Skip to main content

Origin and evolution of candidate mental retardation genes on the human X chromosome (MRX)



The human X chromosome has a biased gene content. One group of genes that is over-represented on the human X are those expressed in the brain, explaining the large number of sex-linked mental retardation (MRX) syndromes.


To determine if MRX genes were recruited to the X, or whether their brain-specific functions were acquired after relocation to the mammalian X chromosome, we examined the location and expression of their orthologues in marsupials, which diverged from human approximately 180 million years ago. We isolated and mapped nine tammar wallaby MRX homologues, finding that six were located on the tammar wallaby X (which represents the ancient conserved mammal X) and three on chromosome 5, representing the recently added region of the human X chromosome. The location of MRX genes within the same synteny groups in human and wallaby does not support the hypothesis that genes with an important function in the brain were recruited in multiple independent events from autosomes to the mammalian X chromosome. Most of the tammar wallaby MRX homologues were more widely expressed in tammar wallaby than in human. Only one, the tammar wallaby ARX homologue (located on tammar chromosome 5p), has a restricted expression pattern comparable to its pattern in human. The retention of the brain-specific expression of ARX over 180 million years suggests that this gene plays a fundamental role in mammalian brain development and function.


Our results suggest all the genes in this study may have originally had more general functions that became more specialised and important in brain function during evolution of humans and other placental mammals.


For more than a century, it has been obvious that mental retardation is far more frequent in human males than females, and there have been many claims over the years that inherited mental retardation (MR) syndromes are concentrated on the X chromosome [1, 2]. Several well studied X-borne genes have an effect on general cognitive abilities, including FMR1 (fragile X syndrome) and FMR2 (FRAXE mental retardation), as well as a large number of X-linked mental retardation (MRX) syndromes that have been mapped but not cloned and characterised [3]. Attempts to prove that MRX genes are located disproportionately on the X have suffered from experimental ascertainment bias, since recessive MRX genes are more easily recognised in hemizygous males. However, one analysis of the OMIM database corrected for any ascertainment bias by comparing the proportions of X-linked phenotypes of MR syndromes to that of other abnormalities [4]. Another analysis tested whether the over-representation of MRX syndromes would disappear if as yet unmapped MR genes were evenly distributed across the genome [5]. Both analyses concluded that mental retardation syndromes are significantly concentrated on the human X chromosome. Other gene functions have also been found to be unequally represented on the human X chromosome. For example, early spermatogonial genes, sex and reproduction related (SRR) and prostate-specific genes are over-represented on the X in humans and mice, whereas there is a paucity of genes involved in late spermatogenesis [610].

How this over-representation occurred has been the subject of much speculation, and several alternative hypotheses have been considered. One possibility is that brain function genes, or copies of them, were moved one by one to the X from autosomes, another is that the over-representation of genes on the X was the result of the translocation of a larger autosomal region already rich in brain function genes to the X. Alternatively, it has been suggested that the gene content of the X chromosome has remained unchanged since its autosomal origin, but some X-borne genes have acquired new functions in brain development.

These hypotheses must be tested within the framework of human sex chromosome evolution. Mammals have an XX female: XY male chromosomal sex determination system, in which a gene on the Y chromosome controls male development. Homology between the X and Y chromosomes supports the hypothesis that the mammalian X and Y chromosomes differentiated from a homologous autosomal pair (the proto-X and proto-Y) when one member acquired a male-determining allele. Suppression of recombination between the X and Y, loss of active genes and accumulation of mutations on the Y resulted in the progressive degradation of the Y such that most genes on the X chromosome have no homologue on the Y chromosome.

The X chromosome gene content of different eutherian mammals is highly conserved, perhaps because of the chromosome-wide dosage compensation mechanism that ensures equal expression of X-linked genes in males and females. Mapping human X-borne genes in distantly related mammals [11] showed that only part of the X chromosome is conserved between the eutherians ("placental" mammals) and marsupials (which diverged from eutherians 180 million years ago). The long arm and pericentric region of the human X is equivalent to the marsupial X and is therefore at least 180 million years old. This region of the human X chromosome is known as the conserved region of the X (XCR). However, genes on the short arm of the human X are autosomal in marsupials, implying the addition of a region to the sex chromosomes between 130 and 80 million years ago. This region of the human X chromosome is known as the recently added region (XAR) and it is exposed to the same forces that shaped the ancient region. These building blocks of the human X chromosome are evident as two major autosomal regions in chickens [12]. The different evolutionary histories of the ancient and added regions of the human X can be exploited to test hypotheses of how and why mental retardation genes came to accumulate on the X chromosome.

The presence of the X chromosome as two copies in females, but only a single copy in males may explain the accumulation of certain classes of genes on the X chromosome that confer an advantage to males but are neutral, or even deleterious, in females [13]. Alternative hypotheses to explain the accumulation of MRX genes on the human X may be tested by observing the location and expression of their marsupial orthologues. Mapping will show whether the MRX genes were part of ancient gene blocks, or were recruited to the human X chromosome from autosomes as independent events. If they were part of ancient gene blocks, it would be expected that MRX genes from the conserved region of the human X would also be located on the X chromosome in the tammar wallaby, and that MRX genes from the recently added region of the human X would be found on the short arm of chromosome 5 in the tammar wallaby. If MRX genes were recruited from autosomes to the X chromosome as independent events, their homologues would be likely to be distributed across the genome in the tammar wallaby. Examination of the expression profiles of marsupial orthologues of MRX genes on the conserved and the recently added regions of the human X chromosome will test the whether the function of these genes has changed due to their location on the X. If genes on both the tammar wallaby X chromosome and chromosome 5p have brain-restricted expression patterns like their human counterparts, then this would support the hypothesis that recently added region of the human X chromosome was rich in brain function genes prior to its translocation to the ancient X, and their function was retained after relocation to the X. If genes located on the wallaby X have brain-specific expression like their human counterparts, but genes on the wallaby 5p have a different expression pattern, this supports the hypothesis that the function of these genes has changed in the eutherian lineage upon relocation to the X chromosome.

To test this hypothesis we studied a number of MRX genes, and candidate MRX genes involved in brain function distributed along the human X chromosome.


Choice of human genes for this study

We chose genes that are more or less evenly distributed along the human X chromosome and are involved in a number of biological pathways or neuronal processes (Table 1). They include genes such as OPHN1, ARHGEF6 and TSPAN7, which play a role in the formation and dismantling of the actin cytoskeleton to control growth of neurons, and genes such as RSK2, JARID1C and probably RSK4, which play a role in the control of gene expression through modulation of chromatin structure. Other genes are likely to regulate transcription and translation, such as ARX, FMR1 and FMR2, or encode receptor proteins, such as SREB3 and AGTR2. Most of these genes are human MRX genes, specific mutations in which cause mental retardation. Mutations that cause mental retardation have not yet been found in the RSK4 and SREB3 genes, but RSK4 is strong candidate MRX gene because of its similarity to RSK2, a known MRX gene, and SREB3 because of its brain-specific expression pattern. Some of the MRX genes are ubiquitously expressed and mutations within these genes cause cellular defects in many tissues, as well as predominantly affecting the brain because of its higher sensitivity [5]. Regardless of the role these genes play in the brain of eutherian mammals, many are expressed in the brain more strongly than in other tissues, and many have a period during development when expression is restricted to the brain or nervous system (Table 1).

Table 1 Summary of the location, function and expression patterns of the human genes in this study.

Isolation and mapping of tammar wallaby MRX gene orthologues

To isolate BAC clones containing orthologues of human MRX genes from the tammar wallaby BAC library, homologous human, mouse and Brazilian gray short-tailed opossum (Monodelphis domestica) sequences available from the public databases were compared with the tammar wallaby trace archives to identify highly conserved gene sequences. The availability of tammar wallaby sequences in the trace archive allowed the design of tammar wallaby primer pairs to amplify the RSK4, AGTR2 and ARHGEF6 genes from female tammar wallaby genomic DNA (Table 2). Primer pairs designed from available opossum sequence were used to amplify the RSK2, ARX, OPHN1, and FMR2 genes from female tammar wallaby genomic DNA (Table 2). PCR products of the expected size (Table 2) were cloned and sequenced to verify their identity and were used separately to identify positive BAC clones from the tammar wallaby BAC libraries. To identify BAC clones containing the FMR1 and TSPAN7 gene, 40bp overgos designed from opossum (FMR1) or tammar wallaby (TSPAN7) sequence were used to screen the tammar wallaby BAC library.

Table 2 Summary of primers used for library screening and expression analysis. BAC clone addresses are also given for each BAC clone identified and used in the localisation of the MRX genes.

To verify that the positive BAC clones identified by library screening contained the correct gene, BAC DNA was isolated, and used as the template for PCR amplification of each gene using the primer pairs used to generate the original PCR fragment for library screening. Tammar wallaby trace sequences were used to design primers to amplify an FMR1 gene fragment from the BAC clones. PCR products generated from the BAC clones were sequenced to verify that the BAC clones contained the correct gene sequence. The TSPAN7 positive BAC was verified by sequencing using the overgos as primers in the sequencing reaction. This allowed the identification of tammar wallaby BAC clones containing sequences homologous to nine MRX genes from the human X chromosome. The possibility that these were intronless retroposed copies was eliminated by the amplification and sequencing of intron-containing PCR products from each BAC clone, demonstrating that the sequence of these products was identical to that of the original probes.

Fluorescence in situ hybridisation (FISH) was used to map the verified BAC clones onto tammar wallaby metaphase chromosome spreads. BAC clones containing the tammar wallaby homologues of human genes located in the conserved region of the human X chromosome (OPHN1, RSK4, AGTR2, ARHGEF6, FMR1 and FMR2) hybridised to the long arm of the tammar wallaby X chromosome (Figure 1). BAC clones containing the tammar wallaby homologues of human genes located in the recently added region of the human X chromosome (RSK2, ARX, and TSPAN7) hybridised to the short arm of tammar wallaby chromosome 5.

Figure 1

Localisation of tammar wallaby MRX homologues. BACs containing tammar wallaby MRX homologues hybridised to male metaphase chromosome spreads. Signals are visualised in green, and chromosomes are counterstained with DAPI (4',6-diamidino-2-phenylindole) and visualised in red.

These results imply that these tammar wallaby MRX homologues are part of the previously defined conserved and recently added regions of the human X chromosome, which are represented by the X chromosome and the short arm of chromosome 5 in the tammar wallaby [11]. They are clearly parts of ancient gene blocks, not the result of independent or more recent transposition events to the mammalian X chromosome, which is consistent with what we already know about the evolution of the eutherian X chromosome [14].

Expression of MRX homologues in the tammar wallaby

We examined the expression profiles of all the tammar wallaby orthologues of human MRX and candidate MRX genes. This included XAR genes RSK2, ARX, and TSPAN7 from the short arm of tammar wallaby chromosome 5, and XCR genes OPHN1, RSK4, AGTR2, ARHGEF6, FMR1 and FMR2 from the tammar wallaby X chromosome. Two other genes previously localised to the tammar wallaby X chromosome, SREB3 and JARID1C (Delbridge in preparation), were also included in this analysis.

We found that RSK2, TSPAN7, SREB3, JARID1C, OPHN1, ARHGEF6, FMR1, FMR2, RSK4, and AGTR2 transcripts could be amplified by RT-PCR from RNA extracted from all adult tissues tested (Figure 2). For some genes the amount of RT-PCR product varied in different tissues. Tammar wallaby SREB3, RSK2 and AGTR2 were only weakly expressed in the brain and some other tissues (Figure 2). Tammar wallaby OPHN1, FMR2 and SREB3 were expressed at a lower level in muscular tissues such as the heart and the skeletal muscle, whereas RT-PCR products produced by amplifying other genes from the same samples gave bands of similar intensity in all tissues. Despite these differences in the levels of expression the presence of an RT-PCR product in all tissues implies that these genes are widely expressed in tammar wallaby, in contrast to their tissue-specific expression in human and mouse (Table 3).

Figure 2

Expression profiles of tammar wallaby MRX homologues. Ce: cerebellum, Cx: cortex, H: heart, K: kidney, Li: liver, Lu: lung, Ov: ovary, Sk: skeletal muscle, Sp: spleen, T: testis, -ve: negative control. M: 1.0 kb marker (Roche, Australia).

Table 3 Tammar wallaby localisation and expression data compared to human. Ad: adrenal medulla, B: brain, H: heart, K: kidney, Ov: ovary, Pl: placenta, Sk: skeletal muscle, Sp: spleen, Te: testis.

In contrast, ARX expression was restricted to the brain (cortex), testis and ovary tissues in the adult tammar wallaby (Figure 2). Two pairs of primers were used to amplify RT-PCR products within exon 5 (Figure 2) and spanning exons 2 to 5 (results not shown), and include most of the coding region of ARX. Both primer pairs amplified only a single product from cortex, testis and ovary tissues from both tammar wallaby adult and pouch young (day 97 after birth), indicating that restricted ARX expression occurs at both stages. Our experiments would not detect the different isoforms of ARX that have been proposed to result from changes in the 3' untranslated region rather than the coding region [15]. The tammar wallaby ARX expression profile more closely reflects the brain and testis specific expression pattern of ARX in human and mouse embryos, rather than the more widespread expression profile observed in human adults. Unlike its expression profile in eutherian mammals, ARX was expressed in the tammar wallaby ovary.


Did human MRX genes originate from autosomal sites?

One hypothesis to explain the over-representation of brain-expressed genes on the human X is that brain-specific genes were transferred to the X from autosomal sites. We tested this hypothesis by determining the chromosomal location of the tammar wallaby orthologues of nine X linked human MRX genes. Tammar wallaby orthologues of XCR genes on the long arm of the human X chromosome (OPHN1, RSK4, AGTR2, ARHGEF6, FMR1, and FMR2) were located on the X chromosome in the tammar wallaby. Two other genes (SREB3 and JARID1C) lie close to the centromere of the short arm of the human X. This region is part of the ancient therian X, but its separate location in chickens and fish mean that it represents a separate evolutionary block [16]. Tammar wallaby orthologues of these genes also lie on the tammar wallaby X (Delbridge in preparation). Thus all the MRX genes in the conserved region of the human X were part of the original therian X chromosome.

Human RSK2, ARX and TSPAN7 are located on the short arm of the human X chromosome in a region that is autosomal in marsupials, and therefore represents a recent addition to the eutherian X. As expected, tammar wallaby orthologues of these XAR genes were located on the short arm of chromosome 5, mapping among other genes from this region. This confirms that these MRX genes were part of the recently added region that was transferred to the eutherian X chromosome following the divergence of eutherians from marsupials.

We conclude, therefore, that these eleven human MRX genes were part of two previously known conserved blocks of genes, the XAR and XCR, which make up the human X chromosome. None were transferred to the human X chromosome from other locations as independent acquisitions, or as different evolutionary blocks. This is also consistent with the available mapping data from another marsupial, the Brazilian short-tailed grey opossum (Monodelphis domestica), in which XCR genes lie on the X and XAR genes on opossum chromosome 4 [17]. In the more distantly related platypus (Ornithorhynchus anatinus), XCR genes lie on chromosome 6 [18], and XAR genes on two smaller chromosomes (Veyrunes, in preparation).

Did human MRX genes originate from genes with more general function?

Given that MRX genes are part of ancient conserved blocks, their over-representation on the X could be due either to an over-representation on the autosomal blocks that evolved into sex chromosomes, or the acquisition of more specialised function by genes with generalised expression. We distinguished between these hypotheses by examining the expression patterns of the MRX genes in the tammar wallaby. The hypothesis that these genes had brain-specific function in the ancestral mammal predicts that their expression will be the same in marsupials as eutherians. The hypothesis that genes with a more general function acquired brain-specific functions predicts that, at least for a few genes, expression patterns in marsupials and eutherians will be different. Moreover, genes more recently recruited to the X (those mapping to tammar wallaby 5p) might show less specialization, and fewer differences.

We obtained expression profiles from the homologues of the eleven genes in the tammar wallaby (Figure 2). Ten of these (SREB3, JARID1C, OPHN1, RSK4, AGTR2, ARHGEF6, FMR1, FMR2, RSK2, and TSPAN7) were widely expressed in tammar wallaby; RT-PCR products were detected in most of the tissue samples tested, including the brain (Table 3). Of the human XCR genes, four (JARID1C, RSK4, ARHGEF6 and FMR1) are also widely expressed in humans, so no difference in expression was detected. However, the wide expression of tammar wallaby orthologues of four human XCR genes (SREB3, OPHN1, AGTR2 and FMR2) contrasts with a more restricted expression pattern in human, suggesting that the brain functions, at least of these genes, were recently acquired in the therian lineage.

Tammar wallaby orthologues of two human Xp genes lying in the added region (RSK2 and TSPAN7) were also widely expressed, as they are in humans. The wide expression of these MRX genes from the added region of the human X suggests that they acquired a specific function more recently, only in the human brain.

The ARX gene in the added region of the human X is particularly interesting because it alone has a restricted expression pattern (cortex of the brain, testis and ovary) in the tammar wallaby. This reflects the restricted expression pattern in eutherian embryos, but differs from the wide expression in adults. Thus, ARX expression is restricted to the developing brain and reproductive tissues in all therian mammals. This pattern of expression appears to have been retained in the adult tammar wallaby, but has been relaxed to include expression in other tissues in adult human and mouse. ARX is therefore an example of a gene that has always played a critical role in development of the therian brain. Since ARX lies on tammar wallaby chromosome 5p, this ancient brain-specific function was not a consequence of its location on the X chromosome.

Expression patterns of MRX homologues have not yet been examined in a wide range of tissue types from the platypus or the chicken so we cannot deduce expression patterns of the MRX genes in an ancestral tetrapod. The expression patterns of OPHN1, ARHGEF6 and FMR1 have been examined in detail in the chicken brain [19] and found to be similar in the ancient regions of the mouse and chicken brain such as the cerebellum, but very different in the younger regions of the brain such as the telencephalon. This suggested that at least these three X-borne genes independently evolved specialised functions in the brain following the divergence of birds and mammals [19]. We found that these three genes were expressed widely in adult tammar wallaby tissues, including the brain, but since we did not examine expression in the corresponding different regions of the brain, we cannot tell whether this change in expression occurred before or after the marsupial-eutherian divergence.


In conclusion, our results are not consistent with the hypothesis that the over-representation on the X chromosome of genes with a function in brain resulted from relocation or copying of brain function genes from autosomes, either independently or as transposed blocks of independent origin. It remains possible that the over-representation of these genes was a property of the ancient autosomal regions that became the sex chromosomes. At least some brain-specific genes on the human X chromosome, such as ARX, already had a brain-specific function when they were located on the autosomal proto-X chromosome. However, we present four examples of the narrowing of the expression patterns of human XCR genes. This suggests that the acquisition of brain-specific function by originally widely expressed genes is responsible for the over-representation of brain-specific genes on the human X chromosome.



PCR amplifications were carried out using 15 pmol of each primer (Geneworks, Adelaide, Australia), 2.0 mM each of dATP, dCTP, dGTP, dTTP (Roche, Sydney, Australia), and 0.625U Taq Polymerase in the recommended buffer containing 1.5 mM MgCl2 (Promega, Sydney Australia). Following an initial denaturation at 94°C for 2 minutes, cycling conditions were 35 cycles of 94°C for 30 seconds; 50–60°C annealing for 30 seconds; 72°C for 1 minute; with a final extension of 10 minutes at 72°C. Annealing temperatures are listed in Table 2. All PCR products were cloned into the TA TOPO Cloning Kit (Invitrogen, Australia) for sequencing and verification of their identity. Sequencing was done at the Australian Genomic Research Facility (AGRF), Brisbane, Australia.

BAC libraries

BAC clones were isolated from either a male tammar wallaby (Macropus eugenii) BAC library (constructed at the Victorian Institute of Animal Sciences, VIA prefix, [20]) or the commercially available female tammar wallaby BAC library (Arizona Genomics Institute, AGI prefix).

Library screening

Gene specific DNA probes generated by PCR (Table 2) were radioactively labelled using 32-P dATP or 32-P dCTP using the Megaprime DNA labelling system (Amersham, Australia). DNA probes were hybridised to BAC filters for 16 hours at 60°C in Church's buffer [21] and washed twice in 2×SSC/0.1% SDS at 60°C. DNA probes generated from mouse genomic DNA were hybridised and washed at 50°C. Overgo probes were designed using the Overgo Maker tool available for download through the Washington University Genome Sequencing Centre website, and used to screen the BAC library as previously described [22].

Direct Sequencing

400 ng BAC DNA was used in a sequencing reaction containing 4 μl BigDye Terminator version 3.1 (Applied Biosystems) and 5 pmol primer. Cycling conditions for sequencing reactions were: 95°C for 5 minutes followed by 99 cycles of 96°C for 10 seconds, 50°C for 10 seconds and 60°C for 4 minutes. Reactions were precipitated and sent to AGRF for capillary separation.

RNA isolation

Tissue was collected under The Australian National University Animal Experimentation Ethics Committee proposal numbers R.CG.08.03 and R.CG.11.06. RNA was isolated from tissue using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, Sydney, Australia).

Reverse transcription

First strand synthesis reactions were carried out using a random hexamer primer in the SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen, Australia). The integrity of the RNA and success of the first strand synthesis reaction was tested by PCR using the Quantum RNA 18S Internal Standards (Ambion). Control PCR amplification of 18S standards was carried out for all RNA samples. An 18S product was amplified from all first strand synthesis reactions (RT+), which confirmed the integrity of the RNA, and the quality of the first strand synthesis reaction. Control 18S products could not be amplified from any RNA samples on which a first strand synthesis reaction had not been performed (RT-), ensuring that there was no genomic DNA contamination of the RNA samples (results not shown). Control reactions were followed by RT-PCR amplification of marsupial MRX genes using gene-specific primers (Table 2).

Fluorescence in situ hybridisation

Male tammar wallaby fibroblast cells were cultured and metaphase chromosome spreads prepared on glass slides as previously described [23]. BAC DNA was labelled by nick translation and hybridised to the chromosome preparations as previously described [17]. Fluorescence was visualised with a Zeiss Axioplan epifluorescence microscope fitted with a 100-W mercury lamp and a SPOT RT Monochrome CCD camera (Diagnostic Instruments Inc., Sterling Heights, MI, USA). IPLab imaging software (Scanalytics Inc., Fairfax, VA, USA) was used to capture and enhance images.

A localisation was confirmed by capture of images of at least 10 metaphase spreads on which a specific localisation could be observed on two X chromatids or at least three chromosome 5 chromatids.


  1. 1.

    Lehrke R: Theory of X-linkage of major intellectual traits. Am J Ment Defic. 1972, 76 (6): 611-619.

    PubMed  Google Scholar 

  2. 2.

    Turner G: Intelligence and the X chromosome. Lancet. 1996, 347 (9018): 1814-1815. 10.1016/S0140-6736(96)91623-2.

    PubMed  Article  Google Scholar 

  3. 3.

    Lubs HA, Chiurazzi P, Arena JF, Schwartz C, Tranebjaerg L, Neri G: XLMR genes: update 1996. Am J Med Genet. 1996, 64 (1): 147-157. 10.1002/(SICI)1096-8628(19960712)64:1<147::AID-AJMG25>3.0.CO;2-M.

    PubMed  Article  Google Scholar 

  4. 4.

    Zechner U, Wilda M, Kehrer-Sawatzki H, Vogel W, Fundele R, Hameister H: A high density of X-linked genes for general cognitive ability: a run-away process shaping human evolution?. Trends Genet. 2001, 17 (12): 697-701. 10.1016/S0168-9525(01)02446-5.

    PubMed  Article  Google Scholar 

  5. 5.

    Inlow JK, Restifo LL: Molecular and comparative genetics of mental retardation. Genetics. 2004, 166 (2): 835-881. 10.1534/genetics.166.2.835.

    PubMed  PubMed Central  Article  Google Scholar 

  6. 6.

    Saifi GM, Chandra HS: An apparent excess of sex- and reproduction-related genes on the human X chromosome. Proc R Soc Lond B Biol Sci. 1999, 266 (1415): 203-209. 10.1098/rspb.1999.0623.

    Article  Google Scholar 

  7. 7.

    Wang PJ, McCarrey JR, Yang F, Page DC: An abundance of X-linked genes expressed in spermatogonia. Nat Genet. 2001, 27 (4): 422-426. 10.1038/86927.

    PubMed  Article  Google Scholar 

  8. 8.

    Betran E, Long M: Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics. 2003, 164 (3): 977-988.

    PubMed  PubMed Central  Google Scholar 

  9. 9.

    Pallavicini A, Zimbello R, Tiso N, Muraro T, Rampoldi L, Bortoluzzi S, Valle G, Lanfranchi G, Danieli GA: The preliminary transcript map of a human skeletal muscle. Hum Mol Genet. 1997, 6 (9): 1445-1450. 10.1093/hmg/6.9.1445.

    PubMed  Article  Google Scholar 

  10. 10.

    Ko MS, Threat TA, Wang X, Horton JH, Cui Y, Wang X, Pryor E, Paris J, Wells-Smith J, Kitchen JR, Rowe LB, Eppig J, Satoh T, Brant L, Fujiwara H, Yotsumoto S, Nakashima H: Genome-wide mapping of unselected transcripts from extraembryonic tissue of 7.5-day mouse embryos reveals enrichment in the t-complex and under-representation on the X chromosome. Hum Mol Genet. 1998, 7 (12): 1967-1978. 10.1093/hmg/7.12.1967.

    PubMed  Article  Google Scholar 

  11. 11.

    Graves JAM: The origin and function of the mammalian Y chromosome and Y-borne genes--an evolving understanding. Bioessays. 1995, 17 (4): 311-320. 10.1002/bies.950170407.

    PubMed  Article  Google Scholar 

  12. 12.

    Kohn M, Kehrer-Sawatzki H, Vogel W, Graves JAM, Hameister H: Wide genome comparisons reveal the origins of the human X chromosome. Trends Genet. 2004, 20 (12): 598-603. 10.1016/j.tig.2004.09.008.

    PubMed  Article  Google Scholar 

  13. 13.

    Fisher RA: The evolution of dominance. Biological Reviews. 1931, 6: 345-368. 10.1111/j.1469-185X.1931.tb01030.x.

    Article  Google Scholar 

  14. 14.

    Graves JAM: Sex chromosome specialization and degeneration in mammals. Cell. 2006, 124 (5): 901-914. 10.1016/j.cell.2006.02.024.

    PubMed  Article  Google Scholar 

  15. 15.

    Gecz J, Cloosterman D, Partington M: ARX: a gene for all seasons. Curr Opin Genet Dev. 2006, 16 (3): 308-316. 10.1016/j.gde.2006.04.003.

    PubMed  Article  Google Scholar 

  16. 16.

    Kohn M, Hogel J, Vogel W, Minich P, Kehrer-Sawatzki H, Graves JAM, Hameister H: Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet. 2006, 22 (4): 203-210. 10.1016/j.tig.2006.02.008.

    PubMed  Article  Google Scholar 

  17. 17.

    Alsop AE, Miethke P, Rofe R, Koina E, Sankovic N, Deakin JE, Haines H, Rapkins RW, Graves JAM: Characterizing the chromosomes of the Australian model marsupial Macropus eugenii (tammar wallaby). Chromosome Res. 2005, 13 (6): 627-636. 10.1007/s10577-005-0989-2.

    PubMed  Article  Google Scholar 

  18. 18.

    Waters PD, Delbridge ML, Deakin JE, El-Mogharbel N, Kirby PJ, Carvalho-Silva DR, Graves JA: Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution. Chromosome Res. 2005, 13 (4): 401-410. 10.1007/s10577-005-0978-5.

    PubMed  Article  Google Scholar 

  19. 19.

    Kohn M, Kehrer-Sawatzki H, Steinbach P, Graves JAM, Hameister H: Recruitment of old genes to new functions: evidences obtained by comparing the orthologues of human XLMR genes in mouse and chicken. Cytogenet Genome Res. 2007, 116 (3): 173-180. 10.1159/000098183.

    PubMed  Article  Google Scholar 

  20. 20.

    Sankovic N, Delbridge ML, Grutzner F, Ferguson-Smith MA, O'Brien PC, Graves JAM: Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes. Chromosome Res. 2006, 14 (6): 657-664. 10.1007/s10577-006-1076-z.

    PubMed  Article  Google Scholar 

  21. 21.

    Church GM, Gilbert W: Genomic sequencing. Proc Natl Acad Sci U S A. 1984, 81 (7): 1991-1995. 10.1073/pnas.81.7.1991.

    PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Ross MT, LaBrie S, McPherson J, Stanton Jr. VP: Screening large insert libraries by hybridisation. Current Protocols in Human Genetics. 1999, John Wiley & Sons, Inc, 5.6.1-5.6.52.

    Google Scholar 

  23. 23.

    Koina E, Wakefield MJ, Walcher C, Disteche CM, Whitehead S, Ross M, Graves JAM: Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals. Chromosome Res. 2005, 13 (7): 687-698. 10.1007/s10577-005-1006-5.

    PubMed  PubMed Central  Article  Google Scholar 

  24. 24.

    Kohn M, Hameister H, Vogel M, Kehrer-Sawatzki H: Expression pattern of the Rsk2, Rsk4 and Pdk1 genes during murine embryogenesis. Gene Expr Patterns. 2003, 3 (2): 173-177. 10.1016/S1567-133X(03)00004-8.

    PubMed  Article  Google Scholar 

  25. 25.

    Jacquot S, Zeniou M, Touraine R, Hanauer A: X-linked Coffin-Lowry syndrome (CLS, MIM 303600, RPS6KA3 gene, protein product known under various names: pp90(rsk2), RSK2, ISPK, MAPKAP1). Eur J Hum Genet. 2002, 10 (1): 2-5. 10.1038/sj.ejhg.5200738.

    PubMed  Article  Google Scholar 

  26. 26.

    Zeniou M, Ding T, Trivier E, Hanauer A: Expression analysis of RSK gene family members: the RSK2 gene, mutated in Coffin-Lowry syndrome, is prominently expressed in brain structures essential for cognitive function and learning. Hum Mol Genet. 2002, 11 (23): 2929-2940. 10.1093/hmg/11.23.2929.

    PubMed  Article  Google Scholar 

  27. 27.

    Stromme P, Mangelsdorf ME, Shaw MA, Lower KM, Lewis SM, Bruyere H, Lutcherath V, Gedeon AK, Wallace RH, Scheffer IE, Turner G, Partington M, Frints SG, Fryns JP, Sutherland GR, Mulley JC, Gecz J: Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy. Nat Genet. 2002, 30 (4): 441-445. 10.1038/ng862.

    PubMed  Article  Google Scholar 

  28. 28.

    Ohira R, Zhang YH, Guo W, Dipple K, Shih SL, Doerr J, Huang BL, Fu LJ, Abu-Khalil A, Geschwind D, McCabe ER: Human ARX gene: genomic characterization and expression. Mol Genet Metab. 2002, 77 (1-2): 179-188. 10.1016/S1096-7192(02)00126-9.

    PubMed  Article  Google Scholar 

  29. 29.

    Miura H, Yanazawa M, Kato K, Kitamura K: Expression of a novel aristaless related homeobox gene 'Arx' in the vertebrate telencephalon, diencephalon and floor plate. Mech Dev. 1997, 65 (1-2): 99-109. 10.1016/S0925-4773(97)00062-2.

    PubMed  Article  Google Scholar 

  30. 30.

    Kitamura K, Miura H, Yanazawa M, Miyashita T, Kato K: Expression patterns of Brx1 (Rieg gene), Sonic hedgehog, Nkx2.2, Dlx1 and Arx during zona limitans intrathalamica and embryonic ventral lateral geniculate nuclear formation. Mech Dev. 1997, 67 (1): 83-96. 10.1016/S0925-4773(97)00110-X.

    PubMed  Article  Google Scholar 

  31. 31.

    Zemni R, Bienvenu T, Vinet MC, Sefiani A, Carrie A, Billuart P, McDonell N, Couvert P, Francis F, Chafey P, Fauchereau F, Friocourt G, des Portes V, Cardona A, Frints S, Meindl A, Brandau O, Ronce N, Moraine C, van Bokhoven H, Ropers HH, Sudbrak R, Kahn A, Fryns JP, Beldjord C, Chelly J: A new gene involved in X-linked mental retardation identified by analysis of an X;2 balanced translocation. Nat Genet. 2000, 24 (2): 167-170. 10.1038/72829.

    PubMed  Article  Google Scholar 

  32. 32.

    Matsumoto M, Saito T, Takasaki J, Kamohara M, Sugimoto T, Kobayashi M, Tadokoro M, Matsumoto S, Ohishi T, Furuichi K: An evolutionarily conserved G-protein coupled receptor family, SREB, expressed in the central nervous system. Biochem Biophys Res Commun. 2000, 272 (2): 576-582. 10.1006/bbrc.2000.2829.

    PubMed  Article  Google Scholar 

  33. 33.

    Matsumoto M, Beltaifa S, Weickert CS, Herman MM, Hyde TM, Saunders RC, Lipska BK, Weinberger DR, Kleinman JE: A conserved mRNA expression profile of SREB2 (GPR85) in adult human, monkey, and rat forebrain. Brain Res Mol Brain Res. 2005, 138 (1): 58-69. 10.1016/j.molbrainres.2005.04.002.

    PubMed  Article  Google Scholar 

  34. 34.

    Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A, Janecke AR, Tariverdian G, Chelly J, Fryns JP, Van Esch H, Kleefstra T, Hamel B, Moraine C, Gecz J, Turner G, Reinhardt R, Kalscheuer VM, Ropers HH, Lenzner S: Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am J Hum Genet. 2005, 76 (2): 227-236. 10.1086/427563.

    PubMed  PubMed Central  Article  Google Scholar 

  35. 35.

    Kutsche K, Yntema H, Brandt A, Jantke I, Nothwang HG, Orth U, Boavida MG, David D, Chelly J, Fryns JP, Moraine C, Ropers HH, Hamel BC, van Bokhoven H, Gal A: Mutations in ARHGEF6, encoding a guanine nucleotide exchange factor for Rho GTPases, in patients with X-linked mental retardation. Nat Genet. 2000, 26 (2): 247-250. 10.1038/80002.

    PubMed  Article  Google Scholar 

  36. 36.

    Billuart P, Bienvenu T, Ronce N, des Portes V, Vinet MC, Zemni R, Carrie A, Beldjord C, Kahn A, Moraine C, Chelly J: Oligophrenin 1 encodes a rho-GAP protein involved in X-linked mental retardation. Pathol Biol (Paris). 1998, 46 (9): 678-

    Google Scholar 

  37. 37.

    Govek EE, Newey SE, Akerman CJ, Cross JR, Van der Veken L, Van Aelst L: The X-linked mental retardation protein oligophrenin-1 is required for dendritic spine morphogenesis. Nat Neurosci. 2004, 7 (4): 364-372. 10.1038/nn1210.

    PubMed  Article  Google Scholar 

  38. 38.

    Yntema HG, van den Helm B, Kissing J, van Duijnhoven G, Poppelaars F, Chelly J, Moraine C, Fryns JP, Hamel BC, Heilbronner H, Pander HJ, Brunner HG, Ropers HH, Cremers FP, van Bokhoven H: A novel ribosomal S6-kinase (RSK4; RPS6KA6) is commonly deleted in patients with complex X-linked mental retardation. Genomics. 1999, 62 (3): 332-343. 10.1006/geno.1999.6004.

    PubMed  Article  Google Scholar 

  39. 39.

    Dummler BA, Hauge C, Silber J, Yntema HG, Kruse LS, Kofoed B, Hemmings BA, Alessi DR, Frodin M: Functional characterization of human RSK4, a new 90-kDa ribosomal S6 kinase, reveals constitutive activation in most cell types. J Biol Chem. 2005, 280 (14): 13304-13314. 10.1074/jbc.M408194200.

    PubMed  Article  Google Scholar 

  40. 40.

    Vervoort VS, Beachem MA, Edwards PS, Ladd S, Miller KE, de Mollerat X, Clarkson K, DuPont B, Schwartz CE, Stevenson RE, Boyd E, Srivastava AK: AGTR2 mutations in X-linked mental retardation. Science. 2002, 296 (5577): 2401-2403.

    PubMed  Google Scholar 

  41. 41.

    Grady EF, Sechi LA, Griffin CA, Schambelan M, Kalinyak JE: Expression of AT2 receptors in the developing rat fetus. J Clin Invest. 1991, 88 (3): 921-933. 10.1172/JCI115395.

    PubMed  PubMed Central  Article  Google Scholar 

  42. 42.

    Kohn M, Steinbach P, Hameister H, Kehrer-Sawatzki H: A comparative expression analysis of four MRX genes regulating intracellular signalling via small GTPases. Eur J Hum Genet. 2004, 12 (1): 29-37. 10.1038/sj.ejhg.5201085.

    PubMed  Article  Google Scholar 

  43. 43.

    Kutsche K, Gal A: The mouse Arhgef6 gene: cDNA sequence, expression analysis, and chromosome assignment. Cytogenet Cell Genet. 2001, 95 (3-4): 196-201. 10.1159/000059346.

    PubMed  Article  Google Scholar 

  44. 44.

    Oostra BA, Willemsen R: A fragile balance: FMR1 expression levels. Hum Mol Genet. 2003, 12 Spec No 2: R249-57. 10.1093/hmg/ddg298.

    PubMed  Article  Google Scholar 

  45. 45.

    Bachner D, Steinbach P, Wohrle D, Just W, Vogel W, Hameister H, Manca A, Poustka A: Enhanced Fmr-1 expression in testis. Nat Genet. 1993, 4 (2): 115-116. 10.1038/ng0693-115.

    PubMed  Article  Google Scholar 

  46. 46.

    Tamanini F, Willemsen R, van Unen L, Bontekoe C, Galjaard H, Oostra BA, Hoogeveen AT: Differential expression of FMR1, FXR1 and FXR2 proteins in human brain and testis. Hum Mol Genet. 1997, 6 (8): 1315-1322. 10.1093/hmg/6.8.1315.

    PubMed  Article  Google Scholar 

  47. 47.

    Chakrabarti L, Bristulf J, Foss GS, Davies KE: Expression of the murine homologue of FMR2 in mouse brain and during development. Hum Mol Genet. 1998, 7 (3): 441-448. 10.1093/hmg/7.3.441.

    PubMed  Article  Google Scholar 

  48. 48.

    Miller WJ, Skinner JA, Foss GS, Davies KE: Localization of the fragile X mental retardation 2 (FMR2) protein in mammalian brain. Eur J Neurosci. 2000, 12 (1): 381-384. 10.1046/j.1460-9568.2000.00921.x.

    PubMed  Article  Google Scholar 

Download references


This study was supported by an ARC discovery project grant awarded to MLD.

Author information



Corresponding author

Correspondence to Margaret L Delbridge.

Additional information

Authors' contributions

RJD and MLD carried out the library screening. DAM and RJD carried out the localisation experiments. DAM carried out the expression analysis. JED localised TSPAN7. MLD participated in the design and coordination of the study, and drafted and revised the manuscript. JAMG contributed to the design of the study, and preparation and revision of the manuscript. All authors read and approved the final and revised manuscript.

Authors’ original submitted files for images

Below are the links to the authors’ original submitted files for images.

Authors’ original file for figure 1

Authors’ original file for figure 2

Rights and permissions

This article is published under license to BioMed Central Ltd. 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 work is properly cited.

Reprints and Permissions

About this article

Cite this article

Delbridge, M.L., McMillan, D.A., Doherty, R.J. et al. Origin and evolution of candidate mental retardation genes on the human X chromosome (MRX). BMC Genomics 9, 65 (2008).

Download citation


  • Tammar Wallaby
  • Australian Genomic Research Facility
  • Restricted Expression Pattern
  • Mental Retardation Gene
  • Strand Synthesis Reaction