Advertisement
Browse Subject Areas
?

Click through the PLOS taxonomy to find articles in your field.

For more information about PLOS Subject Areas, click here.

  • Loading metrics

Open Access

Peer-reviewed

Research Article

Regulation of Emx2 Expression by Antisense Transcripts in Murine Cortico-Cerebral Precursors

Abstract

Background

Emx2 encodes for a transcription factor expressed in the embryonic intermediate mesoderm and central nervous system (CNS). It is implicated in several aspects of cerebral cortex development, including morphogenetic field specification, arealization, precursor proliferation and lamination. Four Emx2-associated antisense transcripts have been found in the urogenital system; one of them, Emx2OS, has been also detected in the adult brain. Until now, however, nothing is known about expression and function of Emx2OS in the developing CNS.

Methodology/Principal Findings

By quantitative RT-PCR and in situ hybridization, we reconstructed the Emx2OS expression profile in the embryonic CNS, paying special attention to the developing cerebral cortex. Emx2OS was observed in a number of CNS structures expressing also Emx2. Within the cortex, Emx2OS was detectable in periventricular precursors, expressing the sense transcript, and peaked in newly born post-mitotic neurons not expressing such transcript. By integrating lentiviral gene delivery, RNAi, TetON technology, morpholino-mediated gene knock-down, drug-induced perturbation of gene expression, and quantitative RT-PCR, we addressed possible roles of Ex2 antisense RNA in Emx2 regulation, in primary CNS precursor cultures. We found that, in both cortical precursors and their neuronal progenies, Emx2 antisense RNA contributes to post-transcriptional down-regulation of its sense partner, possibly by a Dicer-promoted mechanism. The same RNA, when delivered to rhombo-spinal precursors, stimulates ectopic expression of Emx2, whereas Emx2 knock-out dramatically impairs Emx2OS transcription. This suggests that, within the developing CNS, a reciprocal Emx2/Emx2OS regulatory loop may normally sustain transcription at the Emx2 locus.

Conclusions/Significance

This study shows that antisense transcripts may contribute to developmental regulation of a key transcription factor gene implicated in CNS patterning, possibly by complex and multilevel mechanisms. The activation of Emx2 by a short antisense transcript may be a prototype of a method for overexpressing single specific genes, without introducing additional copies of them into the genome.

Citation: Spigoni G, Gedressi C, Mallamaci A (2010) Regulation of Emx2 Expression by Antisense Transcripts in Murine Cortico-Cerebral Precursors. PLoS ONE 5(1): e8658. https://doi.org/10.1371/journal.pone.0008658

Editor: Bernadette Breant, INSERM, France

Received: October 15, 2009; Accepted: December 14, 2009; Published: January 11, 2010

Copyright: © 2010 Spigoni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was entirely supported by intramural SISSA funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Introduction

Emx2 is a transcription factor gene expressed in the developing urogenital and central nervous systems (CNS) [1], [3], crucial for proper morphogenesis of these structures [4], [6]. It is implicated in dorso-ventral specification of the rostral neural tube, conferring cortico-cerebral identity to precursors in the dorsal telencephalic vesicle and repressing the activation of striatal morphogenetic programs [7]. Expressed by cortical periventricular precursors along a caudal/medialhigh-to-rostral/laterallow gradient, it further promotes the specification of hippocampus and occipital cortex, while antagonizing rostral-lateral areal programs [8]–[10]. Within the embryonic brain, it stimulates neural precursors' self-renewal, at expenses of neuronal differentiation; these effects are apparently reverted in post-natal neural stem cells [11]–[14]. Finally, Emx2 is crucial to proper inside-out layering of the neocortical primordium. In its absence, pioneer Cajal-Retzius cells orchestrating such process are severely reduced and the neocortical lamination profile is deeply distorted, in a reeler-like way [15], [16].

Four main Emx2 antisense transcripts of 6.0, 5.0, 2,3 and 1,8 kb have been detected in the murine urogenital system by Northern blotting and a cDNA corresponding to the second of them, Emx2OS, has been isolated. Emx2OS expression has been studied by in situ hybridisation in the uro-genital system: like Emx2-mRNA, Emx2OS-ncRNA is abundant in normal postmenopausal endometrium, reduced in premenopausal endometrium, absent/reduced in many primary endometrial tumors [17]. Moreover, its human counterpart has been specifically detected in the adult brain, by Northern blot [17]. However, the Emx2OS expression profile has not been studied in the developing CNS and little is known about possible implication of Emx2OS in fine regulation of Emx2.

Several transcription factor genes implicated in CNS development harbor antisense transcripts. Antisense transcripts are encoded by Six3 [18], Msx1 [19]–[23], Pax6, Pax2, Six3, Six6, Otx2, Crx, Rax, Vax2 [24], Dlx 5/6 [25] and Hox loci [26]–[28]. More generally, antisense transcription is a genome-wide phenomenon, estimated to be associated with at least 10–40% of polypeptide-encoding genes [29]–[38]. Antisense/Sense (AS/S) pairs may be structurally classified as divergent, overlapping and convergent and it has been shown that they may display concordant, discordant or more complex expression patterns [39].

Based on various relationships occurring among AS expression levels and those of their sense partners, it has been predicted that the former ones might differentially promote or antagonize the expression of such partners, depending on the gene and on the context. Such prediction has been substantially confirmed in a variety of functional studies, indicating that: (1) AS transcription is not simple transcriptional noise or epiphenomenon of S transcription [36], but often results a prerequisite for proper regulation of “coding” sense genes; (2) molecular mechanisms by which AS transcripts act are extremely complex and largely diversified [39], [40].

In some cases, poor sequence conservation but similar exon/intron organisation characterizing antisense transcripts from different species suggests that transcription per se, and not the AS RNA molecule, may be crucial to the function. That has been demonstrated in the case of the silent human provirus HERV-K18, where AS transcription promotes S transcription [41], as well as in a variety of other cases, where AS transcription conversely inhibits S transcription, because of competition between the two transcriptional machineries for shared cofactors, or due to collision between them [42].

However, the AS transcript may also work as such, acting at distinctive regulatory levels. First, it may regulate the epigenetic state of chromatine, modulating the methylation state of DNA and/or histones [27], [43], [44]. Second, it may facilitate recruitment of transcription factors to enhancers impinging on the partner sense gene, so promoting its transcription. This is the case of the Evf2 ncRNA, cooperating with the homeoprotein Dlx2 in stimulating transcription of its sense partner Dlx6 [25]. Third, the AS ncRNA may modulate the splicing of its partner sense pre-mRNA, as reported for the TRa2 and Zeb2 loci [45], [46]. Fourth, AS transcripts may regulate the half-life of their sense partners. Pairing of retrotransposon sense and antisense transcripts paves the way to Dicer-dependent cutting of resulting dsRNAs, followed by siRNA-instructed silencing of sense transcripts, from the same or paralogous loci [47]–[49]. Fifth, antisense RNAs may modulate translation [50]. Last, they may be necessary for proper activity of their sense partners, as shown for the Xist/Tsix pair [51].

In this study, we investigated the expression pattern of Emx2OS-ncRNA in the developing CNS, by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in situ hybridisation (ISH). Then, by integrating lentiviral cDNA delivery, drug-induced perturbation of patterning pathways and gain- or loss-of-function (GOF and LOF, respectively) designs, we addressed possible roles of this transcript on regulation of its partner gene, Emx2, on primary CNS cultures as well as on cell lines. We found that Emx2 antisense transcripts may both stimulate and refine Emx2 expression. Moreover, such effects seem to be exerted at two distinct regulatory levels, transcriptional and post-transcriptional.

These results, beyond their contribution to the comprehension of mechanisms regulating cortico-cerebral development, suggest a possible general exploitation of AS-based methods, as a tool for artificial triggering of endogenous gene expression.

Results

Expression Pattern of Emx2OS-ncRNA

To get a first insight into expression and putative functions of Emx2OS-ncRNA, we compared its abundance with that of Emx2-mRNA, in cortico-cerebral and rhomboencephalic tissues, at four embryonic developmental ages, E10.5, E12.5, E14.5 and E18.5. As expected, Emx2-mRNA was specifically detectable in the cortex, where its levels went progressively down from E10.5 up to E18.5 [3], [52]. Interestingly, Emx2OS-ncRNA displayed similar spatial specificity and similar temporal progression (Fig. 1A and 2).

thumbnail
Download:
Figure 1. Synopsis of molecular tools used for studying expression and function of Emx2OS.

(A) Representation of the murine Emx2 locus, with the Emx2-mRNA and the Emx2OS-ncRNA transcription units (red). Genomic localization of the riboprobe used for in situ hybridization analysis of Emx2OS (blue bar). Genomic localization of the oligonucleotides employed for quantitative RT-PCR evaluation of Emx2OS-ncRNA (P1 and P3), Emx2-mRNA (N2F and N2R) and Emx2-pre-mRNA (I1, I2, I3 and I4) (blue arrowheads). (B) Structure of the bi-cistronic plasmids employed for assaying activities of artificial miRNAs against Emx2OS-ncRNA in HeLa cells and of lentivectors for overexpressing these miRNAs in primary cells. Localization of miR-αEmx2OS-542 and -774 (blue arrowheads) as well as of their responsive element, miR-RE, with respect to the antisense transcript. miR-RE (dark yellow), showed enlarged over the antisense transcript, extends across the 3rd and the 4th exons of it. (C) Structure of the “driver” lentivector, guiding constitutive expression of rtTA2S-M2, and of “expressor” lentivectors, guiding rtTA/doxycycline-dependent expression of ncRNA/IRES/eGFPcds modules. Genomic localization of OS1-179(+) and OS1-179(−) ncRNAs (blue arrows), as compared to Emx2OS-ncRNA and Emx2-mRNA (for sake of clarity, the sense/antisense ovarlapping region and its surroundings are represented enlarged; red, non coding sequences; violet, coding sequences).

https://doi.org/10.1371/journal.pone.0008658.g001

thumbnail
Download:
Figure 2. Time-course quantitative RT-PCR analysis of Emx2-mRNA and Emx2OS-ncRNA expression in the developing cortex and rhombencephalon.

Sense and antisense transcripts display concordant spatial distributions (abundant in the cortex, absent in rhombencephalon), from E10.5 to E18.5. Within the cortex, they share a similar temporal trend, being progressively down-regulated from the pre-neuronogenic (E10.5) to post-neuronogenic stages (E18.5). RTs are primed by random hexamers and PCRs by oligos shown in Fig. 1. Data are normalized on E10.5 cortical samples. Abbreviations: c, cortex; r, rhombencephalon.

https://doi.org/10.1371/journal.pone.0008658.g002

Then, we studied the Emx2OS-ncRNA expression pattern in the developing central nervous system (CNS), by non-radioactive in situ hybridisation (Fig. 1A). At E12.5, within the CNS, the transcript was detectable in the telencephalon (Fig. 3A,B), including both pallium and basal ganglia (Fig. 4A), in the mammillary recess of the hypothalamus (Fig. 3A, arrowhead) and in the midbrain, including tectum and tegmentum (Fig. 3C). No signal was detectable within the rhombo-spinal domain (Fig. 3A,D). Emx2OS was also expressed by the nasal pits (Fig. 3E), the otic vesicle (Fig. 3G), the choroid plexus of II and IV ventricle (Fig. 3A,D), as well as by two clusters of head mesenchyme cells, in the snout region (Fig. 3A, asterisk) and in the surroundings of the hypothalamic optic recess (Fig. 3F, arrowheads).

thumbnail
Download:
Figure 3. Distribution of Emx2OS transcripts in the embryonic E12.5 mouse brain.

(A–D) Within the E12.5 developing CNS, Emx2OS-ncRNA is detectable in telencephalon (A,B), mesencephalon (me), including both tectum (te) and tegmentum (tg), (panels A,C) and diencephalon, including the mammillary recess (arrowhead in panel A). It is not present in rhombencephalon (rh, panel G), except the choroid plexus of the IV ventricle (chp, panels A,D). Outside the CNS, Emx2OS is expressed in primordia of sense organs, nasal pits (np, panel E) and otic vesicle (ov, panel G), as well as in mesenchyme underlying snout epidermis (A, asterisk) and surrounding the hypothalamic (hy) optic recess (F, arrowheads). Scalebars, 200 µm in A–C, 50 µm in D–G.

https://doi.org/10.1371/journal.pone.0008658.g003

thumbnail
Download:
Figure 4. In situ hybridization profile of Emx2OS-ncRNA in the developing mouse telencephalon.

Distribution of Emx2OS-ncRNA (A–I) and Reln-mRNA (J–L) on mid-frontal sections of E12.5 (A), E14.5 (B) and E18.5 (C,G,J) mouse telencephalons. (D), (E) and (F) are magnifications of boxed areas in (A), (B) and (C), respectively. (H) and (I) are enlargements of boxed areas of panel (G), respectively; the same applies to panels (K) and (L) with respect to (J); (G) and (J) are adjacent sections from the same brain. Emx2OS is expressed in periventricular proliferative layers at all ages subject of analysis (A–C). An additional signal is detectable within the cortical plate starting from E14.5 (B) and gets confined to its marginal-most part at E18.5 (C). No Emx2OS expression can be detected in the neocortical marginal zone (G,H, empty arrowheads) as well as in the archicortical stratum lacunosum-moleculare (G,I), both rich of Reln+ Cajal-Retzius cells (J–L, solid arrowheads). Some aspecific staining may be found in meninges, at the edge of sections. Abbreviations: CA1, cornu Ammonis field 1; CA3, cornu Ammonis field 3; cp, CP, cortical plate; DG, dentate gyrus; HF, hippocampal fissure; iz, intermediate zone; mz, MZ, marginal zone; ppl, preplate; SLM, stratum lacunosum-moleculare; sp, subplate; svz, subventricular zone; vz, ventricular zone; Scalebars, 200 µm.

https://doi.org/10.1371/journal.pone.0008658.g004

Focussing our attention on the developing cerebral cortex, we found Emx2OS transcripts within periventricular proliferative layers, from E12.5 to E18.5 (Fig. 4A–F), as well as in the cortical plate (CP), especially in its more superficial part (Fig. 4E,F). Conversely, no signal was detectable within the preplate (PPL) and its derivatives, marginal zone (MZ) and subplate (SP) (Fig. 4D–F). In particular, no Emx2OS transcripts could be found within Cajal-Retzius (CR) cells, aligned beneath the pia mater and specifically expressing Reln mRNA, in both neocortex and hippocampus (Fig. 4G–L, empty and solid arrowheads).

Emx2OS Antagonizes Emx2 Expression

The mutually exclusive distribution of Emx2-mRNA and Emx2OS-ncRNA among cortico-cerebral neurons (the former expressed by CR neurons, the latter by CP neurons) suggested to us that reciprocal down-regulation between them might occur and that, in particular, Emx2OS-ncRNA might be implicated in repression of Emx2mRNA.

We first assayed this hypothesis by a LOF approach, i.e., by knocking-down Emx2OS-ncRNA in primary neurospheres derived from E12.5 cortical tissue, via RNAi, and monitoring consequences of that on Emx2-mRNA levels. For this purpose, we used a lentivirus constitutively expressing miR-αEmx2OS-774 (Fig. 1B), an artificial miR able to target Emx2OS sequences in HeLa cells (Fig. 5A). Under miR-αEmx2OS-774, Emx2OS-ncRNA signal was reduced by more than 2 times (p<0.002; n = 9) (Fig. 5B, left). Concomitantly, we observed a modest (+25%), but statistically significant (p<0.03; n = 9) increase of Emx2-mRNA.

thumbnail
Download:
Figure 5. Emx2OS knock-down in HeLa cells and dissociated cortico-cerebral precursors.

(A) Down-regulation of the miR-RE-sensitized DsRed2 reporter in Hela cells, upon overexpression of artificial miRNAs designed against Emx2OS. (B) Down-regulation of Emx2OS-ncRNA, up-regulation of mature Emx2-mRNA and unchanged levels of immature Emx2-pre-mRNA in E12.5-derived cortical primary cells (cx), acutely infected by miR-αEmx2OS-774-expressor lentivirus, kept in Sato medium and harvested 72 hours later. Data are normalized on control-miR-treated samples (miR-C). (C) Neuronal differentiation of lentivirus-transduced neural precursors kept 72 hours under 5% serum, as assessed by β-tubulin immunoprofiling. Down-regulation of Emx2-mRNA in miR-C-infected neural precursors, kept 72 hours under 5% serum in place of growth factors (GFs). Rescue of such down-regulation, elicited via miR-αEmx2OS-774-induced knock-down of Emx2OS-ncRNA. qRT-PCR data are normalized on control-miR-treated samples (miR-C), kept under GFs.

https://doi.org/10.1371/journal.pone.0008658.g005

To assess if upregulation of Emx2 induced by miR-αEmx2OS-774 took place at transcriptional or post-transcriptional level, we then measured Emx2 pre-mRNA levels, following infection of neurospheres with miR-αEmx2OS-774 or negative control lentiviruses. For sake of sensitivity and specificity, measurements were done by two-step quantitative RT-PCR, using two sets of nested primers annealing within the first Emx2 intron (Fig. 1A). Interestingly, no change in Emx2 pre-mRNA levels was found (Fig. 5B, right), suggesting that Emx2OS-dependent regulation of Emx2 took place at post-transcriptional level.

Remarkably, in previous sets of experiments, neural cultures were performed in DMEM/F12/N2 medium, containing the standard growth factors (GFs) mix which promotes the intermitotic/stem state [53]. As during embryonic development Emx2-mRNA disappears in post-mitotic neurons, where Emx2OS-ncRNA is transiently upregulated, the question arises: is Emx2OS-ncRNA able to down-regulate Emx2-mRNA also in nascent neurons? To address this issue, the Emx2OS-LOF tests were repeated culturing the infected cells in the presence of 5% serum, which stimulates neuronal differentiation, in place of GFs. Moreover, in this new experiment an aliquot of miR-C-infected cells was kept under GFs, as a control. Consistently with our expectations, under 5% serum plus miR-C lentivirus, neuronal differentiation was dramatically stimulated, as confirmed by massive activation of neuron-specific β-tubulin (Fig. 5C, top), Emx2-mRNA level decreased, by about 30% (Fig. 5C, bottom-right), and Emx2OS-ncRNA was only slightly downregulated (Fig. 5C, bottom-left). Remarkably, knock-down of Emx2OS induced by miR-αEmx2OS-774 rescued the Emx2-mRNA decrease to large extent (Fig. 5C, bottom-right), suggesting that Emx2OS-ncRNA substantially contributes to Emx2 down-regulation at the time when CP neurons are born.

Then, to confirm this model, we verified it by a complementary GOF approach, i.e. by delivering antisense Emx2 cDNA to embryo-derived neurospheres, via lentiviral vectors, and scoring consequences of that.

Unfortunately, the full-length 5.0 kb Emx2OS cDNA harbors several canonical polyadenylation signals, which make it hardly suitable for our lentiviral expression system. So, in place of it, we overexpressed its 5′-most 179 bp fragment, coinciding with the Emx2-mRNA/Emx2OS-ncRNA overlapping region minus a low-complexity 74 bp polypyrimidine tract. Assuming - in fact - that Emx2OS-ncRNA works by interacting with Emx2-mRNA via Watson&Crick base-pairing, this short fragment could recapitulate key regulative properties of the full-length Emx2OS-ncRNA. Moreover, in order to assay both consequences of antisense overexpression and their reversibility, we performed Emx2OS-GOF manipulations by a dual, TetON-based, lentiviral delivery system, triggered by doxycycline. Neurospheres were infected by a “driver virus”, harboring a constitutively expressed rtTA2S-M2 transactivator gene, plus an “expressor virus”, harboring the cDNA sequence subject of investigation (Fig. 1C).

Compared to the control, the Emx2 antisense-encoding lentivirus OS1-179(+) reduced the Emx2-mRNA level by 24.2% (p<0.001). OS1-179(−), encoding for the corresponding reverse-complementary sequence, increased it by 34.2% (while not reaching statistical significance). Moreover, Emx2-mRNA levels under OS1-179(+) and OS1-179(−) differred by −43.7% (p<0.01). Remarkably, these changes of Emx2-mRNA levels were mirrored by opposite concomitant changes of Emx2OS-ncRNA (Fig. 6A). In synthesis, OS1-179(+) both down-regulates Emx2-mRNA and promotes the expression of the endogenous antisense transcript, which may in turn contribute to Emx2 down-regulation.

thumbnail
Download:
Figure 6. Emx2 and Emx2OS expression in dissociated cortico-cerebral precursors and NIH/3T3 cells upon OS1-179(+) delivery.

(A) Emx2-mRNA and Emx2OS-ncRNA expression in primary neural precursor cells, derived from E12.5 cortices (cx) and acutely infected with the “driver” lentivector, plus “expressor” lentivectors [OS1-179(+), OS1-179(–) and control (C)] in different combinations. One day after sample dissociation, cells are administered with doxycycline and, two more days later, profiled for RNA. Data are normalized on control lentivirus-treated samples. OS1-179(+) induces a moderate, but statistically significant down-regulation of Emx2-mRNA, as well as a moderate up-regulation of the endogenous antisense transcript. (B) Emx2-mRNA expression in NIH/3T3 cells, acutely infected with the “driver” lentivector plus each of the three “expressor” lentivectors [OS1-179(+), OS1-179(-) or C]. Cells are administered 6 hours after infection with an anti-Dicer1 or a control (C) morpholino and 18 more hours later with doxycycline. Two more days later, they are RNA-profiled by qRT-PCR. Data reported in the histogram are normalized on samples infected by control lentivirus and exposed to control morpholino. Compared with lentivirus-C-treated controls, levels of Emx2-mRNA change upon OS1-179(+) infection by a factor of 0.56/1 = 0.56 (p<0.001) and 1.42/1.65 = 0.87 (p<0.01), in NIH/3T3 cells treated by control morpholino and α-Dicer1, respectively. Compared with morpholino-C-treated controls, levels of Emx2-mRNA change upon α-Dicer1 administration by a factor of 1.42/0.56 = 2.54 (p<0.001), 1.65/1 = 1.65 (p<0.001), and 1.82/1.31 = 1.39 (p<0.01), in cells infected by OS1-179(+), control or OS1-179(–) lentiviruses, respectively. Two-ways ANOVA data analysis suggests the occurrence of a functional interaction between Dicer1 and OS1-179(+), with p<0.025 (Fig. 6B).

https://doi.org/10.1371/journal.pone.0008658.g006

As for molecular mechanisms mediating Emx2OS-dependent Emx2-mRNA down-regulation, we hypothesized that the antisense ncRNA might destabilize the sense mRNA, forming a double strand with it and so preparing its degradation by double-strand ribonucleases. Among these enzymes, a reasonable candidate might be Dicer1, involved in dsRNA-mediated destabilization of retrotransposon transcripts [47]-[49] and crucial to generation and survival of cortico-cerebral neurons [54]. To test this hypothesis, we decided to repeat the GOF experiments described above in cells alternatively provided with Dicer1 activity or deprived of it, by morpholino technology [55], [56]. To get the best Dicer1 knock-down, NIH/3T3 cells, among the easiest to transfect by established morpholino reagents, were selected as a substrate.

Combined Dicer1-knock-down (DicerKD) by α-Dicer1 morpholino and OS1-179(+)/OS1-179(-)-GOF manipulations were performed, according to the schedule in Fig. 6B. Results were as follows. Lentivirus OS1-179(+) downregulated Emx2-mRNA in all tested conditions. Compared with lentivirus-C treated controls, relative levels of Emx2-mRNA upon OS1-179(+) infection, changed by a factor of 0.56/1 = 0.56 (p<0.001) - and 1.42/1.65 = 0.87 (p<0.01), in wild type and Dicer1-KD NIH/3T3 cells, respectively. Morpholino α-Dicer1 gave conversely rise to a robust increase of Emx2-mRNA. Compared with morpholino-C-treated controls, relative levels of Emx2-mRNA under α-Dicer1 changed by a factor of 1.42/0.56 = 2.54 (p<0.001), 1.65/1 = 1.65 (p<0.001), and 1.82/1.31 = 1.39 (p<0.01), in cells infected by OS1-179(+), control or OS1-179(−) lentiviruses, respectively.

The stronger effect elicited by OS1-179(+) in the presence of normal levels of Dicer1 and the more pronounced effect elicited by α-Dicer1 when associated to OS1-179(+) suggested that a specific functional interaction could occur between Dicer1 and the antisense transcript. Remarkably, two-ways ANOVA re-analysis of Emx2 expression data confirmed this suspect, with p<0.025 (Fig. 6B).

Summarizing: (1) Emx2-mRNA is normally down-regulated by Dicer1; (2) the antisense RNA fragment overlapping Emx2-mRNA destabilizes it; (3) Dicer1 promotes such antisense-dependent mRNA destabilization.

Emx2OS Transcripts Promote Both Emx2-mRNA and Emx2OS-ncRNA Expression

The specific co-expression of Emx2OS-ncRNA and Emx2-mRNA by neural precursors belonging to defined regions of the developing CNS suggested that antisense transcripts, in addition to trigger destabilization of Emx2-mRNA, might be also basically implicated in promoting its transcription. This hypothesis was tested by over-expressing Emx2 antisense sequences in neural precursors from the rhombo-spinal tract, a CNS segment which normally does not express Emx2 [1], [2] (Fig. 1C). As basal expression levels of Emx2 in rhombo-spinal precursors are very low (near the experimental background) and this might make it difficult to estimate the relative change of transcript level elicited by OS1-179(+), the following device was adopted. The experiment was alternatively run under standard neurosphere medium [15], or upon addition of a specific lithium/cyclopamine drug mix, which, stabilizing the transcription factor (TF) beta-catenin [57] and preventing inhibition of the TF Gli3 [58], promotes Emx2 transcription [59]–[61], so as to increase the baseline of the assay and ameliorate its signal-to-noise ratio (Fig. 7A).

thumbnail
Download:
Figure 7. Ectopic activation of Emx2-mRNA and Emx2OS-ncRNA in rhombo-spinal neurospheres, upon OS1-179(+) delivery.

(A) Ectopic activation of the endogenous Emx2 locus by OS1-179(+). The two graphs show Emx2-mRNA and Emx2OS-ncRNA expression levels in primary neural precursors from distinctive portions of the E10.5 CNS, rhombo-spinal tract (rh/sc) and telencephalon (te), acutely infected with “driver” and “expressor” lentivectors (Fig. 1C), kept under doxycycline and added or not with the Li+/cyclopamine mix. Samples are RNA-profiled 72 hours after infection. Data are normalized on telencephalic precursors exposed to Li+/cyclopamine, infected by control lentivirus and kept under doxycycline. Basal Emx2 expression by rhombo-spinal cells, very low as compared to telencephalic precursors, rises about 2 (p<0.01), 4 (p<0.001) and 30 times (p<0.001), upon treatment of these cells with the OS1-179(+) virus, the drug mix, or both, respectively. Two-ways ANOVA indicates that a specific interaction between OS1-179(+) and the drug mix takes place, with p<0.001. A similar course is shown by Emx2OS-ncRNA. (B) Reversibility of OS1-179(+)-dependent activation of the endogenous Emx2 transcription unit. The four panels to the top show time course analysis of eGFP fluorescence in neural precursors, infected by driver and OS1-179(+) lentiviruses and kept under doxycycline for 72 or 120 hours. The absence of fluorescence in the bottom-right panel means that withdrawal of doxycycline at 72 hours is sufficient to reset levels of the eGFP/OS1-179(+) chimaeric transcript to zero by 120 hours. The two graphs to the bottom show Emx2-mRNA and Emx2OS-ncRNA expression levels in primary neural precursors from the E10.5 rhombo-spinal (rh/sc) tract, acutely infected with “driver” and “expressor” lentivectors (Fig. 1C), kept under doxycycline for 72 or 120 hours and chronically exposed to Li+/cyclopamine throughout the experiment. Samples are RNA-profiled 120 hours after infection. Data are normalized on rhombo-spinal cells exposed to Li+/cyclopamine, infected by OS1-179(+) lentivirus and kept under doxycycline throughout the experiment. Removal of doxycycline at 72 hours abolishes (p<0.01) the 4-fold up-regulation of Emx2-mRNA, detectable in Li/cyclopamine-treated rhombo-spinal precursors, upon their further infection by lentivirus OS1-179(+) (p<0.01). Similar consequences are elicited by doxycycline removal on levels of Emx2OS-ncRNA.

https://doi.org/10.1371/journal.pone.0008658.g007

As expected, the Emx2 expression level in rhombo-spinal cells, infected with control virus and kept in the absence of drugs, resulted far lower than in telencephalic cells exposed to lithium/cyclopamine. The Emx2 level slightly rose, upon treatment of rhombo-spinal cells by either the OS1-179(+) virus or the lithium/cyclopamine mix (about 2 and 4 times, with p<0.01 and p<0.001, respectively). Interestingly, simultaneous exposure of rhombo-spinal cells to both OS1-179(+) virus and lithium/cyclopamine elicited a much more dramatic up-regulation effect (almost 30 times, with p≪0.001), so confirming the effectiveness of the OS1-179(+) virus and further suggesting a powerful synergy between such virus and the drug cocktail (p<0.001) (Fig. 7A, upper histograms). In other words, as hypothesized, Emx2OS transcripts may activate Emx2 expression and the amplitude of this phenomenon is much more prominent, upon appropriate pharmacological modulation of the nuclear TF milieu impinging on Emx2 regulation [57], [59]. Noticeably, changes of Emx2-mRNA levels elicited by pharmacological and genetic manipulations described above were paralleled by strikingly similar changes of Emx2OS-ncRNA (Fig. 7A, lower histograms). This indicates that both reasonably originated from concerted stimulation of sense and antisense transcription at the Emx2 locus. This also suggests that the upregulation of Emx2-mRNA triggered by artificial OS1-179(+) administration might be further sustained by endogenous antisense transcripts from the same locus, induced by OS1-179(+) itself (Fig. 7A).

As the previous experiment was done by keeping the OS1-179(+) transgene chronically on, it was poorly informative about the kinetics and, in particular, the reversibility of the Emx2 activation triggered by antisense transcripts. To address this issue, we repeated the OS1-179(+) overexpression test over 120 hours, limiting neural precursors exposure to doxycycline to the first 72 hours (Fig. 7B).

Results of this test were as follows. Withdrawal of doxycycline at 72 hours allowed full shutting off of OS1-179(+)-ncRNA at 120 hours, as witnessed by the absence of associated eGFP fluorescence (Fig. 7B, panels to the top). Remarkably, this was accompanied by a collapse of endogenous Emx2 sense and antisense transcripts to levels peculiar to rhombo-spinal cells infected by the control virus (Fig. 7B, histograms).

In other words, even low, but persisting levels of antisense transcripts seem to be sufficient and strictly necessary for proper firing of the Emx2 transcription unit. This might explain why Emx2 sense and antisense transcripts have normally to be co-expressed in proliferative layers of the early developing CNS.

Absence of Emx2 Sense Transcription and/or Its Products Impairs Emx2OS-ncRNA Expression

The association between Emx2OS and Emx2 transcripts might also imply a reciprocal, complementary dependence of Emx2OS-ncRNA expression on Emx2 sense transcription. To address this issue, we compared levels of Emx2OS transcripts in E12.5 cortices from Emx2+/+, Emx2+/− and Emx2−/− mouse embryos [4]. The Emx2 null allele of these mutants - in fact - lacks only a 250bp genomic fragment encoding for the C-term of the homeodomain (not provided of any known cis-regulatory activities), has an intact divergent-promoter region and still harbors the two main enhancers which drive transcription in the developing telencephalon [4], [57]. As such, it should in principle be able to normally drive the synthesis of its antisense transcript.

Notwithstanding that, we found that Emx2OS-ncRNA was down-regulated by more than 80% in homozygous null mutants and by 50% in heterozygous mutants (Fig. 8), suggesting that - as suspected - Emx2 sense transcription and/or its products are in turn necessary for proper expression of Emx2OS-ncRNA.

thumbnail
Download:
Figure 8. Down-regulation of Emx2-mRNA and Emx2OS-ncRNA in acutely dissected cortices from E12.5 Emx2 null mutant embryos.

Abbreviations: wt, wild type; he, heterozygous; ko, knock-out.

https://doi.org/10.1371/journal.pone.0008658.g008

Discussion

In this study we investigated the expression pattern of Emx2OS-ncRNA, the antisense transcript associated to the transcription factor gene Emx2, in the developing mouse CNS. Then, we preliminarly addressed its involvement in regulation of Emx2 expression.

As shown by qRT-PCR (Fig. 2) and in situ hybridisation (Fig. 3), Emx2OS is specifically expressed by a number of CNS substructures and sense organs also expressing Emx2. Among them: telencephalon, mammillary recess, optic tectum, olfactory placode, otic vesicle [1], [3]. Such colocalization of the two transcripts in periventricular layers of defined neural tube domains recalls the identical expression patterns they display in the uterine endometrium [17]. Emx2/Emx2OS colocalization might be an epiphenomenon of shared regulatory mechanisms impinging on both. Alternatively, transcription of one or both units might specifically promote the other and, in particular, antisense transcription might contribute to specifically keep Emx2 on in neural precursors of defined spatial domains.

Remarkably, the two transcripts, both expressed by periventricular neural precursors of the cortical primordium, display a mutually exclusive pattern in post-mitotic progenies of such precursors. Newborn neurons belonging to the cortical plate strongly express Emx2OS-ncRNA, expecially at the end of their radial migration (Fig. 4E,F), but not Emx2-mRNA (while still harboring residual Emx2 immunoreactivity) [1]-[3]. Pioneer Cajal-Retzius neurons lying in the marginal zone conversely express huge amounts of Emx2 mRNA and protein [3], but no antisense transcript at all (Fig. 4G,L). Such mutual distribution recalls the complementary expression patterns displayed by Otx2/Otx2OS and Crx/CrxOS pairs in the adult retina, with the sense transcription factor genes expressed predominantly in photoreceptors and the corresponding OS genes in bipolar interneurons and ganglionic projection neurons [24]. The mutual distribution of Emx2 and Emx2OS RNA products points to a possible negative cross-regulation between them and, in particular, to an involvement of the former in fine control of post-mitotic silencing of the latter.

As for the biological meaning of Emx2/Emx2OS co-expression, we tested the hypothesis that sense and antisense transcription from the Emx2 locus might reciprocally sustain each other.

To assay if Emx2OS-ncRNA is able to promote Emx2-mRNA expression, a 5′ fragment of the former was overexpressed in rhombo-spinal precursors, normally expressing none of them. As suspected, delivery of this fragment, OS1-179(+)-ncRNA, into such cells elicits strong Emx2 upregulation. No direct assessment of the level, transcriptional or post-transcriptional, at which this phenomenon takes place, was performed. However two considerations suggests that the former possibility may hold good. First, OS1-179(+) synergizes with a drug mix specifically up-regulating beta-catenin, a key trans-activator binding the two telencephalic enhancers of Emx2 [59]. Second, up-regulation of Emx2 is faithfully paralleled by Emx2OS up-regulation.

Concerning mechanisms mediating transactivating properties of OS1-179(+) (as well of Emx2OS-ncRNA), two hypotheses may be taken into accont. Both molecules might interact with transcription factors impinging on the Emx2 locus, ameliorating their binding to the chromatin and/or their processivity (like the Evf2-ncRNA at the Dlx5/6 locus) [25]. Alternatively, antisense transcripts or their by-products might make the epigenetic state of Emx2 chromatine more permissive to gene expression, by recruiting appropriate modifier enzymes to it. However, modifier enzymes recruited by antisense RNAs, rather than facilitating gene expression, often make chromatine less prone to transcription [27], [43], [44]. Consistent with these considerations, the need of persistent OS1-179(+) expression to get Emx2 activation and the capability of the only drug cocktail to elicit weak but reproducible Emx2 upregulation induce us to rule out the latter hypothesis and to consider the former more likely. Beyond mechanics of OS1-179(+) action, such activation of Emx2 by a short antisense transcript is nonetheless remarkable, as possible prototype of a general method for overexpressing single specific genes, without any need to introduce additional copies of them into the genome, similarly to classical RNAa [62]–[65].

To ascertain if Emx2OS-ncRNA expression reciprocally depends on Emx2 transcription (and/or its products), Emx2OS levels were scored in Emx2 mutant mice, not harboring any gene lesions obviously incompatible with Emx2OS transcription. Remarkably, in such mice, both Emx2 and Emx2OS transcripts are dramatically down-regulated, echoing the collapse of Vax2OS (Vax2 opposite strand) occurring in mice knock-out for the cognate transcription factor gene Vax2 [24]. Multiple are mechanisms possibly underlying such down-regulation. Among the most likely ones, the depression of the Emx2/Wnt mutually-sustaining loop [9], [59], leading to a decrease of the nuclear beta-catenin pool which normally stimulates transcription at the Emx2 locus [59]. Such mechanisms - however - were not addressed at all in this study; they will be subject of a further dedicated one.

So, based on Emx2OS down-regulation in Emx2-null mutants as well as on consequences of OS1-179(+) overexpression in rhombo-spinal precursors, we can speculate now that mutual promotion of sense and antisense transcription at the Emx2 locus may be a crucial pre-requisite for proper activation and expression of Emx2. Maybe that is why Emx2 sense and antisense transcripts have to be co-expressed in defined domains of the early neural tube.

We also tested whether Emx2OS is also implicated in downregulation of Emx2, by artificially modulating Emx2 antisense levels in cortico-cerebral neural precursors. An inverse correlation was found between levels of Emx2OS and Emx2 transcripts, confirming that the former may normally contribute to down-regulation of the latter. Changes of Emx2-mRNA levels elicited by Emx2OS-RNAi are not reflected by the course of the corresponding pre-mRNA, that remains stable as found by intronic qRT-PCR. This further indicates that Emx2OS-dependent modulation of Emx2 takes place post-transcriptionally. Antisense-promoted down-regulation of Emx2 is weakened by Dicer1 knock-down, suggesting that Dicer1 might promote such process by “dicing” the Emx2-mRNA/Emx2OS-ncRNA hybrid, similarly to retrotransposon silencing [47], [49]. Consistently with this model, the concomitant up-regulation of Emx2OS-ncRNA caused by OS1-179(+) might reflect a reduced degradation rate of the endogenous antisense molecule, following the competition by OS1-179(+) for sense transcript binding.

Remarkably, Emx2OS-dependent down-regulation of Emx2 is not limited to proliferating neural precursors. It takes place also in differentiating neuronal progenitors, where a surplus of Emx2OS-ncRNA is available to trigger this process (Fig. 5C, bottom left). Here, an up-regulation of key enzymes involved in sense RNA degradation, occurring during neuronal differentiation [66], might make the Emx2OS impact on Emx2-mRNA degradation predominant over its positive effects on sense transcription, so accelerating the shutting off of the sense transcript. Actually, the amplitude of Emx2OS-dependent Emx2 downregulation is apparently not huge. Notwithstanding that, such regulation might be instrumental to proper progression of cortico-cerebral morphogenesis. In fact, as Emx2 finely regulates the balance between symmetric, self-renewing divisions undergone by embryonic neural stem cells and asymmetrical, neuronogenic ones [12], an accurate regulation of its expression levels and, in particular, a finely tuned decay of its mRNA may be crucial to proper growth of the neocortical primordium [14]. A moderate contribution of Emx2OS-ncRNA to Emx2-mRNA destabilization might be just required, for optimal tuning of this process.

Materials and Methods

Ethics Statement

Animals handling and subsequent procedures were in accordance with European laws [European Communities Council Directive of November 24, 1986 (86/609/EEC)] and with National Institutes of Health guidelines.

Animal Handling

Wt mice (strain CD1, purchased from Harlan-Italy) and Emx2 null mutants [4] used in this study are maintained at the SISSA-CBM mouse facility. Embryos were staged by timed breeding and vaginal plug inspection. Embryos (E10.5-E18.5) were harvested from pregnant dames killed by cervical dislocation.

Preparation of Histological Samples

Dissected embryos were immersion-fixed overnight in 4% paraformaldehyde in 1X phosphate saline buffer (PBS) and then cryoprotected by immersion in 30% sucrose in PBS 1X overnight at 4°C. Tissues were frozen in OCT compound, sectioned at 10 µm in a cryostat, collected on slides SuperFrost Plus (Fischer), air dried for about 30 min, and stored at – 80°C until use.

Cell Cultures

Primary cells.

Cortical primordia and rhombo-spinal tracts were dissected from E12.5 mouse embryos and mechanically dissociated to single cells, by gentle pipetting. Dissociated neural precursor cells were cultured at 700 cells/µl, in DMEM/F12/Glutamax medium (Invitrogen™), integrated with N2 supplement (Invitrogen™), 1 mg/ml BSA, 0.6% w/v glucose, 2 µg/ml heparin, 10 pg/ml Fgf2, 20 pg/ml Egf, 1X Pen/Strept (Gibco), 10 pg/ml fungizone. Cultures were usually blocked and underwent RNA extraction 72 hours after dissection. When a longer culturing time was required, primary neurospheres were dissociated to single cells by trypsin-DNAseI and re-plated at the same initial density. When required, doxycycline, lithium chloride and cyclopamine were added to the culture medium, at 2 µg/µl, 1mM and 1 µM, respectively.

HeLa cells and NIH/3T3 cells.

Cells were cultured in DMEM-Glutamax-I™ (Gibco) plus 10%FBS, according to standard protocols. When appropriate, α-Dicer (5′ GGCTT TTCAA TCATC CAGTG TTTCT 3′) and control (5′ TCTTT GTGAC CTACT AACTT TTCGG 3′) morpholinos were delivered to cells at 10 µM, by 6 µM EndoPorter™ carrier (GeneTools), according to manifacturer's instructions. When required, doxycycline was added to the culture medium, at 2 µg/µl.

Immunofluorescence

Neural cells were detached form plates by 1X trypsin (Gibco) for 5 minutes at RT, centrifuged at 100 g for 7 min at RT, resuspended in Sato medium and finally left 60 min to attach to Superfrost® slides, previously kept for 60 min under 20 µg/ml poly-D-lysine at RT. Immunofluorescence was performed as previously described [66], with minor modifications. Briefly, after fixation by 4% paraformaldehyde for 10 min at 4°C and three washes in 1X PBS, 5 min each, cells were incubated for 1 h at RT under blocking mix (1X PBS; 10% FBS; 1 mg/ml BSA; 0.1% Triton-X100) and then incubated at 4°C overnight with primary antibody in blocking mix. Mouse anti-neuron-specific class III β-tubulin-primary antibody (clone Tuj1, Covance), was used, 1∶600. Immunoreactivity was revealed after a 2 h incubation with secondary Alexa-594 antibody, 1∶600.

In Situ Hybridization

Not radioactive in situ hybridization was performed as previously described, with minor modifications [67]. Two riboprobes were used: Emx2OS, corresponding to mouse chromosome 19: nt 59,500,768-59,501,561, and Reln, corresponding to the 3.3 kb EcoRI fragment from the BS6 clone (a gift by A.Bulfone). Hybridized embryo sections were imaged and analyzed using a fluorescent Nikon (Tokyo, Japan) Eclipse 80i microscope and a DS-2MBWC digital microscope camera. All images were processed by Adobe Photoshop CS3 software.

Quantitative RT-PCR

RNA preparation.

RNA was extracted from CNS explants and cell cultures by Trizol™ (Invitrogen), according to manifacturer's instructions.

cDNA prepration.

At least 1 µg of RNA from each sample was retrotranscribed by SuperScriptIII™ (Invitrogen) in the presence of random hexamers, according to manifacturer's instructions, with minor modifications. In the case of pre-mRNA levels evaluation, at least 4 µg of RNA preparation from each sample, previously treated by DNAseI™ (Promega), were used.

Quantitative PCR.

1/25 of each cDNA sample was analyzed by the SybrGreen™ qPCR platform (Biorad). Each PCR reaction was run at least in triplicate and results averaged. Averages were further normalized against Tbp, except data in Fig. 5B (left and middle graphs), conversely normalized against GAPDH. Specifically in the case of pre-mRNA levels evaluation (reported in Fig. 5B, right graph), to reconcile sensitivity and specificity, 1/2 of each cDNA sample was linearly pre-amplified and 1/100 of the resulting primary reaction product was used as substrate of the subsequent quantitative PCR reaction, driven by nested, internal primers. Finally, supplementary amplifications on not-retrotranscribed samples were run, as negative controls.

Oligonucleotides.

Genomic localization of oligonucleotides used in this study are shown in Fig. 1A. Amplicons and corresponding oligos were as follows: Emx2-mRNA (E2S/N2F: 5′ GGAAA GGAAG CAGCT GGCTC ACAGT CTCAG TCTTA C 3′; E2S/N2R: 5′ GTGGT GTGTC CCTTT TTTCT TCTGT TGAGA ATCTG AGCCT TC 3′); Emx2OS-ncRNA (Emx2OS/P1: 5′ CCCGC GCCCG GGTCA CTGAG ATGGC TTCG 3′; Emx2OS/P3: 5′ GATGA GCAGG TGAGT GGTAG ATGGT TGTAA GCTGT AC 3′); Emx2-pre-mRNA-primary PCR (I1: 5′ GTCTC TGAAG CTCGT TTGGG TTACT G 3′; I4: 5′ AGTGA GTGTA GAGCA GAGTT GAAGT CC 3′); Emx2-pre-mRNA-secondary PCR (I2: 5′ GCGAG GTCTT TGAAT CCTGT TTC 3′; I3: 5′ GCAGA GTTGA AGTCC AGTGA ACC 3′); Tbp-mRNA (Tbp-b/Fw: 5′ ATTCT CAAAC TCTGA CCACT GCACC GTTG 3′; Tbp-b/Rev: 5′ TTAGG TCAAG TTTAC AGCCA AGATT CACGG TAG 3′); Gapdh-mRNA (Gapd/FW: 5′ CAACA GCAAC TCCCA CTCTT CCACC TTCG 3′; Gapd/REV: 5′ GGTGG TCCAG GGTTT CTTAC TCCTT GGAGG 3′); Tbp-pre-mRNA-primary PCR (TBP-FW/EXT: 5′ CTCAG TTTGA TGGCT CAGTT TCC 3′; TBP-REV/EXT: 5′ GTATA ACCAG TTATT TATCC AGATC TC 3′); Tbp-pre-mRNA- secondary PCR (TBP-FW/INT: 5′ CAAAA GATGA AAACC CAGAA AACAG CC 3′; TBP-REV/INT: 5′ GTTTA CTGAA CGCTT GATTA TATAG 3′).

Plasmids Construction

All basic DNA manipulations (extraction, purification, ligation) as well as bacterial cultures and transformation, media and buffer preparations were performed according to standard methods. DNAs were transformed in the E.Coli TOP-10 strains (Invitrogen).

Loss-of-Function Constructs and Their Validation

To knock-down Emx2OS by RNAi, we selected the best two siRNAs suggested by the Invitrogen “BLOCK-iT™ RNAi Designer“ software (miR-aEmx2OS-542 and miR-aEmx2OS-774) plus the BLOCK-iT™ negative control-miR (miR-C) and compared their activities on Hela cells. For this purpose, we built up a set of three bicistronic plasmids, each harboring two distinct transcription units and designed to assay the activity of one specific miR. The former transcription unit, the “sensor”, included the CMV promoter, the DsRed2 coding sequence, the cDNA corresponding to the Emx2OS-ncRNA fragment targeted in silico by the two miRs above (Genbank AY117414.1: nt796-1289) and the SV40 polyA site. The latter unit, the “miR expressor”, harbored the CMV promoter, the eGFP coding sequence, a modified 230bp fragment from pri-mmu-miR-155 (where the miR-155 and miR-155* moieties are replaced by those of the artificial miR in order) and the TK polyA site. A fourth plasmid was built up as well, similar to the previous three, but harboring in cis sequences encoding for both miR-αEmx2OS-542 and miR-αEmx2OS-774 (Fig.1B). The pri-miR fragments included in the above mentioned plasmids were prepared as follows. Each of the two sequences 5′ TGCTG CATAT TTGCA CTTCT CCGAA GGTTT TGGCC ACTGA CTGAC CTTCG GAGGT GCAAA TATGC AGG 3′ and 5′ TGCTG CGAAC TTAGA CTCAG ATTCC CGTTT TGGCC ACTGA CTGAC GGGAA TCTGT CTAAG TTCGC AGG 3′ was cloned into pcDNA™6.2-GW/EmGFP-miR (Invitrogen), inbetween mmu-miR-155 flanking regions, according to manifacturer's instructions, and the resulting SalI-XhoI chimeric pri-miR cDNA fragments, encoding for miR-αEmx2OS-542 and miR-αEmx2OS-774, respectively, were obtained. Finally, the SalI-XhoI cDNA fragment from “pcDNA™6.2-GW/EmGFP-miR_neg_control_ plasmid” was used as control pri-miR.

We transfected HeLa cells with these four bicistronic plasmids, counted fluorescent cells and calculated for each plasmid the ratio between red cells and total fluorescent cells, as a comprehensive index of pri-miR processing efficiency and mature miR activity. The DsRed2+/(total fluorescent cells) ratio varied from 65% (negative control miR), to 39% (miR-αEmx2OS-542), 10% (miR-αEmx2OS-774) and 2% (miR-αEmx2OS-542 & miR-αEmx2OS-774), suggesting that the combination in cis of the two miRs, -542 and -774, would be the best choice (Fig. 5A). However, we noticed that, using the -542/-774 plasmid, the ratio between eGFP+ cells and total cells in the plate was consistently lower (data not shown), possibly because of enhanced Drosha-dependent destabilization of the chimaeric eGFP-cds/Pri-miR molecule. As this might pose serious problems in subsequent production of miR-encoding lentiviruses as well as in tracing cells infected by these virions, we prudently opted for simple miR-αEmx2OS-774 for the knocking-down experiments.

Finally, the pri-miR-αEmx2OS-774 and “control pri-miR” SalI/XhoI cDNA fragments were transferred into the SalI-digested, pCCLsin.PPT.hPGK.GFP.pre plasmid [68], inbetween the pPgk1/GFP and Wpre modules, so obtaining the genomic plasmids used for subsequent production of miR-expressor lentiviruses (Fig. 1B).

Conditional Gain-of-Function Constructs

Emx2OS/Emx2 RNA sequences were conditionally overexpressed by lentiviral vectors and TetON technology.

The “driver lentivector” encoded for a constitutively expressed rtTA transactivator. Its genomic plasmid was obtained by replacing the BamHI/SalI eGFP cassette of pCCLsin.PPT.hPGK.GFP.pre by a BamHI/XhoI rtTA2S-M2 module.

“Expressor viruses” encoded for a doxycycline-controlled chimaeric transgene, including the cDNA fragment subject of analysis plus an IRES/eGFP module. Its genomic plasmid was obtained starting from pCCLsin.PPT.hPGK.GFP.pre, replacing the pPgk1 promoter by an “tTA/rtTA responsive element, tight” (TREt), the eGFP cds by an IRES/eGFP module and finally cloning the cDNA in order inbetween TREt and IRES/eGFP. Two “expressor viruses” were built up: the former harbored the cDNA fragment corresponding to nucleotides 1–179 of Emx2OS-ncRNA [OS1-179(+)], the latter the reverse-complementary sequence [OS1-179(−)]. A third virus, not including any Emx2 sense or antisense sequences was used as a negative control (Fig. 1C).

Morpholino Reagents and Their Validation

Sequences of anti-Dicer1 morpholino and its reverse negative control were obtained from the Gene-Tools free design service (α-Dicer1 and C, respectively) and the former molecule was validated, by testing its capability to inhibit Dicer1-dependent pri-miR-124a maturation [56]. This was assayed by a DsRed2 sensor gene linked to a miR-124a responsive element, co-trasfected into NIH/3T3 cells with pri-miR-expressor plasmids (Fig. S1).

Lentiviruses Preparation, Titration and Usage

Lentiviruses were prepared and titrated as previously described [68]–[70], with minor modifications.

Cell infections were performed without polybrene. In gain-of-function experiments, each virus was used at “multiplicity of infection” (m.o.i.) = 10, which resulted in trasduction of almost the totality of cortical precursors [71]. The m.o.i. was raised to 20 in loss-of-function experiments, in order to get a more robust downregulation of the target RNA.

Statistical Analysis

All experiments were performed at least in biological triplicate. Tbp- (or GAPDH-) normalized qRT-PCR data relative to each treatment were further averaged and the corresponding s.e.m.'s ae determined. Resulting averages were finally normalized against the control treatment, as reported in Figure Legends. Statistical significance of differences among results was evaluated by one- or two-ways ANOVA.

Supporting Information

Figure S1.

Validation of α-Dicer1 morpholino in NIH/3T3 cells. (A) Rationale of the assay: α-Dicer1-dependent suppression of pri-miR-124a-dependent DsRed2 inhibition. (B) Molecular tools for validating α-Dicer1 activity: inserts of pri-miR-expressor and miR-124a-sensor plasmids; sequences of α-Dicer1 and control morpholinos. The miR-124a responsive element (miR-124a-RE) corresponds to the 477-bp 3′UTR fragment of mouse Lhx2-mRNA (chr2 (+):38224759-38225235); Pri-miR-124a corresponds to the 285-bp mouse Pri-miR-124(2) genomic fragment (chr3 (+):17695562-17695846); control Pri-miR contains the Pri-miR155 sequence from the BLOCK-iT™ expression vector (Invitrogen). (C) Rescue of miR124a-dependent DsRed2 inhibition by α-Dicer1 morpholino, in NIH/3T3 cells.

https://doi.org/10.1371/journal.pone.0008658.s001

(8.78 MB TIF)

Acknowledgments

We thank Marco Brancaccio for technical help in viruses preparation and Nicola Antonio Maiorano for the kind gift of pri-miR-expressor and miR-124a-sensor plasmids.

Author Contributions

Conceived and designed the experiments: AM. Performed the experiments: GS CG. Analyzed the data: GS AM. Wrote the paper: GS AM.

References

  1. 1. Simeone A, Gulisano M, Acampora D, Stornaiuolo A, Rambaldi M, et al. (1992a) Two vertebrate homeobox genes related to the Drosophila empty spiracles gene are expressed in the embryonic cerebral cortex. EMBO 11: 2541–2550.
  2. 2. Simeone A, Acampora D, Gulisano M, Stornaiuolo A, Boncinelli E (1992b) Nested expression domains of four homeobox genes in developing rostral brain. Nature 358: 687–690.
  3. 3. Mallamaci A, Iannone R, Briata P, Pintonello L, Mercurio S, et al. (1998) EMX2 protein in the developing mouse brain and olfactory area. Mech Dev 77: 165–172.
  4. 4. Pellegrini M, Mansouri A, Simeone A, Boncinelli E, Gruss P (1996) Dentate gyrus formation requires Emx2. Development 122: 3893–3898.
  5. 5. Miyamoto N, Yoshida M, Kuratani S, Matsuo I, Aizawa S (1997) Defects of urogenital development in mice lacking Emx2. Development 124: 1653–1664.
  6. 6. Yoshida M, Suda Y, Matsuo I, Miyamoto N, Takeda N, et al. (1997) Emx1 and Emx2 functions in development of dorsal telencephalon. Development 124: 101–111.
  7. 7. Muzio L, Di Benedetto B, Stoykova A, Boncinelli E, Gruss P, et al. (2002b) Conversion of cerebral cortex into basal ganglia in Emx2(-/-) Pax6(Sey/Sey) double-mutant mice. Nat Neurosci 5: 737–745.
  8. 8. Bishop KM, Goudreau G, O'Leary DD (2000) Regulation of area identity in the mammalian neocortex by Emx2 and Pax6. Science 288: 344–349.
  9. 9. Muzio L, Di Benedetto B, Stoykova A, Boncinelli E, Gruss P, et al. (2002a) Emx2 and Pax6 control regionalization of the pre-neuronogenic cortical primordium. Cereb Cortex 12: 129–139.
  10. 10. Mallamaci A, Muzio L, Chan CH, Parnavelas J, Boncinelli E (2000b) Area identity shifts in the early cerebral cortex of Emx2-/- mutant mice. Nat Neurosci 3: 679–686.
  11. 11. Gangemi RM, Daga A, Marubbi D, Rosatto N, Capra MC, et al. (2001) Emx2 in adult neural precursor cells. Mech Dev 109: 323–329.
  12. 12. Heins N, Cremisi F, Malatesta P, Gangemi RM, Corte G, et al. (2001) Emx2 promotes symmetric cell divisions and a multipotential fate in precursors from the cerebral cortex. Mol Cell Neurosci 18: 485–502.
  13. 13. Galli R, Fiocco R, De Filippis L, Muzio L, Gritti A, et al. (2002) Emx2 regulates the proliferation of stem cells of the adult mammalian central nervous system. Development 129: 1633–1644.
  14. 14. Muzio L, Soria JM, Pannese M, Piccolo S, Mallamaci A (2005) A mutually stimulating loop involving Emx2 and canonical Wnt signalling specifically promotes expansion of occipital cortex and hippocampus. Cereb Cortex 15: 2021–2028.
  15. 15. Mallamaci A, Mercurio S, Muzio L, Cecchi C, Pardini CL, et al. (2000a) The lack of Emx2 causes impairment of Reelin signaling and defects of neuronal migration in the developing cerebral cortex. J Neurosci 20: 1109–1118.
  16. 16. Shinozaki K, Miyagi T, Yoshida M, Miyata T, Ogawa M, et al. (2002) Absence of Cajal-Retzius cells and subplate neurons associated with defects of tangential cell migration from ganglionic eminence in Emx1/2 double mutant cerebral cortex. Development 129: 3479–3492.
  17. 17. Noonan FC, Goodfellow PJ, Staloch LJ, Mutch DG, Simonc TC (2003) Antisense transcripts at the EMX2 locus in human and mouse. Genomics 81: 58–66.
  18. 18. Geng X, Lavado A, Lagutin OV, Liu W, Oliver G (2007) Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns 7: 252–257.
  19. 19. Blin-Wakkach C, Lezot F, Ghoul-Mazgar S, Hotton D, Monteiro S, et al. (2001) Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc Natl Acad Sci U S A 98: 7336–7341.
  20. 20. Berdal A, Lezot F, Pibouin L, Hotton D, Ghoul-Mazgar S, et al. (2002) Msx1 homeogene antisense mRNA in mouse dental and bone cells. Connect Tissue Res 43: 148–152.
  21. 21. Coudert AE, Pibouin L, Vi-Fane B, Thomas BL, Macdougall M, et al. (2005) Expression and regulation of the Msx1 natural antisense transcript during development. Nucleic Acids Res 33: 5208–5218.
  22. 22. Babajko S, Petit S, Fernandes I, Méary F, LeBihan J, et al. (2009) Msx1 expression regulation by its own antisense RNA: consequence on tooth development and bone regeneration. Cells Tissues Organs 189: 115–121.
  23. 23. Petit S, Meary F, Pibouin L, Jeanny JC, Fernandes I, et al. (2009) Autoregulatory loop of Msx1 expression involving its antisense transcripts. J Cell Physiol 220: 303–310.
  24. 24. Alfano G, Vitiello C, Caccioppoli C, Caramico T, Carola A, et al. (2005) Natural antisense transcripts associated with genes involved in eye development. Human Molecular Genetics 14: 913–923.
  25. 25. Feng J, Bi C, Clark BS, Mady R, Shah P, et al. (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes & Development 20: 1470–1484.
  26. 26. Mainguy G, Koster J, Woltering J, Jansen H, Durston A, et al. (2007) Extensive polycistronism and antisense transcription in the Mammalian Hox clusters. PLOS ONE 2: e356.
  27. 27. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129: 1311–1323.
  28. 28. Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, et al. (2007) Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 13: 223–239.
  29. 29. Shendure J, Church GM (2002) Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol 3: 0044.1–0044.14.
  30. 30. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379–386.
  31. 31. Chen J, Sun M, Kent WJ, Huang X, Xie H, et al. (2004) Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32: 4812–4820.
  32. 32. RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium 2005 Antisense Transcription in the Mammalian Transcriptome. Science 309: 1564–1566.
  33. 33. Engstrçm PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex Loci in human and mouse genomes. PLOS Genet 2: e47.
  34. 34. Li YY, Qin L, Guo ZM, Liu L, Xu H, et al. (2006) In silico discovery of human natural antisense transcripts. BMC Bioinformatics 7: 18.
  35. 35. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters. Science 322: 1845–1848.
  36. 36. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The Antisense Transcriptomes of Human Cells. Science 322: 1855–1857.
  37. 37. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, et al. (2008) RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoter. Science 322: 1851–1854.
  38. 38. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al. (2008) Divergent Transcription from Active Promoters. Science 322: 1849–1851.
  39. 39. Beitera T, Reicha E, Williamsb RW, Simon P (2009) Antisense transcription: A critical look in both directions. Cell Mol Life Sc 66: 94–112.
  40. 40. Munroe SH, Zhu J (2006) Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective. Cell Mol Life Sci 63: 2102–2118.
  41. 41. Leupin O, Attanasio C, Marguerat S, Tapernoux M, Antonarakis SE, et al. (2005) Transcriptional activation by bidirectional RNA polymerase II elongation over a silent promoter. EMBO 6: 956–960.
  42. 42. Mazo A, Hodgson JW, Petruk S, Sedkov Y, Brock HW (2007) Transcriptional interference: An unexpected layer of complexity in gene regulation. J. Cell Sci 120: 2755–2761.
  43. 43. Sleutels F, Ronald Zwart R, Barlow DP (2001) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415: 810–813.
  44. 44. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32: 232–246.
  45. 45. Hastings ML, Ingle HA, Lazar MA, Munroe SH (2000) Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. J Biol Chem 275: 11507–11513.
  46. 46. Beltran M, Puig I, PeÇa C, GarcPeÇa R, Bonilla F, et al. (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22: 756–769.
  47. 47. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, et al. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453: 534–538.
  48. 48. Okamura K, Balla S, Martin R, Liu N, Lai EC (2008) Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol 15: 581–590.
  49. 49. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453: 539–543.
  50. 50. Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008) Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Mol Cell 32: 827–837.
  51. 51. Ogawa Y, Sun BK, Lee JT (2008) Intersection of the RNA Interference and X-Inactivation Pathways. Science 320: 1336–1341.
  52. 52. Gulisano M, Broccoli V, Pardini C, Boncinelli E (1996) Emx1 and Emx2 show different patterns of expression during proliferation and differentiation of the developing cerebral cortex in the mouse. Eur J Neurosci 8: 1037–1050.
  53. 53. Gritti A, Parati EA, Cova L, Frolichsthal P, Galli R, et al. (1996) Multipotential stem cells from the adult mouse brain proliferate and self-renew in response to basic fibroblast growth factor. J Neurosci 16: 1091–1100.
  54. 54. De Pietri Tonelli D, Pulvers JN, Haffner C, Murchison EP, Hannon GJ, et al. (2008) miRNAs are essential for survival and differentiation of newborn neurons but not for expansion of neural progenitors during early neurogenesis in the mouse embryonic neocortex. Development 135: 3911–3921.
  55. 55. Summerton J (2007) Morpholino, siRNA, and S-DNA Compared: Impact of Structure and Mechanism of Action on Off-Target Effects and Sequence Specificity. Med Chem 7: 651–660.
  56. 56. Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11: 228–234.
  57. 57. Clément-Lacroix P, Ai M, Morvan F, Roman-Roman S, Vayssière B, et al. (2005) Lrp5-independent activation of Wnt signaling by lithium chloride increases bone formation and bone mass in mice. Proc Natl Acad Sci U S A 102: 17406–17411.
  58. 58. Incardona JP, William Gaffield W, Raj P, Kapur RP, Henk Roelink H (1998) The teratogenic Veratrumalkaloid cyclopamine inhibits Sonic hedgehog signal transduction. Development 125: 3553–3562.
  59. 59. Theil T, Aydin S, Koch S, Grotewold L, Rüther U (2002) Wnt and Bmp signalling cooperatively regulate graded Emx2 expression in the dorsal telencephalon. Development 129: 3045–3054.
  60. 60. Theil T, Alvarez-Bolado G, Walter A, Ruther U (1999) Gli3 is required for Emx gene expression during dorsal telencephalon development. Development 126: 3561–3571.
  61. 61. Rallu M, Machold R, Gaiano N, Corbin JG, McMahon AP, et al. (2002) Dorsoventral patterning is established in the telencephalon of mutants lacking both Gli3 and Hedgehog signaling. Development 129: 4963–4974.
  62. 62. Li LC, Okino ST, Zhao H, Pookot D, Place RF, et al. (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103: 17337–17342.
  63. 63. Chen Z, Place RF, Jia ZJ, Pookot D, Dahiya R, et al. (2008) Antitumor effect of dsRNA-induced p21(WAF1/CIP1) gene activation in human bladder cancer cells. Mol Cancer Ther 7: 698–703.
  64. 64. Mao Q, Li Y, Zheng X, Yang K, Shen H, et al. (2008) Up-regulation of E-cadherin by small activating RNA inhibits cell invasion and migration in 5637 human bladder cancer cells. Biochem Biophys Res Commun 375: 566–570.
  65. 65. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 105: 1608–1613.
  66. 66. Potenza N, Papa U, Russo A (2009) Differential expression of Dicer and Argonaute genes during the differentiation of human neuroblastoma cells. Cell Biology International 33: 734–738.
  67. 67. Muzio L, Mallamaci A (2005) Foxg1 confines Cajal-Retzius neuronogenesis and hipoccampal morphogenesis to the dorso-medial pallium. J Neurosci 25: 435–441.
  68. 68. De Palma M, Naldini L (2002) Transduction of a gene expression cassette using advanced generation lentiviral vectors. Methods Enzymol 346: 514–529.
  69. 69. Follenzi A, Naldini L (2002) Generation of HIV-1 derived lentiviral vectors. Methods Enzymol: 346: 454–465.
  70. 70. Sastry L, Johnson T, Hobson MJ, Smucker B, Cornetta K, et al. (2006) Titering lentiviral vectors: comparison of DNA, RNA and marker expression methods. Gene Ther 9: 1155–1162.
  71. 71. Capowski EE, Schneider BL, Ebert AD, Seehus CR, Szulc J, et al. (2007) Lentiviral vector-mediated genetic modification of human neural progenitor cells for ex vivo gene therapy. J Neurosci Methods 163: 338–349.