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Long noncoding RNAs, emerging players in muscle differentiation and disease

Long noncoding RNAs, emerging players in muscle differentiation and disease The vast majority of the mammalian genome is transcribed giving rise to many different types of noncoding RNAs. Among them, long noncoding RNAs are the most numerous and functionally versatile class. Indeed, the lncRNA repertoire might be as rich as the proteome. LncRNAs have emerged as key regulators of gene expression at multiple levels. They play important roles in the regulation of development, differentiation and maintenance of cell identity and they also contribute to disease. In this review, we present recent advances in the biology of lncRNAs in muscle development and differentiation. We will also discuss the contribution of lncRNAs to muscle disease with a particular focus on Duchenne and facioscapulohumeral muscular dystrophies. Keywords: Chromatin, DMD, FSHD, Muscular dystrophy, ncRNA, Repeat Review polymerase II and may share mRNA-like features such as Long non protein-coding RNAs (lncRNAs) 5’cap, polyA tail and splicing sites [12,13]. Alternatively, In mammals, the vast majority of the transcriptional out- non-polyadenylated lncRNAs are likely generated by RNA put is noncoding [1]. While 75% of the genome is tran- polymerase III [14,15]. scribed, only 2% encodes for proteins [2]. Non protein- In terms of transcriptional profile, lncRNAs are gener- coding RNAs (ncRNAs) are operationally divided in two ally expressed at lower levels than protein-coding tran- classes according to their size. Small ncRNAs are below scripts and, compared to the latter, their pattern of 200 bp and include transfer RNA (tRNA), ribosomal RNA expression is more developmental stage- and cell type- (rRNA), small nuclear RNAs (snRNA), small nucleolar specific [2,16]. The intrinsic nature and complex secon- RNAs (snoRNA), microRNAs, siRNAs and Piwi-inter- dary structures of lncRNAs enable them to specifically acting RNAs (piRNA) [3-7]. Long ncRNAs (lncRNAs) in- interact with DNA, RNA and proteins. Since lncRNAs clude all ncRNA transcripts greater than 200 bp with little are localized both in the nucleus and the cytosol, they or no coding potential. Although discovered relatively re- can act at virtually every level of gene expression [17,18]. cently, lncRNAs are considered the most numerous and functionally diverse class of RNAs [8]. Up to 15,000 LncRNA, a molecular ‘passepartout’ lncRNAs have been identified so far [9] and, as the num- LncRNAs can be divided into multiple functional cat- ber constantly increases, the lncRNA assortment might egories based on the site of action and the level of gene turn out to be as rich as the proteome. expression at which they act. However, as our knowledge LncRNAs loci are often in close association with of lncRNAs increases, new functional groups emerge protein-coding genes as they are encoded from exonic or and the distinction between classes is not always ad- intronic sequences in both sense and antisense orientation equate. Here, we present a very brief classification to or even from gene regulatory regions [10]. LncRNAs can provide a framework for the examples of lncRNAs acting also arise from intergenic regions including repetitive se- in muscle differentiation and disease later described. quences [11]. Most lncRNAs are transcribed by RNA Nuclear lncRNAs can be subdivided into cis-acting RNAs that work in proximity to their site of transcription, * Correspondence: gabellini.davide@hsr.it and trans-acting RNAs that operate at distant loci. Both Dulbecco Telethon Institute at San Raffaele Scientific Institute, Division of cis-and trans-acting lncRNAs can activate or repress Regenerative Medicine, Stem cells, and Gene therapy, DIBIT2, 5A3, Via Olgettina 58, 20132 Milano, Italy transcription through the recruitment of chromatin © 2014 Neguembor et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 2 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 remodelers and modifiers, thus shaping the chromatin sta- post-transcriptional regulation in the nucleus. For ex- tus of a particular locus or even of an entire chromosome ample, lncRNAs can interact with the splicing machinery (Figure 1A) [19-24]. Besides, lncRNAs are able to recruit or directly with nascent mRNAs to guide particular spli- or prevent the binding of the transcriptional machinery cing events (Figure 1C) [33-35]. In addition to the cis ver- and transcription factors directly impacting the transcrip- sus trans distinction, lncRNAs can shape the subnuclear tional output of a region (Figure 1B) [25-28]. Among architecture in different ways. Certain lncRNAs regu- these, enhancer RNAs (eRNAs), are encoded by extragenic late chromosome looping, favoring or disrupting chro- enhancer regions and promote transcription of surroun- mosomal interactions (Figure 1D) [36,37]. Others act as ding genes [29-32]. LncRNAs also participate in co- and structural scaffolds for the formation and regulation of Figure 1 Mechanisms for long noncoding RNA (lncRNA) function. (A) LncRNAs (in red) are able to recruit chromatin modifiers mediating the deposition of activatory (green dots) or repressive (red dots) histone marks. (B) LncRNAs control the recruitment of transcription factors and core components of the transcriptional machinery. (C) LncRNAs can directly bind mRNAs and modulate splicing events. (D-E) LncRNAs participate in the higher order organization of the nucleus by mediating chromatin looping (D) and as structural components for the formation and function of nuclear bodies (E). (F) LncRNAs control translation rates favoring or inhibiting polysome loading to mRNAs. (G) LncRNAs modulate mRNA decay protecting mRNA from degradation or, alternatively, mediating the recruitment of degradation machinery. (H) LncRNAs can act as miRNA sponges, thus favoring the expression of the mRNAs targeted by the sequestered miRNA. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 3 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 nuclear compartments such as speckles [33], paraspeckles enormous literature provides evidence that the myogenic [38] and Polycomb bodies [39] (Figure 1E). gene expression program is orchestrated by a trans- In the cytoplasm, lncRNAs influence translational out- criptional hierarchy, including the Myogenic Regulatory put in different ways. Firstly, they can modulate the trans- Factors (MyoD, Myf5, Myogenin, and MRF4) and the lational rate by regulating polysome loading to an mRNA Myocyte Enhancer Factor-2 (MEF2A-D) families of tran- molecule (Figure 1F) or through the control of internal scription factors (reviewed in [51] and [52]). In a stage- ribosomal entry sites (IRES) [40-42]. Secondly, they can specific manner, these factors act in coordination with regulate gene expression by reducing or stimulating other transcriptional regulators, including epigenetic fac- mRNA decay (Figure 1G) [43,44]. A particular class of tors, to execute the muscle differentiation program [53]. cytoplasmic lncRNAs, the competing endogenous RNAs Still, this scenario is not complete as new players are grad- (ceRNA), regulates both the translation and the degra- ually emerging. Indeed, there is increasing evidence that dation rates of mRNAs by acting as molecular sponges for ncRNAs are also part of the muscle regulatory network. miRNAs, thus modulating the repressive activity of So far, miRNAs are the most extensively studied and cha- miRNA on their mRNA targets (Figure 1H) [45-49]. racterized [54]. However, in the last years lncRNAs are Altogether, lncRNAs exhibit remarkable functional flexi- emerging as critical regulators of muscle differentiation bility and tightly regulated expression that confer on them (Table 1). an enormous potential as fine tuners of cell function and identity. Due to their versatility, they are able to control LncRNAs mediating the activity of chromatin modifiers different aspects of cellular development, from stem cell and transcription factors maintenance to commitment and differentiation and we An increasing body of work indicates that many nuclear anticipate their biological role in a great variety of cell types lncRNAs regulate the activity of enhancers at various to be uncovered in the near future [50]. In this review, we levels. Enhancers are distal regulatory elements that play will focus on the fascinating discoveries regarding the role an essential role for the proper temporal and tissue- of lncRNAs in muscle differentiation and disease, with a specific expression of protein-coding genes. Typically, ac- particular focus on Duchenne muscular dystrophy (DMD) tive enhancers display increased chromatin accessibility and facioscapulohumeral muscular dystrophy (FSHD). and are enriched for monomethyl histone H3 lysine 4 (H3K4me1) and acetylated H3K27 (H3K27ac). Intri- LncRNAs in myogenic differentiation guingly, RNA polymerase II (RNAPII) is also enriched at Myogenesis is the process where progenitor cells give rise active enhancers where it drives localized transcription of to myoblasts that fuse onto multi-nucleated myofibers lncRNAs called enhancer-derived RNAs (eRNAs) [31,66]. endowed with contractile ability. This complex and tightly Many eRNAs regulate enhancer/promoter communica- regulated process starts from extra/intra cellular signals tion by directly recruiting chromatin modifiers and remo- impinging on the myogenic transcription program. An delers and the transcriptional machinery, thus favoring Table 1 Long noncoding RNAs (lncRNAs) involved in muscle differentiation LncRNA Site of action Function Effector molecule Regulation during References muscle differentiation CE and DRR eRNAs ( RNAs) Nucleus Transcriptional activation MyoD Up [30] Gtl2/Meg3 Nucleus Epigenetic repression PRC2 Up [55,56] H19 Nucleus and Epigenetic repression, miRNAs sponge PRC2, let-7 miRNAs Up [57] cytoplasm Linc-MD1 Cytoplasm miRNAs sponge HuR Up [46,58] Malat1 Nucleus Epigenetic repression, pre-mRNA Cbx4 and SR family Up [59] splicing of splicing factors Neat1 Nucleus Structural integrity of nuclear Various RNA-binding Up [60] paraspeckles proteins Nctc1 Nucleus? Unknown Unknown Up [61] SRA Nucleus Scaffold factor MyoD Up [62,63] SINE containing Cytoplasm mRNA decay STAU1 and STAU2 Up [64] lncRNAs Yams Nucleus Transcriptional activation Unknown Up/down [65] CE and DRR eRNAs: enhancer RNAs; RNAs: Core Enhancer and Distal Regulatory Region RNAs; Gtl2/Meg3: Gene trap locus 2/Maternally expressed gene 3; Malat1: Metastasis associated lung adenocarcinoma transcript 1; Neat1: Nuclear enriched abundant transcript 1; Nctc1: Noncoding transcript 1; SRA: Steroid receptor RNA Activator; SINE containing lncRNAs: Short Interspersed Elements containing lncRNAs; Yams: YY1-associated muscle lincRNAs. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 4 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 the activation of gene expression in cis or in trans upstream regulatory regions of MyoD (CE and DRR)regu- (Figure 1B) [29,32,36,67-70]. Recently, a key role for eRNAs late the expression of MyoD and MyoG (Figure 2A and in the regulation of muscle differentiation was uncovered Table 1) [71,72]. Both eRNAs are involved in the activa- [30]. In myotubes, ChIP-seq analyses revealed that the tion of gene expression, but they differ in their mode CE myogenic regulatory factors MyoD and MyoG display a of action. While the RNA functions in cis to activate DRR very similar genome-wide binding profile and are mostly expression of MyoD, RNA works in trans to promote associated with extragenic regions, many of which exhibit MyoG transcription and muscle differentiation (Figure 2A). eRNA features [30]. Several of these eRNAs are prefe- At their site of action, both eRNAs mediate increased rentially localized to the nucleus and are mainly regulated chromatin accessibility and recruitment of RNAPII [30]. by MyoD, as MyoG silencing has a marginal effect on Collectively, these findings suggest that eRNAs regulate their expression [30]. In turn, two eRNAs generated by myogenesis by directing chromatin-remodeling events, CE and DRR Figure 2 Distinct roles of long noncoding RNAs (lncRNAs) in muscle differentiation. (A) Enhancer RNAs (eRNAs) RNAs can induce expression of myogenic regulators MyoD and MyoG acting in cis or in trans, respectively. (B) LncRNA SRA acts as a scaffold molecule for MyoD, p68 and p72 at the promoter region of myogenic genes to activate their expression. (C) LncRNAs Malat1, H19 and Gtl-Meg3 interact with PRC1/2 complex to modulate their target genes. (D) As a molecular sponge H19 inhibits let-7 mediated mRNA degradation of myogenic negative regulators Hmga2 and Igfbp2. (E) Short interspersed element (SINE) containing lncRNAs can bind to UTR region of Cdc6 and Traf6 mRNAs and promote their decay at different stages of muscle differentiation. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 5 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 controlling the hierarchy within the myogenic gene regu- predominant isoform in myotubes [63]. SRAP works at latory network. least in part by regulating SRA lncRNA coactivator func- The transcription factor Yin Yang 1 (YY1) is another im- tion. Indeed, SRAP is an RNA-binding protein that speci- portant regulator of myogenesis at multiple levels [73-77]. fically binds SRA lncRNA, thus preventing SRA-mediated By comparing YY1 ChIP-seq results in proliferating and regulation of MyoD transcriptional activity [63]. Hence, differentiated C2C12 muscle cells, a number of lncRNAs the correct balance between coding and noncoding SRA regulated by YY1 (YY1-associated muscle lincRNAs or molecules is important for normal muscle differentiation. Yams) have been recently identified [65]. Yams display dis- Intriguingly, aberrant SRA splicing is present in myotonic tinct expression patterns during muscle differentiation dystrophy patients. Whether impaired splicing of SRA and affect myogenesis differently (Table1). For example, contributes to the pathogenesis of muscular dystrophy re- while Yam-2 and -3 promote C2C12 muscle differen- mains to be elucidated [63]. tiation, Yam-1 and -4 inhibit it [65]. The mechanism of action of Yam-1 was investigated in more detail. Yam-1 is Subnuclear structure-specific lncRNAs a single exon transcript, regulated during in vitro and A number of lncRNAs are enriched in and contribute to in vivo myogenesis and equally distributed in the nucleus organize specific subnuclear domains (Figure 1E) [82-88]. and cytoplasm. Throughout development, in muscle re- The lncRNA Malat1 is enriched in nuclear speckles, generation and in tissue culture, Yam-1 is downregulated abundantly expressed in cancer cells and a strong pre- during terminal muscle differentiation [65]. Yam-1 knock- dictor of tumor metastasis [89]. Malat1 has been shown down promotes muscle differentiation in tissue cul- to regulate gene transcription and pre-mRNA splicing by ture and accelerates regeneration following muscle injury respectively interacting with the epigenetic repressor Poly- in vivo [65]. Importantly, Yam-1 knockdown rescues the comb protein Cbx4 [39] and with the SR family of splicing myogenic defects caused by YY1 overexpression indicating factors (Figure 2C and Table 1) [33]. Malat1 is upregu- that Yam-1 is an important mediator of YY1 activity in lated during early differentiation of C2C12 mouse myo- muscle [65]. Silencing of Yam-1 reduces the expression of blasts and primary human skeletal muscle cells, while its several nearby genes, suggesting that it could be a positive knockdown leads to suppression of myoblast proliferation cis-regulator of surrounding genes similar to eRNAs by arresting cells in the G0/G1 phase [59], suggesting a (Figure 1B) [65]. One of the nearby genes co-regulated role for Malat1 in the transition from the proliferative with Yam-1 encodes for miR-715, a miRNA targeting phase to the permanent cell cycle exit, as well as in the Wnt7b. Since Wnt signaling is a critical modulator of ske- commitment to differentiation. Intriguingly, Malat1 has letal muscle formation [78], it is tempting to speculate that been recently identified as a novel downstream target of Yam-1 could function, at least in part, by activating miR- myostatin [59], an important regulator of myoblast prolif- 715 in cis leading to Wnt7b downregulation. eration, differentiation and skeletal muscle mass [90]. Fu- Besides regulating chromatin accessibility like eRNAs, ture work will indicate how relevant Malat1 is for nuclear lncRNAs can also control gene expression by dir- myostatin activity. ectly affecting the activity of sequence-specific transcrip- tion factors. This is the case for steroid receptor RNA Imprinted lncRNAs activator (SRA) [79], the first example of lncRNA regula- The Dlk1-Dio3 region is a very complex, imprinted locus ting myogenesis [62]. SRA likely functions as a scaffold, involved in tissue growth regulation and human cancers bringing together multiple factors that modulate gene ex- [91]. Aberrant repression of the Dlk1-Dio3 imprinted clus- pression [80] including the master regulator of muscle dif- ter is present in most induced pluripotent stem cell (iPSC) ferentiation MyoD (Figure 2B and Table1) [62]. In muscle, lines and is responsible for the failure of iPSCs to form a complex composed by SRA, MyoD and the RNA heli- viable mice [92]. Intriguingly, postnatal aberrant expres- cases p68 and p72 has been identified (Figure 2B) [62]. sion of this locus is responsible for muscle hypertrophy in Knockdown and overexpression studies indicate that p68/ mouse and sheep [93,94]. The locus contains protein- p72 and SRA are coactivators required for the trans- coding RNAs, lncRNAs, miRNAs and snoRNAs expressed cription of a subset of MyoD target genes and for muscle from either the paternal or the maternal allele. Several of differentiation [62]. The SRA gene produces multiple the lncRNAs transcribed from the Dlk1-Dio3 region are transcripts through alternative splicing. While retention of enriched in the nucleus and have been reported to bind to intron 1 gives rise to the non protein-coding SRA tran- Polycomb Repressive Complex 1 (PRC1), PRC2 and other script, splicing of the intron creates an open reading frame epigenetic repressors [95-97]. Expression of the various that generates the SRA protein (SRAP) [81]. The ratio bet- Dlk1-Dio3 transcripts is reciprocally regulated. For ex- ween the coding and noncoding SRA transcripts varies ample, the Glt2/Meg3 lncRNA binds to PRC2 recruiting it during muscle differentiation with SRAP mRNA being to the Dlk1-Dio3 locus to repress the protein-coding gene more abundant in myoblasts and SRA lncRNA being the Dlk1 and the lncRNA Gtl2-as (Figure 2C and Table 1). Neguembor et al. Skeletal Muscle 2014, 4:8 Page 6 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 Consistently, Glt2/Meg3 knockdown leads to a decreased including Cdc6 and Traf6 (Figure 2E and Table 1) [64]. PRC2 recruitment at the Dlk1 promoter with subsequent Both STAU1 and STAU2 interact directly with the ATP- increased expression of Dlk1 and Gtl2-as [95]. During dependent RNA helicase UPF1, a key SMD factor, enhan- development, Gtl2/Meg3 is abundantly expressed in the cing its helicase activity to promote effective SMD. Because paraxial mesoderm suggesting a role in myogenesis [55]. both SMD and the mechanistically related nonsense-me- Indeed, Gtl2/Meg3 knockout mice develop skeletal muscle diated mRNA decay (NMD) employ UPF1, SMD and developmental defects along with perinatal death [56], NMD are competitive pathways. This competition plays an promoting Gtl2/Meg3 as an example of a nuclear, cis- important role in the control of muscle differentiation. In- acting lncRNA regulating muscle development. deed, during myogenesis, the efficiency of NMD decreases H19 was the first lncRNA described in mammalian cells while the efficiency of SMD increases. Interestingly, Myo- [98]. It is transcribed from the maternal allele of the H19/ genin and PAX3 are differentially targeted by these two Igf2 locus producing a lncRNA predominantly enriched in pathways of degradation and this different susceptibility the cytoplasm [98]. H19 is highly expressed in developing contributes to their relative abundance during differenti- embryo and adult muscle in human and mouse [99,100], ation. PAX3 mRNA is an SMD target and its increased and is upregulated during myoblast differentiation and decay promotes myogenesis, whereas decreased degrad- muscle regeneration [57,101]. H19 works at multiple ation of the NMD target Myogenin is required for myogen- levels. Through binding to the PRC2 epigenetic repressor esis [109]. Importantly, since close to one third of all complex [95], H19 can mediate the transcriptional repres- lncRNAs contains at least one SINE [64,110], lncRNAs sion of Igf2 (Figure 2C) [102,103]. Moreover, H19 can bind containing SINE sequences could be at the heart of Igf2 mRNA binding-protein (IMP) family members to many physiologically important processes in addition to regulate Igf2 post-transcriptionally [104]. Also, H19 con- myogenesis. tains several binding sites for the let-7 family of micro- RNAs suggesting that H19 may act as a miRNA sponge LncRNAs in muscle diseases for let-7 (Figure 2D and Table 1) [57]. Among let-7 Growing evidence shows that the vast majority of disease- targets, Hmga2 and Igfbp2 have an important role in myo- associated genetic variations occur in the noncoding por- blasts proliferation and myogenesis but must be downreg- tion of the genome. In fact, whereas only 7% of disease- ulated to allow the formation of multinucleated myofibers associated SNPs localize in protein-coding exons, the (Figure 2D) [105]. Finally, H19 exon 1 encodes the con- remaining 93% arise in noncoding areas of the genome, of served microRNAs miR-675-3p and miR-675-5p [106]. which 43% fall in intergenic regions [111]. Considering Recent results indicate that, by targeting Smad1, Smad5, the extensive transcription of these areas, it is reasonable and Cdc6, these miRNAs play an important role in the to predict that a significant and yet unknown number of skeletal muscle differentiation and regeneration activities lncRNAs are involved in a variety of human diseases. associated to H19 [101]. LncRNAs can either have a primary role in the patho- genesis of a disease or rather act as modulators of disease LncRNAs containing repetitive sequences controlling penetrance, explaining, at least in part, the inter-personal mRNA decay variability observed in virtually every disorder. So far, the Short interspersed elements (SINEs) are among the most contribution of lncRNAs to disease has mostly been inves- abundant repetitive sequences in mammalian genomes tigated in cancer and neurological disorders [112-114] but [107]. While initially thought of as ‘junk’ DNA, SINEs can the first examples of lncRNA involved in myopathies are be transcribed as individual elements by RNA polymerase now unveiled. Here, we focus on the recent discoveries re- III or as part of longer transcripts synthesized by RNA garding the role of lncRNAs in Duchenne muscular dys- polymerase II and they can regulate gene expression by di- trophy and facioscapulohumeral muscular dystrophy. verse mechanisms [41,108]. It has recently been discovered that a SINE within the 3′ UTR of a protein-coding RNA Duchenne muscular dystrophy can form intermolecular base pairing with a partially com- Duchenne muscular dystrophy (DMD) is the most com- plementary SINE within one or more lncRNAs [43,64]. mon and severe myopathy affecting 1:3,500 males. It is Extensive yet imperfect stretches of double-stranded RNA inherited in an X-linked recessive manner but, in very (dsRNA) can be bound at multiple sites by dsRNA-binding rare cases, heterozygous females can be mildly affected proteins, including Staufen 1 and 2 (STAU1 and STAU2). [115]. DMD is characterized by severe muscle wasting Staufen recruitment activates Staufen-mediated mRNA from early childhood that usually arises in leg and pelvic decay (SMD), an important mRNA degradation process in muscles and later extends to the trunk of the body, com- mammalian cells. Using this mechanism, lncRNAs con- promising the heart and respiratory muscles. DMD is taining SINEs regulate the stability of several mRNAs caused by a variety of out-of-frame mutations in the dys- encoding for proteins with a role in muscle differentiation, trophin (DMD) gene encoded on the X chromosome Neguembor et al. Skeletal Muscle 2014, 4:8 Page 7 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 (Xp21.2) resulting in the lack of a functional dystrophin DMD mutations may impact the expression of the protein in skeletal muscle. With 79 exons and 2.4 Mb in lncRNAs. size, DMD is the largest gene of our genome and up to The mutations occurring in DMD patients could also 2,900 types of mutations have been reported in DMD deregulate the expression of lncRNAs located outside the patients so far [116,117]. Despite the mutations trig- dystrophin gene or could even give rise to new lncRNAs gering the disease being well characterized, the regula- as a result of translocation events. This could modulate tion of dystrophin is in part unknown and appears much the severity of the muscle degeneration or contribute to more complex than previously thought. Moreover, the the development of additional symptoms such as the inter-individual variability in the severity and the disease neurological complications observed in around one third progression is only partially explained by the types of of the patients [120,121]. A single case study recently pub- mutations and the occurrence of female patients remains lished explores this hypothesis and describes how an in- enigmatic. Therefore, the regulation of DMD is an area of trachromosomal inversion (inv(X)p21.2;q28) disrupts the intense research that in the last few years has led to the novel lncRNA KUCG1 in a DMD patient with moderate characterization of miRNA and lncRNA involvement [118]. mental retardation [122]. KUCG1 is a 648-bp nuclear Using custom-made tiling arrays, 14 lncRNAs tran- lncRNA expressed in a tissue specific manner [122]. Since scribed from intronic sequences of the DMD gene both it is normally expressed in the brain, its deregulation could in sense and antisense orientations were recently identi- contribute to the neurological impairment of the patient fied [119]. These lncRNAs are expressed concomitantly [122] as already reported for other pathologies [114]. Al- with dystrophin in at least one of the tissues that nor- though a functional characterization of this transcript has mally express it: skeletal muscle, heart and brain [119]. not been performed, this study underscores the patho- Ectopic expression and promoter binding assays suggest logical potential of mutations in noncoding loci that often that the lncRNAs can function in trans by downregulat- follow genomic rearrangements. ing the expression of specific dystrophin isoforms target- Another lncRNA associated with DMD is long intergenic ing their promoters (Figure 3A). Interestingly, an inverse noncoding RNA-muscle differentiation 1 (linc-MD1) [46]. correlation was found between the levels of dystrophin Linc-MD1 is a muscle-specific lncRNA required to acti- and a subset of lncRNAs in female carriers, both symp- vate late stages of the myogenic program. Linc-MD1 is a tomatic and asymptomatic [119]. It remains to be inves- cytoplasmic ceRNA that acts as a molecular sponge for tigated if these lncRNAs act in an allele-specific manner miR-133 and miRNA-135 (Figure 3B and Table 1) [46]. or whether they may also modulate the expression of the Through this mechanism, linc-MD1 promotes the expres- wild type dystrophin allele in female carriers. Additio- sion of myocyte-specific enhancer factor 2C (MEF2C) and nally, it would be interesting to define how different mastermind-like protein 1 (MAML1), two transcription Figure 3 Proposed roles for long noncoding RNAs (lncRNAs) in Duchenne muscular dystrophy. (A) In the nucleus, sense and antisense transcription from intronic sequences of the dystrophin (DMD) gene gives rise to lncRNAs that play a repressive effect at specific DMD promoters. (B) In the cytoplasm, the muscle specific lncRNA linc-MD1 acts as a competitive endogenous RNA (ceRNA) by sequestering miRNAs away from their target mRNAs. Linc-MD1 contributes to muscle differentiation by sponging miRNA-135 and -133, and thus promoting the expression of MEF2C and MAML1. Linc-MD1 is strongly reduced in muscle cells from DMD patients. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 8 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 factors with an important role in muscle differentiation is highly polymorphic, displaying 11 to more than 100 (Figure 3B) [46]. Interestingly, the levels of linc-MD1 are units [128,129]. On the contrary, FSHD patients carry strongly reduced in primary myoblasts of DMD patients deletions reducing D4Z4 copy number between one and and its ectopic expression rescues the myogenic differenti- ten units [129,130]. D4Z4 deletion is associated with a ation potential of these cells, restoring the correct expres- profound change in the epigenetic status of the 4q35 re- sion pattern of MAML1, MEF2C, MYOG and MHC [46]. gion [131]. A recently identified lncRNA plays a key role Linc-MD1 can have a double life as lncRNA or as miRNA, in this transition [37]. In healthy subjects, the FSHD locus since its primary transcript harbors the pri-miR-133b se- is under a repressive chromatin status, with high levels of quence. The balance between linc-MD1 and miR-133 bio- DNA methylation, histone de-acetylation and enrichment genesis is regulated by HuR, an RNA-binding protein with for repressive histone marks such as H2Aub1, H3K9me3 a crucial role in myogenesis (Table 1) [123]. Moreover, and H3K27me3. Indeed, D4Z4 has been recently identi- HuR facilitates the linc-MD1-miRNA interaction, enhan- fied as a novel Polycomb (PcG) target region, suggesting cing its sponge activity, thus affecting this ceRNA circuitry that the presence of a high number of D4Z4 units leads to potentially relevant for DMD [58]. the extensive recruitment of PcG and the consequent re- pression of 4q35 genes in healthy subjects (Figure 4). In Facioscapulohumeral muscular dystrophy FSHD patients, instead, the reduction in number of D4Z4 Facioscapulohumeral muscular dystrophy (FSHD) is the units under a critical threshold leads to a reduced PcG third most common muscular dystrophy (1:14,000). binding with decreased levels of H3K27me3, particularly FSHD is transmitted in an autosomal dominant manner in the region immediately proximal to the D4Z4 repeat and affects both sexes but presents a gender bias, as array. As a result, this region becomes more prone to males are usually more severely affected [124]. FSHD transcription and gives rise to the activatory lncRNA displays a more restricted pattern of muscle weakness DBE-T. DBE-T is mainly produced in FSHD patients and compared to DMD, mainly confined to the facial mimic mediates the aberrant activation of the FSHD locus [37]. and shoulder girdle muscles but extending to abdominal DBE-T is a nuclear transcript that acts in cis as it re- and leg muscles in the most severe cases [125,126]. The mains associated with the chromatin of the FSHD locus genetic lesion involved in FSHD is unusual as it does (Figure 4) [37]. DBE-T directly binds to the Trithorax not target a protein-coding gene, but rather affects the (TrxG) protein ASHL1 recruiting it to the FSHD locus copy number of the 3.3 kb macrosatellite D4Z4 mapping where it mediates the accumulation of H3K36me2 [37], a at the subtelomeric region of chromosome 4 (4q35) histone modification that counteracts PcG repressive ac- [127]. In the general population, D4Z4 copy number tivity [132-134]. Consequently, this leads to altered higher Figure 4 Role of DBE-T long noncoding RNA (lncRNA) in facioscapulohumeral muscular dystrophy (FSHD). In healthy individuals, the D4Z4 array displays from 11 to more than 100 units and is extensively bound by Polycomb group proteins (PcG), leading to the repression of the locus. In FSHD patients, the reduction of D4Z4 copy number to below 11 units causes decreased PcG binding and hence reduced silencing. This allows the transcription of the lncRNA DBE-T that remains associated to the FSHD locus and recruits the TrxG protein ASHL1 leading to activation of FSHD candidate genes. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 9 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 order chromatin organization and derepression of FSHD Received: 14 February 2014 Accepted: 11 March 2014 Published: 31 March 2014 candidate genes localized nearby the D4Z4 array and unleashing FSHD pathogenesis [37]. References 1. 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Shahrizaila N, Wills AJ: Significance of Beevor's sign in facioscapulohumeral dystrophy and other neuromuscular diseases. Submit your manuscript at J Neurol Neurosurg Psychiatry 2005, 76:869–870. www.biomedcentral.com/submit http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Skeletal Muscle Springer Journals

Long noncoding RNAs, emerging players in muscle differentiation and disease

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Copyright © 2014 by Neguembor et al.; licensee BioMed Central Ltd.
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Life Sciences; Cell Biology; Developmental Biology; Biochemistry, general; Systems Biology; Biotechnology
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2044-5040
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10.1186/2044-5040-4-8
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24685002
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Abstract

The vast majority of the mammalian genome is transcribed giving rise to many different types of noncoding RNAs. Among them, long noncoding RNAs are the most numerous and functionally versatile class. Indeed, the lncRNA repertoire might be as rich as the proteome. LncRNAs have emerged as key regulators of gene expression at multiple levels. They play important roles in the regulation of development, differentiation and maintenance of cell identity and they also contribute to disease. In this review, we present recent advances in the biology of lncRNAs in muscle development and differentiation. We will also discuss the contribution of lncRNAs to muscle disease with a particular focus on Duchenne and facioscapulohumeral muscular dystrophies. Keywords: Chromatin, DMD, FSHD, Muscular dystrophy, ncRNA, Repeat Review polymerase II and may share mRNA-like features such as Long non protein-coding RNAs (lncRNAs) 5’cap, polyA tail and splicing sites [12,13]. Alternatively, In mammals, the vast majority of the transcriptional out- non-polyadenylated lncRNAs are likely generated by RNA put is noncoding [1]. While 75% of the genome is tran- polymerase III [14,15]. scribed, only 2% encodes for proteins [2]. Non protein- In terms of transcriptional profile, lncRNAs are gener- coding RNAs (ncRNAs) are operationally divided in two ally expressed at lower levels than protein-coding tran- classes according to their size. Small ncRNAs are below scripts and, compared to the latter, their pattern of 200 bp and include transfer RNA (tRNA), ribosomal RNA expression is more developmental stage- and cell type- (rRNA), small nuclear RNAs (snRNA), small nucleolar specific [2,16]. The intrinsic nature and complex secon- RNAs (snoRNA), microRNAs, siRNAs and Piwi-inter- dary structures of lncRNAs enable them to specifically acting RNAs (piRNA) [3-7]. Long ncRNAs (lncRNAs) in- interact with DNA, RNA and proteins. Since lncRNAs clude all ncRNA transcripts greater than 200 bp with little are localized both in the nucleus and the cytosol, they or no coding potential. Although discovered relatively re- can act at virtually every level of gene expression [17,18]. cently, lncRNAs are considered the most numerous and functionally diverse class of RNAs [8]. Up to 15,000 LncRNA, a molecular ‘passepartout’ lncRNAs have been identified so far [9] and, as the num- LncRNAs can be divided into multiple functional cat- ber constantly increases, the lncRNA assortment might egories based on the site of action and the level of gene turn out to be as rich as the proteome. expression at which they act. However, as our knowledge LncRNAs loci are often in close association with of lncRNAs increases, new functional groups emerge protein-coding genes as they are encoded from exonic or and the distinction between classes is not always ad- intronic sequences in both sense and antisense orientation equate. Here, we present a very brief classification to or even from gene regulatory regions [10]. LncRNAs can provide a framework for the examples of lncRNAs acting also arise from intergenic regions including repetitive se- in muscle differentiation and disease later described. quences [11]. Most lncRNAs are transcribed by RNA Nuclear lncRNAs can be subdivided into cis-acting RNAs that work in proximity to their site of transcription, * Correspondence: gabellini.davide@hsr.it and trans-acting RNAs that operate at distant loci. Both Dulbecco Telethon Institute at San Raffaele Scientific Institute, Division of cis-and trans-acting lncRNAs can activate or repress Regenerative Medicine, Stem cells, and Gene therapy, DIBIT2, 5A3, Via Olgettina 58, 20132 Milano, Italy transcription through the recruitment of chromatin © 2014 Neguembor et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 2 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 remodelers and modifiers, thus shaping the chromatin sta- post-transcriptional regulation in the nucleus. For ex- tus of a particular locus or even of an entire chromosome ample, lncRNAs can interact with the splicing machinery (Figure 1A) [19-24]. Besides, lncRNAs are able to recruit or directly with nascent mRNAs to guide particular spli- or prevent the binding of the transcriptional machinery cing events (Figure 1C) [33-35]. In addition to the cis ver- and transcription factors directly impacting the transcrip- sus trans distinction, lncRNAs can shape the subnuclear tional output of a region (Figure 1B) [25-28]. Among architecture in different ways. Certain lncRNAs regu- these, enhancer RNAs (eRNAs), are encoded by extragenic late chromosome looping, favoring or disrupting chro- enhancer regions and promote transcription of surroun- mosomal interactions (Figure 1D) [36,37]. Others act as ding genes [29-32]. LncRNAs also participate in co- and structural scaffolds for the formation and regulation of Figure 1 Mechanisms for long noncoding RNA (lncRNA) function. (A) LncRNAs (in red) are able to recruit chromatin modifiers mediating the deposition of activatory (green dots) or repressive (red dots) histone marks. (B) LncRNAs control the recruitment of transcription factors and core components of the transcriptional machinery. (C) LncRNAs can directly bind mRNAs and modulate splicing events. (D-E) LncRNAs participate in the higher order organization of the nucleus by mediating chromatin looping (D) and as structural components for the formation and function of nuclear bodies (E). (F) LncRNAs control translation rates favoring or inhibiting polysome loading to mRNAs. (G) LncRNAs modulate mRNA decay protecting mRNA from degradation or, alternatively, mediating the recruitment of degradation machinery. (H) LncRNAs can act as miRNA sponges, thus favoring the expression of the mRNAs targeted by the sequestered miRNA. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 3 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 nuclear compartments such as speckles [33], paraspeckles enormous literature provides evidence that the myogenic [38] and Polycomb bodies [39] (Figure 1E). gene expression program is orchestrated by a trans- In the cytoplasm, lncRNAs influence translational out- criptional hierarchy, including the Myogenic Regulatory put in different ways. Firstly, they can modulate the trans- Factors (MyoD, Myf5, Myogenin, and MRF4) and the lational rate by regulating polysome loading to an mRNA Myocyte Enhancer Factor-2 (MEF2A-D) families of tran- molecule (Figure 1F) or through the control of internal scription factors (reviewed in [51] and [52]). In a stage- ribosomal entry sites (IRES) [40-42]. Secondly, they can specific manner, these factors act in coordination with regulate gene expression by reducing or stimulating other transcriptional regulators, including epigenetic fac- mRNA decay (Figure 1G) [43,44]. A particular class of tors, to execute the muscle differentiation program [53]. cytoplasmic lncRNAs, the competing endogenous RNAs Still, this scenario is not complete as new players are grad- (ceRNA), regulates both the translation and the degra- ually emerging. Indeed, there is increasing evidence that dation rates of mRNAs by acting as molecular sponges for ncRNAs are also part of the muscle regulatory network. miRNAs, thus modulating the repressive activity of So far, miRNAs are the most extensively studied and cha- miRNA on their mRNA targets (Figure 1H) [45-49]. racterized [54]. However, in the last years lncRNAs are Altogether, lncRNAs exhibit remarkable functional flexi- emerging as critical regulators of muscle differentiation bility and tightly regulated expression that confer on them (Table 1). an enormous potential as fine tuners of cell function and identity. Due to their versatility, they are able to control LncRNAs mediating the activity of chromatin modifiers different aspects of cellular development, from stem cell and transcription factors maintenance to commitment and differentiation and we An increasing body of work indicates that many nuclear anticipate their biological role in a great variety of cell types lncRNAs regulate the activity of enhancers at various to be uncovered in the near future [50]. In this review, we levels. Enhancers are distal regulatory elements that play will focus on the fascinating discoveries regarding the role an essential role for the proper temporal and tissue- of lncRNAs in muscle differentiation and disease, with a specific expression of protein-coding genes. Typically, ac- particular focus on Duchenne muscular dystrophy (DMD) tive enhancers display increased chromatin accessibility and facioscapulohumeral muscular dystrophy (FSHD). and are enriched for monomethyl histone H3 lysine 4 (H3K4me1) and acetylated H3K27 (H3K27ac). Intri- LncRNAs in myogenic differentiation guingly, RNA polymerase II (RNAPII) is also enriched at Myogenesis is the process where progenitor cells give rise active enhancers where it drives localized transcription of to myoblasts that fuse onto multi-nucleated myofibers lncRNAs called enhancer-derived RNAs (eRNAs) [31,66]. endowed with contractile ability. This complex and tightly Many eRNAs regulate enhancer/promoter communica- regulated process starts from extra/intra cellular signals tion by directly recruiting chromatin modifiers and remo- impinging on the myogenic transcription program. An delers and the transcriptional machinery, thus favoring Table 1 Long noncoding RNAs (lncRNAs) involved in muscle differentiation LncRNA Site of action Function Effector molecule Regulation during References muscle differentiation CE and DRR eRNAs ( RNAs) Nucleus Transcriptional activation MyoD Up [30] Gtl2/Meg3 Nucleus Epigenetic repression PRC2 Up [55,56] H19 Nucleus and Epigenetic repression, miRNAs sponge PRC2, let-7 miRNAs Up [57] cytoplasm Linc-MD1 Cytoplasm miRNAs sponge HuR Up [46,58] Malat1 Nucleus Epigenetic repression, pre-mRNA Cbx4 and SR family Up [59] splicing of splicing factors Neat1 Nucleus Structural integrity of nuclear Various RNA-binding Up [60] paraspeckles proteins Nctc1 Nucleus? Unknown Unknown Up [61] SRA Nucleus Scaffold factor MyoD Up [62,63] SINE containing Cytoplasm mRNA decay STAU1 and STAU2 Up [64] lncRNAs Yams Nucleus Transcriptional activation Unknown Up/down [65] CE and DRR eRNAs: enhancer RNAs; RNAs: Core Enhancer and Distal Regulatory Region RNAs; Gtl2/Meg3: Gene trap locus 2/Maternally expressed gene 3; Malat1: Metastasis associated lung adenocarcinoma transcript 1; Neat1: Nuclear enriched abundant transcript 1; Nctc1: Noncoding transcript 1; SRA: Steroid receptor RNA Activator; SINE containing lncRNAs: Short Interspersed Elements containing lncRNAs; Yams: YY1-associated muscle lincRNAs. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 4 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 the activation of gene expression in cis or in trans upstream regulatory regions of MyoD (CE and DRR)regu- (Figure 1B) [29,32,36,67-70]. Recently, a key role for eRNAs late the expression of MyoD and MyoG (Figure 2A and in the regulation of muscle differentiation was uncovered Table 1) [71,72]. Both eRNAs are involved in the activa- [30]. In myotubes, ChIP-seq analyses revealed that the tion of gene expression, but they differ in their mode CE myogenic regulatory factors MyoD and MyoG display a of action. While the RNA functions in cis to activate DRR very similar genome-wide binding profile and are mostly expression of MyoD, RNA works in trans to promote associated with extragenic regions, many of which exhibit MyoG transcription and muscle differentiation (Figure 2A). eRNA features [30]. Several of these eRNAs are prefe- At their site of action, both eRNAs mediate increased rentially localized to the nucleus and are mainly regulated chromatin accessibility and recruitment of RNAPII [30]. by MyoD, as MyoG silencing has a marginal effect on Collectively, these findings suggest that eRNAs regulate their expression [30]. In turn, two eRNAs generated by myogenesis by directing chromatin-remodeling events, CE and DRR Figure 2 Distinct roles of long noncoding RNAs (lncRNAs) in muscle differentiation. (A) Enhancer RNAs (eRNAs) RNAs can induce expression of myogenic regulators MyoD and MyoG acting in cis or in trans, respectively. (B) LncRNA SRA acts as a scaffold molecule for MyoD, p68 and p72 at the promoter region of myogenic genes to activate their expression. (C) LncRNAs Malat1, H19 and Gtl-Meg3 interact with PRC1/2 complex to modulate their target genes. (D) As a molecular sponge H19 inhibits let-7 mediated mRNA degradation of myogenic negative regulators Hmga2 and Igfbp2. (E) Short interspersed element (SINE) containing lncRNAs can bind to UTR region of Cdc6 and Traf6 mRNAs and promote their decay at different stages of muscle differentiation. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 5 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 controlling the hierarchy within the myogenic gene regu- predominant isoform in myotubes [63]. SRAP works at latory network. least in part by regulating SRA lncRNA coactivator func- The transcription factor Yin Yang 1 (YY1) is another im- tion. Indeed, SRAP is an RNA-binding protein that speci- portant regulator of myogenesis at multiple levels [73-77]. fically binds SRA lncRNA, thus preventing SRA-mediated By comparing YY1 ChIP-seq results in proliferating and regulation of MyoD transcriptional activity [63]. Hence, differentiated C2C12 muscle cells, a number of lncRNAs the correct balance between coding and noncoding SRA regulated by YY1 (YY1-associated muscle lincRNAs or molecules is important for normal muscle differentiation. Yams) have been recently identified [65]. Yams display dis- Intriguingly, aberrant SRA splicing is present in myotonic tinct expression patterns during muscle differentiation dystrophy patients. Whether impaired splicing of SRA and affect myogenesis differently (Table1). For example, contributes to the pathogenesis of muscular dystrophy re- while Yam-2 and -3 promote C2C12 muscle differen- mains to be elucidated [63]. tiation, Yam-1 and -4 inhibit it [65]. The mechanism of action of Yam-1 was investigated in more detail. Yam-1 is Subnuclear structure-specific lncRNAs a single exon transcript, regulated during in vitro and A number of lncRNAs are enriched in and contribute to in vivo myogenesis and equally distributed in the nucleus organize specific subnuclear domains (Figure 1E) [82-88]. and cytoplasm. Throughout development, in muscle re- The lncRNA Malat1 is enriched in nuclear speckles, generation and in tissue culture, Yam-1 is downregulated abundantly expressed in cancer cells and a strong pre- during terminal muscle differentiation [65]. Yam-1 knock- dictor of tumor metastasis [89]. Malat1 has been shown down promotes muscle differentiation in tissue cul- to regulate gene transcription and pre-mRNA splicing by ture and accelerates regeneration following muscle injury respectively interacting with the epigenetic repressor Poly- in vivo [65]. Importantly, Yam-1 knockdown rescues the comb protein Cbx4 [39] and with the SR family of splicing myogenic defects caused by YY1 overexpression indicating factors (Figure 2C and Table 1) [33]. Malat1 is upregu- that Yam-1 is an important mediator of YY1 activity in lated during early differentiation of C2C12 mouse myo- muscle [65]. Silencing of Yam-1 reduces the expression of blasts and primary human skeletal muscle cells, while its several nearby genes, suggesting that it could be a positive knockdown leads to suppression of myoblast proliferation cis-regulator of surrounding genes similar to eRNAs by arresting cells in the G0/G1 phase [59], suggesting a (Figure 1B) [65]. One of the nearby genes co-regulated role for Malat1 in the transition from the proliferative with Yam-1 encodes for miR-715, a miRNA targeting phase to the permanent cell cycle exit, as well as in the Wnt7b. Since Wnt signaling is a critical modulator of ske- commitment to differentiation. Intriguingly, Malat1 has letal muscle formation [78], it is tempting to speculate that been recently identified as a novel downstream target of Yam-1 could function, at least in part, by activating miR- myostatin [59], an important regulator of myoblast prolif- 715 in cis leading to Wnt7b downregulation. eration, differentiation and skeletal muscle mass [90]. Fu- Besides regulating chromatin accessibility like eRNAs, ture work will indicate how relevant Malat1 is for nuclear lncRNAs can also control gene expression by dir- myostatin activity. ectly affecting the activity of sequence-specific transcrip- tion factors. This is the case for steroid receptor RNA Imprinted lncRNAs activator (SRA) [79], the first example of lncRNA regula- The Dlk1-Dio3 region is a very complex, imprinted locus ting myogenesis [62]. SRA likely functions as a scaffold, involved in tissue growth regulation and human cancers bringing together multiple factors that modulate gene ex- [91]. Aberrant repression of the Dlk1-Dio3 imprinted clus- pression [80] including the master regulator of muscle dif- ter is present in most induced pluripotent stem cell (iPSC) ferentiation MyoD (Figure 2B and Table1) [62]. In muscle, lines and is responsible for the failure of iPSCs to form a complex composed by SRA, MyoD and the RNA heli- viable mice [92]. Intriguingly, postnatal aberrant expres- cases p68 and p72 has been identified (Figure 2B) [62]. sion of this locus is responsible for muscle hypertrophy in Knockdown and overexpression studies indicate that p68/ mouse and sheep [93,94]. The locus contains protein- p72 and SRA are coactivators required for the trans- coding RNAs, lncRNAs, miRNAs and snoRNAs expressed cription of a subset of MyoD target genes and for muscle from either the paternal or the maternal allele. Several of differentiation [62]. The SRA gene produces multiple the lncRNAs transcribed from the Dlk1-Dio3 region are transcripts through alternative splicing. While retention of enriched in the nucleus and have been reported to bind to intron 1 gives rise to the non protein-coding SRA tran- Polycomb Repressive Complex 1 (PRC1), PRC2 and other script, splicing of the intron creates an open reading frame epigenetic repressors [95-97]. Expression of the various that generates the SRA protein (SRAP) [81]. The ratio bet- Dlk1-Dio3 transcripts is reciprocally regulated. For ex- ween the coding and noncoding SRA transcripts varies ample, the Glt2/Meg3 lncRNA binds to PRC2 recruiting it during muscle differentiation with SRAP mRNA being to the Dlk1-Dio3 locus to repress the protein-coding gene more abundant in myoblasts and SRA lncRNA being the Dlk1 and the lncRNA Gtl2-as (Figure 2C and Table 1). Neguembor et al. Skeletal Muscle 2014, 4:8 Page 6 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 Consistently, Glt2/Meg3 knockdown leads to a decreased including Cdc6 and Traf6 (Figure 2E and Table 1) [64]. PRC2 recruitment at the Dlk1 promoter with subsequent Both STAU1 and STAU2 interact directly with the ATP- increased expression of Dlk1 and Gtl2-as [95]. During dependent RNA helicase UPF1, a key SMD factor, enhan- development, Gtl2/Meg3 is abundantly expressed in the cing its helicase activity to promote effective SMD. Because paraxial mesoderm suggesting a role in myogenesis [55]. both SMD and the mechanistically related nonsense-me- Indeed, Gtl2/Meg3 knockout mice develop skeletal muscle diated mRNA decay (NMD) employ UPF1, SMD and developmental defects along with perinatal death [56], NMD are competitive pathways. This competition plays an promoting Gtl2/Meg3 as an example of a nuclear, cis- important role in the control of muscle differentiation. In- acting lncRNA regulating muscle development. deed, during myogenesis, the efficiency of NMD decreases H19 was the first lncRNA described in mammalian cells while the efficiency of SMD increases. Interestingly, Myo- [98]. It is transcribed from the maternal allele of the H19/ genin and PAX3 are differentially targeted by these two Igf2 locus producing a lncRNA predominantly enriched in pathways of degradation and this different susceptibility the cytoplasm [98]. H19 is highly expressed in developing contributes to their relative abundance during differenti- embryo and adult muscle in human and mouse [99,100], ation. PAX3 mRNA is an SMD target and its increased and is upregulated during myoblast differentiation and decay promotes myogenesis, whereas decreased degrad- muscle regeneration [57,101]. H19 works at multiple ation of the NMD target Myogenin is required for myogen- levels. Through binding to the PRC2 epigenetic repressor esis [109]. Importantly, since close to one third of all complex [95], H19 can mediate the transcriptional repres- lncRNAs contains at least one SINE [64,110], lncRNAs sion of Igf2 (Figure 2C) [102,103]. Moreover, H19 can bind containing SINE sequences could be at the heart of Igf2 mRNA binding-protein (IMP) family members to many physiologically important processes in addition to regulate Igf2 post-transcriptionally [104]. Also, H19 con- myogenesis. tains several binding sites for the let-7 family of micro- RNAs suggesting that H19 may act as a miRNA sponge LncRNAs in muscle diseases for let-7 (Figure 2D and Table 1) [57]. Among let-7 Growing evidence shows that the vast majority of disease- targets, Hmga2 and Igfbp2 have an important role in myo- associated genetic variations occur in the noncoding por- blasts proliferation and myogenesis but must be downreg- tion of the genome. In fact, whereas only 7% of disease- ulated to allow the formation of multinucleated myofibers associated SNPs localize in protein-coding exons, the (Figure 2D) [105]. Finally, H19 exon 1 encodes the con- remaining 93% arise in noncoding areas of the genome, of served microRNAs miR-675-3p and miR-675-5p [106]. which 43% fall in intergenic regions [111]. Considering Recent results indicate that, by targeting Smad1, Smad5, the extensive transcription of these areas, it is reasonable and Cdc6, these miRNAs play an important role in the to predict that a significant and yet unknown number of skeletal muscle differentiation and regeneration activities lncRNAs are involved in a variety of human diseases. associated to H19 [101]. LncRNAs can either have a primary role in the patho- genesis of a disease or rather act as modulators of disease LncRNAs containing repetitive sequences controlling penetrance, explaining, at least in part, the inter-personal mRNA decay variability observed in virtually every disorder. So far, the Short interspersed elements (SINEs) are among the most contribution of lncRNAs to disease has mostly been inves- abundant repetitive sequences in mammalian genomes tigated in cancer and neurological disorders [112-114] but [107]. While initially thought of as ‘junk’ DNA, SINEs can the first examples of lncRNA involved in myopathies are be transcribed as individual elements by RNA polymerase now unveiled. Here, we focus on the recent discoveries re- III or as part of longer transcripts synthesized by RNA garding the role of lncRNAs in Duchenne muscular dys- polymerase II and they can regulate gene expression by di- trophy and facioscapulohumeral muscular dystrophy. verse mechanisms [41,108]. It has recently been discovered that a SINE within the 3′ UTR of a protein-coding RNA Duchenne muscular dystrophy can form intermolecular base pairing with a partially com- Duchenne muscular dystrophy (DMD) is the most com- plementary SINE within one or more lncRNAs [43,64]. mon and severe myopathy affecting 1:3,500 males. It is Extensive yet imperfect stretches of double-stranded RNA inherited in an X-linked recessive manner but, in very (dsRNA) can be bound at multiple sites by dsRNA-binding rare cases, heterozygous females can be mildly affected proteins, including Staufen 1 and 2 (STAU1 and STAU2). [115]. DMD is characterized by severe muscle wasting Staufen recruitment activates Staufen-mediated mRNA from early childhood that usually arises in leg and pelvic decay (SMD), an important mRNA degradation process in muscles and later extends to the trunk of the body, com- mammalian cells. Using this mechanism, lncRNAs con- promising the heart and respiratory muscles. DMD is taining SINEs regulate the stability of several mRNAs caused by a variety of out-of-frame mutations in the dys- encoding for proteins with a role in muscle differentiation, trophin (DMD) gene encoded on the X chromosome Neguembor et al. Skeletal Muscle 2014, 4:8 Page 7 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 (Xp21.2) resulting in the lack of a functional dystrophin DMD mutations may impact the expression of the protein in skeletal muscle. With 79 exons and 2.4 Mb in lncRNAs. size, DMD is the largest gene of our genome and up to The mutations occurring in DMD patients could also 2,900 types of mutations have been reported in DMD deregulate the expression of lncRNAs located outside the patients so far [116,117]. Despite the mutations trig- dystrophin gene or could even give rise to new lncRNAs gering the disease being well characterized, the regula- as a result of translocation events. This could modulate tion of dystrophin is in part unknown and appears much the severity of the muscle degeneration or contribute to more complex than previously thought. Moreover, the the development of additional symptoms such as the inter-individual variability in the severity and the disease neurological complications observed in around one third progression is only partially explained by the types of of the patients [120,121]. A single case study recently pub- mutations and the occurrence of female patients remains lished explores this hypothesis and describes how an in- enigmatic. Therefore, the regulation of DMD is an area of trachromosomal inversion (inv(X)p21.2;q28) disrupts the intense research that in the last few years has led to the novel lncRNA KUCG1 in a DMD patient with moderate characterization of miRNA and lncRNA involvement [118]. mental retardation [122]. KUCG1 is a 648-bp nuclear Using custom-made tiling arrays, 14 lncRNAs tran- lncRNA expressed in a tissue specific manner [122]. Since scribed from intronic sequences of the DMD gene both it is normally expressed in the brain, its deregulation could in sense and antisense orientations were recently identi- contribute to the neurological impairment of the patient fied [119]. These lncRNAs are expressed concomitantly [122] as already reported for other pathologies [114]. Al- with dystrophin in at least one of the tissues that nor- though a functional characterization of this transcript has mally express it: skeletal muscle, heart and brain [119]. not been performed, this study underscores the patho- Ectopic expression and promoter binding assays suggest logical potential of mutations in noncoding loci that often that the lncRNAs can function in trans by downregulat- follow genomic rearrangements. ing the expression of specific dystrophin isoforms target- Another lncRNA associated with DMD is long intergenic ing their promoters (Figure 3A). Interestingly, an inverse noncoding RNA-muscle differentiation 1 (linc-MD1) [46]. correlation was found between the levels of dystrophin Linc-MD1 is a muscle-specific lncRNA required to acti- and a subset of lncRNAs in female carriers, both symp- vate late stages of the myogenic program. Linc-MD1 is a tomatic and asymptomatic [119]. It remains to be inves- cytoplasmic ceRNA that acts as a molecular sponge for tigated if these lncRNAs act in an allele-specific manner miR-133 and miRNA-135 (Figure 3B and Table 1) [46]. or whether they may also modulate the expression of the Through this mechanism, linc-MD1 promotes the expres- wild type dystrophin allele in female carriers. Additio- sion of myocyte-specific enhancer factor 2C (MEF2C) and nally, it would be interesting to define how different mastermind-like protein 1 (MAML1), two transcription Figure 3 Proposed roles for long noncoding RNAs (lncRNAs) in Duchenne muscular dystrophy. (A) In the nucleus, sense and antisense transcription from intronic sequences of the dystrophin (DMD) gene gives rise to lncRNAs that play a repressive effect at specific DMD promoters. (B) In the cytoplasm, the muscle specific lncRNA linc-MD1 acts as a competitive endogenous RNA (ceRNA) by sequestering miRNAs away from their target mRNAs. Linc-MD1 contributes to muscle differentiation by sponging miRNA-135 and -133, and thus promoting the expression of MEF2C and MAML1. Linc-MD1 is strongly reduced in muscle cells from DMD patients. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 8 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 factors with an important role in muscle differentiation is highly polymorphic, displaying 11 to more than 100 (Figure 3B) [46]. Interestingly, the levels of linc-MD1 are units [128,129]. On the contrary, FSHD patients carry strongly reduced in primary myoblasts of DMD patients deletions reducing D4Z4 copy number between one and and its ectopic expression rescues the myogenic differenti- ten units [129,130]. D4Z4 deletion is associated with a ation potential of these cells, restoring the correct expres- profound change in the epigenetic status of the 4q35 re- sion pattern of MAML1, MEF2C, MYOG and MHC [46]. gion [131]. A recently identified lncRNA plays a key role Linc-MD1 can have a double life as lncRNA or as miRNA, in this transition [37]. In healthy subjects, the FSHD locus since its primary transcript harbors the pri-miR-133b se- is under a repressive chromatin status, with high levels of quence. The balance between linc-MD1 and miR-133 bio- DNA methylation, histone de-acetylation and enrichment genesis is regulated by HuR, an RNA-binding protein with for repressive histone marks such as H2Aub1, H3K9me3 a crucial role in myogenesis (Table 1) [123]. Moreover, and H3K27me3. Indeed, D4Z4 has been recently identi- HuR facilitates the linc-MD1-miRNA interaction, enhan- fied as a novel Polycomb (PcG) target region, suggesting cing its sponge activity, thus affecting this ceRNA circuitry that the presence of a high number of D4Z4 units leads to potentially relevant for DMD [58]. the extensive recruitment of PcG and the consequent re- pression of 4q35 genes in healthy subjects (Figure 4). In Facioscapulohumeral muscular dystrophy FSHD patients, instead, the reduction in number of D4Z4 Facioscapulohumeral muscular dystrophy (FSHD) is the units under a critical threshold leads to a reduced PcG third most common muscular dystrophy (1:14,000). binding with decreased levels of H3K27me3, particularly FSHD is transmitted in an autosomal dominant manner in the region immediately proximal to the D4Z4 repeat and affects both sexes but presents a gender bias, as array. As a result, this region becomes more prone to males are usually more severely affected [124]. FSHD transcription and gives rise to the activatory lncRNA displays a more restricted pattern of muscle weakness DBE-T. DBE-T is mainly produced in FSHD patients and compared to DMD, mainly confined to the facial mimic mediates the aberrant activation of the FSHD locus [37]. and shoulder girdle muscles but extending to abdominal DBE-T is a nuclear transcript that acts in cis as it re- and leg muscles in the most severe cases [125,126]. The mains associated with the chromatin of the FSHD locus genetic lesion involved in FSHD is unusual as it does (Figure 4) [37]. DBE-T directly binds to the Trithorax not target a protein-coding gene, but rather affects the (TrxG) protein ASHL1 recruiting it to the FSHD locus copy number of the 3.3 kb macrosatellite D4Z4 mapping where it mediates the accumulation of H3K36me2 [37], a at the subtelomeric region of chromosome 4 (4q35) histone modification that counteracts PcG repressive ac- [127]. In the general population, D4Z4 copy number tivity [132-134]. Consequently, this leads to altered higher Figure 4 Role of DBE-T long noncoding RNA (lncRNA) in facioscapulohumeral muscular dystrophy (FSHD). In healthy individuals, the D4Z4 array displays from 11 to more than 100 units and is extensively bound by Polycomb group proteins (PcG), leading to the repression of the locus. In FSHD patients, the reduction of D4Z4 copy number to below 11 units causes decreased PcG binding and hence reduced silencing. This allows the transcription of the lncRNA DBE-T that remains associated to the FSHD locus and recruits the TrxG protein ASHL1 leading to activation of FSHD candidate genes. Neguembor et al. Skeletal Muscle 2014, 4:8 Page 9 of 12 http://www.skeletalmusclejournal.com/content/4/1/8 order chromatin organization and derepression of FSHD Received: 14 February 2014 Accepted: 11 March 2014 Published: 31 March 2014 candidate genes localized nearby the D4Z4 array and unleashing FSHD pathogenesis [37]. References 1. 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Shahrizaila N, Wills AJ: Significance of Beevor's sign in facioscapulohumeral dystrophy and other neuromuscular diseases. Submit your manuscript at J Neurol Neurosurg Psychiatry 2005, 76:869–870. www.biomedcentral.com/submit

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Skeletal MuscleSpringer Journals

Published: Mar 31, 2014

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