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Curr Psychiatry Rep (2010) 12:154–161 DOI 10.1007/s11920-010-0102-1 Small RNA-Mediated Gene Regulation in Neurodevelopmental Disorders Abrar Qurashi & Peng Jin Published online: 19 March 2010 # Springer Science+Business Media, LLC 2010 Abstract An expanding assortment of small, noncoding RNAs identified in the nervous system suggests a strong connection between their combinatorial regulatory potential and the complexity of the nervous system. Misregulation of these small regulatory RNAs could contribute to the abnormalities in brain development that are associated with neurodevelopmental disorders. Here we give an overview of the diversity and unexpected abundance of small RNAs, as well as specific examples that illustrate their functional significance in neurodevelopmental disorders. We also discuss an intriguing, albeit elusive area of study: the potential impact of newly discovered classes of small RNAs in the nervous system. Keywords Small RNA . microRNA . Neurodevelopmental disorder . Fragile X syndrome . Rett syndrome . DiGeorge syndrome . Down syndrome Introduction The perception of RNA solely as a messenger between DNA and protein was changed radically when RNA was found to catalyze its own replication and the synthesis of A. Qurashi Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA e-mail: [email protected] P. Jin (*) Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA e-mail: [email protected] other RNA molecules. This led to the idea that RNA might have been the first genetic material on earth, giving rise to the concept of the “RNA world”; it also suggested that RNA could play a more active role in gene expression than previously thought. Since the discovery of the first small RNAs, lin-4 and let-7, and their ability to trigger silencing of a complementary messenger RNA sequence, a new era of RNA function in gene regulation has opened up [1]. With analyses of the human genome showing that 98% of the transcriptional output of the genome does not translate into proteins, noncoding RNA has taken on more importance for humans, with similar findings for mice and other eukaryotes [2–4]. After the initial discovery of lin-4 and let-7, the number of known small RNAs mushroomed, and they have been described as the “dark matter” of the cell. At present, much scientific interest is focused on the small noncoding RNAs because they target both chromatin and transcripts, thereby keeping both the genome and the transcriptome under extensive surveillance [1]. They are involved in a range of physiologic functions, such as developmental transitions and neuronal patterning, apoptosis, fat metabolism, and regulation of hematopoietic lineage differentiation [1, 5–9•]. Although the known small RNAs act to regulate gene expression, they do differ widely in terms of their size, structural and/or sequence features, biogenesis mechanism, type of protein-binding partners, and the manner in which they function. Based on these criteria, they are sorted into three classes: microRNAs (miRNAs), endogenous small interfering RNAs (esiRNAs), and Piwi-interacting RNAs (piRNAs) [1, 9•] (Fig. 1). The human nervous system is sophisticated in its unique ability to achieve higher-order cognitive functions, including learning and memory. This functional property is in turn orchestrated by a complex set of multilayered developmental mechanisms. Alterations to specific components of these Curr Psychiatry Rep (2010) 12:154–161 155 + + – Transcription + + – – + – Transcription – Transcription pri-miRNA Drosha AAAA m 7G DGCR8 esiRNA precursors pre-miRNA piRNA precursors Exportin-5/ RanGTP cisdsRNA Hairpin transdsRNA Nucleus Export Export Export Cytoplasm Dicer Primary processing AGO1–4 TRBP or PACT Miwi2 Dicer TRBP Miwi2 Miwi Ping pong cycle Target p Ago2 Mili AAAAA A esiRNA B Fig. 1 Biogenesis of small regulatory RNAs in mammals. a Genes encoding microRNAs (miRNAs) are initially transcribed by RNA polymerase II or III to generate the primary miRNA transcripts (pri-miRNA) within the nucleus. The stem loop structure of the primiRNA is recognized and cleaved on both strands by a microprocessor complex, which consists of the nuclear RNase III enzyme Drosha and an RNA-binding protein, DGCR8, to yield a precursor miRNA (premiRNA) 60 to 70 nucleotides in length. The pre-miRNA is then exported from the nucleus through a nuclear pore by exportin-5 in a Ran-GTPdependent manner and processed in the cytoplasm by the RNase III Dicer, TRBP (HIV-1 TAR RNA-binding protein). Sliced RNA strands are further unwound by an RNA helicase. One strand of the miRNA/ miRNA* or siRNA duplex (the antisense, or guide strand) is then preferentially incorporated into the RNA-induced silencing complex (or miRNA-containing ribonucleoprotein complex [miRNP] for miRNAs) and will guide the miRNP to a target mRNA in a sequence-specific C manner. b The precursors of Piwi-interacting RNA (piRNA) are derived from intergenic repetitive elements, transposons, or large piRNA clusters. piRNA precursors are transported via an unknown mechanism to the cytoplasm. Once in the cytoplasm, they are associated with Piwi subfamily proteins. After primary processing, these precursors interact with Piwi proteins. Both Miwi and Mili are localized in the cytoplasm. The proteins involved in primary processing remain elusive. Mili introduces a cleavage in the precursor-generating 5′ end of piRNA, which is subsequently accepted by Miwi2. Miwi2 also cleaves the opposite strand precursor, generating the 5′ end of the piRNA that subsequently binds to Mili. The nuclease that creates the 3′ end of piRNA has yet to be determined. c Endogenous siRNA (esiRNA) precursors are derived from repetitive sequences, either sense–antisense pairs or long-stem loop structures. Their biogenesis is mediated by Dicer and Argonaute 2 protein (AGO2) 156 developmental stages and maturational processes lead to a broad spectrum of neurodevelopmental disorders that predispose people to neuropsychiatric disorders, including intellectual disability, autism, attention-deficit/hyperactivity disorder, and epilepsy [10, 11]. Despite their unique etiology and clinical presentation, most neurodevelopmental disorders share a common trait: disease onset occurs during periods of ongoing maturation and development. Importantly, a mixture of genetic mutations and environmental and epigenetic factors seems to impact neurodevelopment, leading to nervous system dysfunction [10, 11]. Small regulatory RNAs, particularly miRNAs, are dynamically regulated in neurogenesis and brain development [1, 10]. It is now well-established that small RNAs, particularly miRNAs, show distinct expression patterns during mammalian brain development and are considered to be key regulators of the nervous system, at least in lower organisms [1, 10]. Tightly controlled miRNA expression is required for proper neurodevelopment; conversely, specific miRNA dysregulation is likely linked to the pathogenesis of neurological disorders [1, 10, 11]. In this review, we focus on our understanding of the functional impact of small regulatory RNAs on brain development in general, as well as in several well-defined genetic disorders. Small Regulatory RNAs in the Genome There are at least three known classes of small regulatory RNAs in mammalian genomes: miRNAs, esiRNAs, and piRNAs. They are classified based on their biogenesis mechanism and protein-binding partners, as well as their structural and/or sequence features [9•] miRNAs: Biogenesis and Mode of Action miRNAs are endogenous 18- to 25-nucleotide (nt), singlestranded, noncoding regulatory RNAs that are known to regulate the translation of target mRNA molecules in a sequence-specific manner [1, 8, 9•, 10, 11]. The biogenesis of miRNAs involves enzymatic machinery that is wellconserved across animals and plants [8, 10]. Typically, RNA polymerase II mediates the transcription of most miRNA genes to generate the primary miRNAs (primiRNAs), which range from hundreds to thousands of nucleotides in length and contain one or more extended hairpin structures [1, 9•]. In the nucleus, a complex containing both the RNase III endonuclease Drosha and DiGeorge syndrome critical region gene 8 (DGCR8) cleaves both strands near the base of the primary stemloop and yields the approximately 65-nt or longer precursor miRNA (pre-miRNA) [1, 9•]. Recent studies indicate that the processing of pri-miRNA may be coupled with Curr Psychiatry Rep (2010) 12:154–161 transcription. In this case, Drosha cleaves the pri-miRNA hairpin to yield pre-miRNA; the rest of the transcript undergoes pre-miRNA splicing and produces mature mRNA for protein synthesis [1, 9•]. Apart from canonical intronic miRNAs, a small group of miRNAs called mirtrons (intronic small RNAs) has been discovered in the introns of flies and mammals. These small RNAs are derived from small introns that resemble pre-miRNAs and can bypass the Drosha-processing step [1, 9•]. Following nuclear processing, pre-miRNAs are transported out of the nucleus by exportin-5/RanGTP and are further processed by Dicer, a double-stranded RNA (dsRNA)-specific endonuclease, along with a dsRNA-binding protein and TRBP (HIV-1 TAR RNA-binding protein) to produce an approximately 22-nt RNA duplex. One strand of the approximately 22-nt RNA duplex is then preferentially incorporated into the effector complex, the RNA-induced silencing complex (RISC), as a mature miRNA (the guide strand or miRNA), whereas the other strand (the sense, or passenger strand) is degraded [1, 9•]. The RISC is a large, heterogeneous, multiprotein complex whose key components include Dicer, TRBP, and Argonaute 2 protein (AGO2). The RISC uses the guide RNA to find complementary mRNA sequences via base-pairing with (in many cases) the 3′untranslated region (3′-UTR) of target mRNAs, which leads to post-transcriptional gene silencing via inhibition of translation initiation or elongation [1, 9•]. miRNA could also negatively regulate protein expression through targeting of mRNA coding regions [1, 9•]. Piwi-Interacting RNAs and Endogenous Small Interfering RNAs piRNAs were first discovered through small RNA profiling of Drosophila melanogaster [5]. High-throughput sequencing uncovered a subset of endogenous, germ cell-specific small RNAs (24–31 nt) that were clearly distinct from miRNAs in size. Most of this longer species corresponded to intergenic repetitive elements, including retrotransposons; they were therefore termed repeat-associated small interfering RNAs (rasiRNAs). Earlier studies in D. melanogaster had suggested that small RNAs that correspond to retrotransposons might be involved in the silencing of transposable elements [5, 9•]. The physical interaction of rasiRNAs with Piwi proteins was revealed by immunoprecipitation of Piwi complexes, including the third member of this subfamily, AGO3. The Piwi subfamily proteins in mice (Miwi2, Mili, and Miwi) as well as in zebrafish (Ziwi and Zili) were also found to be associated with small RNAs that resemble rasiRNAs. These small (24–31 nt) RNAs were termed piRNAs and correspond to transposon sequences, implying that they also function in silencing selfish DNA elements [5, 9•]. Although the biogenesis of piRNAs has not been Curr Psychiatry Rep (2010) 12:154–161 well-characterized, current studies suggest that it requires Piwi proteins, but, unlike miRNAs and siRNAs, they are neither Drosha- nor Dicer-dependent. piRNAs are likely produced from long, single-stranded RNA precursors that are transcribed from intergenic repetitive elements, transposons, or large piRNA clusters by yet-to-be-identified endonucleases [9•, 12••, 13••]. Another recently discovered class of small RNAs expressed more ubiquitously is that of esiRNAs, which are about 21 nt in length. The biogenesis of esiRNAs initiates with bidirectional transcription or the transcription of an inverted repeat [9•, 11]. The resulting dsRNA or the hairpin RNA precursor is then processed by the components of the miRNA pathway [9•, 11]. miRNAs in Neurodevelopment: A General View Although many of the brain-specific miRNAs have been identified, the functions of only a few are known. Nonetheless, the effects of miRNA-mediated modulation on gene expression during normal development, differentiation, and homeostasis, as well as related pathological conditions, are widely accepted [1, 8, 14, 15]. Strong evidence for the biological roles of miRNAs in neural development emerged from their identification within the homeobox (HOX) gene clusters. Hox genes function in patterning the anterior-posterior axis of the central nervous system, and several miRNA genes located within the Hox gene clusters provide control over development [1, 16]. Deletion of both maternal and zygotic Dicer in zebrafish and Dicer-deficient mice supports a role for miRNAs during segmentation and differentiation or maintenance of tissue identity [1, 8, 10, 17, 18]. However, the importance of miRNAs in the establishment of tissue fate came from studies in Drosophila, in which the patterned expression of many miRNAs was seen at the onset of zygotic transcription in early embryos [1]. Similarly, studies in Caenorhabditis elegans have shown that the cell fate decision between two taste receptor neurons and maintenance of their identity arises via a complex regulatory network of interactions between two miRNAs, miR-273 and lsy-6, and their transcription factor targets [1, 6]. As neurons undergo differentiation, changes in the expression of a small number of miRNAs (eg, increased expression of miR-124 and miR-9) do occur [1, 8, 10]. A role for miR124 in neurogenesis has been established definitively in vivo, revealing its critical role in neuronal differentiation from neural precursor cells [1, 8, 10]. miRNAs continue to be expressed or enriched in adult neurons, particularly at dendrites, where they contribute to local translational control in an activity-dependent manner to sculpt the translational profile. The implications of this in 157 brain development and plasticity become clear from rat hippocampus synapses, where miRNA-134 is present at synaptic sites and maintains the translational silencing of the Limkinase1 (LimK1) mRNA until a synaptic input overrides the silencing [19]. LimK1 regulates actin filament dynamics and has important functions in dendrite and spine development and maintenance. Another study demonstrated that miR-138 controls dendritic spine morphogenesis; likewise, miR-132 targets and represses P250GAP, a Rho/ Rac regulator. Ashraf and colleagues [20] have shown that protein synthesis of α-calcium/calmodulin-dependent protein kinase II (α-CaMKII) is controlled by the RISC component Armitage, which is co-localized with α-CaMKII in synaptic punctate. The dsRNA-binding proteins Staufen and kinesin heavy chain are under similar control. When Armitage is degraded in response to neural activity, α-CaMKII mRNA translation is increased [20]. Combined, these studies suggest that the miRNA pathway is involved in the regulation of local protein synthesis, which is in turn required for the neuronal construction and plasticity that ultimately affects higher brain functions (eg, learning and memory) [8]. miRNAs in Neurodevelopmental Disorders Given the role of miRNA in neuronal development and the control of neuronal functional elements, many researchers have sought a link between miRNAs and neurodevelopmental diseases. Indeed, the roles of specific miRNAs have been explored in several neurodevelopmental diseases (eg, fragile X syndrome [FXS], Rett syndrome, DiGeorge syndrome [DGS], and Down syndrome [DS]). Fragile X Syndrome FXS, one of the most common forms of inherited mental impairment, was the first genetic disorder linked to the miRNA pathway [7, 21]. Clinical presentations of FXS include characteristic physical and learning disabilities, as well as more severe cognitive and intellectual disabilities. In 1991, positional cloning of the fragile X mental retardation-1 (FMR1) gene revealed the molecular basis of FXS; the syndrome is associated with a massive unstable CGG trinucleotide repeat expansion within the gene’s 5′-UTR. The disease becomes clinically manifest as the gene is passed from generation to generation and the CGG repeat in the 5′-UTR of an Fmr1 allele expands, shutting down production of the FMR1 gene product, fragile X mental retardation protein (FMRP) [7, 21]. The association of FMRP with the RISC and miRNAs themselves can be drawn through various biochemical and genetic interaction studies. In flies, dFMRP biochemically interacts with functional RISC proteins, including dAgo1, 158 dAgo2, and Dicer [8, 11, 21]. Genetically, dFmr1 dominantly interacts with dAgo1 in both dFmr1 overexpression and loss-of-function models. Pickpocket1 (PPK1) was found to be an mRNA target of dFMRP, and the expression of PPK1 seems to be regulated by both dFMRP and dAgo2 [22]. Other studies supporting the involvement of FMRP in miRNA/RNA interference function come from the identification of P body-like granules in Drosophila neurons that function together with Me31B in an Argonaute-dependent translational repression [23]. Interestingly, FMRP itself can associate with and act as an acceptor protein for Dicerderived miRNAs and, importantly, facilitate the assembly of miRNAs on specific target RNA sequences. In the adult mouse brain, Dicer and eIF2c2 (the mouse homologue of AGO1) also have been found to interact with FMRP at postsynaptic densities [24]. Presumably, this interaction works to regulate translation of target mRNAs in an activity-dependent manner. Based on these findings, it has been proposed that RISC components, including Argonaute and Dicer, could interact with FMRP and use the loaded guide miRNA(s) to interact with target sequences within the 3′-UTR of mRNA bound to FMRP and thereby suppress translation. In this model, FMRP facilitates the interaction between miRNAs and their target mRNA sequences, ensuring proper targeting of guide miRNA-RISC within the 3′-UTRs and proper translational suppression. That FMRP is associated with Dicer, miRNAs, and specific mRNA targets raised the question of whether FMRP could be associated with specific miRNAs and modulate their processing. Although whether specific miRNAs are associated with FMRP in mammals remains to be determined, in flies, dFMRP is required for proper processing of pre-miR-124a; loss of dFmr1 leads to a reduced level of mature miR-124a and an increased level of pre-miR-124a [25]. These results suggest a modulatory role for dFMRP to maintain proper levels of miRNAs during neuronal development. Furthermore, in fly ovaries, bantam miRNA (bantam) is associated with dFMRP physically and genetically for the proper maintenance of germline stem cells, thus supporting the notion that the FMRP-mediated translational pathway functions through specific miRNAs to control stem cell regulation [26, 27]. Rett Syndrome Rett syndrome, an X-linked progressive neurodevelopmental disorder associated with mental retardation, is believed to result from loss of methyl CpG binding protein-2 (MeCP2) in neurons [28, 29]. In a typical case, MeCP2 expression increases as neurons differentiate prior to synaptogenesis. MeCP2 has been shown to function as a transcriptional repressor complex [29, 30]. More recently, MeCP2 was shown to function as a transcriptional activator at certain loci Curr Psychiatry Rep (2010) 12:154–161 [30]. The epigenetic regulation mediated by MeCP2 is also provided through the transcription of noncoding RNA elements such as miRNA. In the absence of MeCP2, some miRNAs may display increased expression, which may result in a negative effect on the translation of mRNAs targeted by that particular miRNA. Importantly, in postnatally cultured rat neurons, miR-132 directly represses the expression of MeCP2. MeCP2 is also known to bind to the methylated brain-derived neurotrophic factor (BDNF) promoter and is released from it after depolarization, resulting in unregulated gene expression [31, 32]. BDNF is also a known activator of the cyclic adenosine monophosphate response element-binding (CREB) protein, a critical transcription factor regulating activity-dependent neuronal plasticity. miR-132 expression is specifically increased by BDNF through the activation of CREB. Based on these findings, a regulatory mechanism involving the transcriptional regulation of miR-132 has been proposed for the homeostatic control of MeCP2 protein during neuronal morphogenesis [31, 32]. It is also interesting that MeCP2 regulates the expression of some imprinted genes, and these imprinted genes show dysregulated expression in Rett syndrome. Moreover, the induction of miR-184 expression in depolarized cultured neurons occurs at the same time as the loss of MeCP2 binding upstream of the miR-184 locus. These data suggest that the regulation of miR-184 expression by MeCP2 is activity dependent; however, the expression of miR-184 is not significantly changed in whole brain tissue derived from MeCP2-deficient mice [33]. DiGeorge Syndrome DGS is a rare congenital disease that results from hemizygous deletion of 1.5 to 3 megabases of DNA on chromosome 22q11.2. DGS arises from de novo deletions about 90% of the time, with the remaining cases inherited in an autosomal dominant fashion from a parent who carries the deletion. DGS is a variable syndrome that commonly includes a history of recurrent infection, heart defects, and characteristic facial features. Individuals with DGS have behavioral and cognitive deficits that lead to childhood pathologies, including attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, and autism spectrum disorder [34–36]. About 40 genes are deleted in DGS and are therefore haploinsufficient in patients with DGS. Interestingly, the Drosha partner, DGCR8, was mapped to this region [9•]. Heterozygotes of DGCR8 knockout mice display cognitive delays and reductions in the full complement of pre-miRNAs and mature miRNAs; however, it remains to be determined whether reduced miRNA levels are an underlying cause of DGS [37]. Identification of the downstream targets that are misregulated in these miRNA- Curr Psychiatry Rep (2010) 12:154–161 deficient mutants would provide further insight into the pathogenesis of DGS as well as a better understanding of learning and cognition in general. Down Syndrome DS is a chromosomal abnormality in which triplication of all or part of human chromosome 21 occurs. DS is the most common genetic cause of cognitive impairment and congenital heart defects in humans [38–40]. Bioinformatic analyses have demonstrated that human chromosome 21 harbors five miRNA genes: MiR-99a, Let-7c, MiR-125b-2, MiR-155, and MiR-802 [41]. Importantly, expression studies found that these miRNAs are overexpressed in fetal brain and heart specimens from individuals with DS compared with those of age- and sex-matched controls. Based on this, the authors hypothesized that trisomic 21 gene dosage overexpression of human chromosome 21derived miRNAs results in the decreased expression of specific target proteins and contributes in part to features of the neuronal and cardiac DS phenotype [41]. A role for miRNAs in DS is further supported by the finding that miR-155 downregulates a human gene associated with hypertension, angiotensin II type-1 receptor (AGTR1) [42]. Indeed, individuals with DS do have lower blood pressure and lower AGTR1 protein levels than those without DS. Interestingly, improved computational and experimental methods now implicate other miRNAs residing on chromosome 21, making them excellent candidates to study for their role in the molecular pathogenesis of DS. In summary, miRNAs are abundant in the nervous system, where they are involved in neural development and are likely an important mediator of neuronal plasticity. Because miRNAs play a role in the fine-tuning of protein production, they could contribute significantly to the molecular pathogenesis of neurodevelopmental disorders. Aside from altered miRNA transcription and biogenesis, the dosage of miRNA genes associated with segmental duplication could contribute to the phenotypes as well. Furthermore, the significant numbers of single nucleotide polymorphisms in the human genome could potentially create or disrupt the putative miRNA target sites. Therefore, variations in the target mRNA sequences could also modulate the activity of specific miRNAs and contribute to phenotypic variation [43, 44]. It is likely that many of these variations would affect neuronal miRNAs. piRNAs and esiRNAs in Neurodevelopmental Disorders High-throughput sequencing has revealed that there are many more distinct piRNAs than miRNAs (>50,000 vs several hundred) [1, 9•]. Most piRNAs map to unique sites 159 in the genome, including intergenic, intronic, and exonic sequences, and only 17% to 20% of mammalian piRNAs map to annotated repeats, including transposons and retrotransposons, suggesting that piRNAs could have diverse functions [1, 9•]. In Drosophila, Piwi protein was found to co-localize with Polycomb group proteins to cluster Polycomb response sequences in the genome and with Rhino (HP1d), one of five heterochromatin-associated protein 1-like proteins, to modulate epigenetic silencing [45–47]. Conversely, Piwi protein and its associated piRNA can also promote the euchromatic character of certain heterochromatin regions and their transcriptional activity [48]. Epigenetic modulations could be the crucial link between external stimuli and gene expression, in which the interplay of environmental factors and non-Mendelian genetics alters gene expression, causing an array of multisystem disorders, particularly neurodevelopmental disorders [49, 50]. Given the involvement of piRNAs in epigenetic modulation, it would be interesting to explore the potential roles of piRNAs in neurodevelopmental disorders. Conclusions The list of small regulatory RNAs that play a part in the seamless way the complex nervous system is assembled is growing steadily. It seems that the roles of small regulatory RNAs in the physiology and development of the brain are diverse. They constitute a hidden layer of internal signals that control various levels of gene expression and epigenetic memory. Understanding the mechanistic function of these RNAs therefore is crucial to our understanding of neurodevelopmental disorders. Acknowledgments The authors would like to thank C. Strauss for help in editing this manuscript. Dr. Jin is supported by the International Rett Syndrome Foundation and the National Institutes of Health. Dr. Jin is also a recipient of the Beckman Young Investigator Award and the Basil O’Connor Scholar Research Award and is an Alfred P. Sloan Research Fellow in Neuroscience. Disclosure No potential conflicts of interest relevant to this article were reported. References Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance 1. Stefani G, Slack FJ: Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 2008, 9:219–230. 160 2. Amaral PP, Dinger ME, Mercer TR, Mattick JS: The eukaryotic genome as an RNA machine. Science 2008, 319:1787–1789. 3. 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