window examination (Figure 1B); and 3) relatively high expression of the internal region (at least 40% of expression of snoRNA pairs). All candidates were manually inspected by comparing the poly(A)+ and poly(A)-/ribo- RNA-seq datasets. This pipeline is independent on known gene annotation and can be successfully employed in human, rhesus and mouse datasets to identify new sno-lncRNAs. RNA-seq datasets used here were from human ESC H9 cells and HeLa cells(GEO:GSE24399), ENCODE cell lines (GEO: GSE26284). RNA-seq files for rhesus ESCs, mouse ESCs and mouse hippocampus can be accessed from the NCBI Sequence Read Archive by Gene Expression Ominbus accession number (GEO:GSE53942).
Genomic sequence comparison with VISTA
VISTA Browser  (http://genome.lbl.gov/vista/) was employed to inspect the conservation landscape for a given region from different genomes, including human (Feb. 2009), Cow (Oct. 2011), Mouse (Dec. 2011 or Jul. 2007), Callithrix jacchus v.2.0.2 (Jun. 2007), Rhesus (Jan. 2006), Pongo pygmaeus abelii v.2.0.2 (Jul. 2007), Gorilla (Dec. 2009), Chimp (Mar. 2006), Rat (Nov. 2004), Dog (May 2005) and Horse (Jan. 2007).
SNURF-SNRPNsequence comparative analysis
Putative rhesus snoRNA116s (Figure 4B) were marked with human and mouse annotations (Figures 4A and C) in UCSC. Locations of putative rhesus SNURF-SNRPN exons were defined according to rhesus poly(A)+ RNA-seq mapping signals. Sequences of human (Figure 4A) and rhesus (Figure 4B) SNURF-SNRPN exons were extracted from UCSC Genome Bioinformatics database (http://genome.ucsc.edu/). Pair-wise sequence alignments were carried out using T-Coffee .
Fox protein binding site prediction on PWS sno-lncRNAs
Sequences of human PWS sno-lncRNAs and rhesus putative PWS sno-lncRNAs were extracted from UCSC Genome Bioinformatics database (http://genome.ucsc.edu/). All these sequences were scanned for Fox hexanucleotide motifs including UGCAUG, GCAUGU, GUGAUG, UGGUGA and GGUGGU .
Conservation analysis with PhastCons
PhastCons scores for multiple alignments of primate genomes (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/phastCons46wayPrimates.txt.gz, updated on 2009/12/6) were downloaded from UCSC and corresponding PhastCons scores for lncRNAs , lincRNAs  and sno-lncRNAs (11 predicted in human, Table 1) were counted separately to inspect the conservation difference of these three datasets. PhastCons scores for nearby exons, snoRNAs at both ends of sno-lncRNAs and internal regions of sno-lncRNAs were also calculated separately to investigate the region-specific conservation difference of sno-lncRNAs.
Cell culture, cell transfection and antisense oligonucleotide treatment
All cell lines were cultured using standard protocols. Plasmid transfection was carried out with X-tremeGENE 9 (Roche) or with nucleofection (Lonza) according to the manufacturer’s instructions. Rhesus rhesus RNAs were extracted from ESC line IVF3.2 . Mouse RNAs were extracted from ESC R1 line or sacrificed mouse hippocampus, respectively. Mice were maintained and used in accordance with the guidelines of the Institutional Animal Care and Use Committee of Shanghai Institutes for Biological Sciences.
SNORD116-14 in pcDNA3-sno-lncRNA2  was replaced with SNORA5A to generate construct pcDNA3-sno-lncRNA2-5A (Figure 2A), and SNORA5A in pcDNA3-sno-lnc5AC was substituted with SNORD116-14 to generate constructs pcDNA3-sno-lnc5C-14 (Figure 2B) with primers listed in Table S1. Mouse sno-lnc33/34 and human sno-lnc5AC flanked by its full length intron, splice sites and exons were cloned into pcDNA3 (Figure 6C).
RNA Isolation, poly(A)-/ribo- fractionation, RNA-seq and Northern Blot
Cultured cell lines or cells with different treatments were harvested in Trizol (Invitrogen) and RNAs were extracted according to the manufacturer’s instruction, followed by DNase I treatment at 37°C for 30 mins (Ambion, DNA-free™ Kit). Poly(A)+ and poly(A)-/ribo- RNA transcripts were fractionated and sequenced as previously described . Raw sequencing dataset and bigWig track file of rhesus and mouse poly(A)-/ribo- RNAs are available for download from NCBI Gene Expression Omnibus under accession number GSE53942 for mouse ESCs, mouse hippocampus and rhesus ESCs. Northern Blot was carried out according to the manufacturer’s protocol (DIG Northern Starter Kit, Roche). Denatured RNAs were loaded on either native agarose gel or denatured PAGE gel with urea for Northern Blots as previous studies [15, 16]. Digoxigenin (Dig) labeled antisense and sense probes were made using either SP6 or T7 RNA polymerase by in vitro transcription with the AmpliScribe™ SP6 and T7 High Yield Transcription Kits (Epicentre). DIG-labeledRNA Molecular Wight Marker III is from Roche.
We are grateful to Gordon Carmichael for critical reading of the manuscript and all lab members for helpful discussion and technical support. H9 cells were obtained from the WiCell Research Institute. RNA-seq was performed at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China. This work was supported by grants 2014CB964800 and 2014CB910600 from MOST, XDA01010206 and 2012OHTP08 from CAS, 31322018, 31271376 and 31271390 from NSFC.
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