- Research article
- Open Access
Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues
- Sandra Schmieder†1,
- Fleur Darré-Toulemonde†1, 4,
- Marie-Jeanne Arguel1, 2,
- Audrey Delerue-Audegond1, 2,
- Richard Christen3 and
- Jean-Louis Nahon1, 2Email author
© Schmieder et al; licensee BioMed Central Ltd. 2008
- Received: 08 August 2008
- Accepted: 09 December 2008
- Published: 09 December 2008
Brain-expressed genes that were created in primate lineage represent obvious candidates to investigate molecular mechanisms that contributed to neural reorganization and emergence of new behavioural functions in Homo sapiens. PMCHL1 arose from retroposition of a pro-melanin-concentrating hormone (PMCH) antisense mRNA on the ancestral human chromosome 5p14 when platyrrhines and catarrhines diverged. Mutations before divergence of hylobatidae led to creation of new exons and finally PMCHL1 duplicated in an ancestor of hominids to generate PMCHL2 at the human chromosome 5q13. A complex pattern of spliced and unspliced PMCHL RNAs were found in human brain and testis.
Several novel spliced PMCHL transcripts have been characterized in human testis and fetal brain, identifying an additional exon and novel splice sites. Sequencing of PMCHL genes in several non-human primates allowed to carry out phylogenetic analyses revealing that the initial retroposition event took place within an intron of the brain cadherin (CDH12) gene, soon after platyrrhine/catarrhine divergence, i.e. 30–35 Mya, and was concomitant with the insertion of an AluSg element. Sequence analysis of the spliced PMCHL transcripts identified only short ORFs of less than 300 bp, with low (VMCH-p8 and protein variants) or no evolutionary conservation. Western blot analyses of human and macaque tissues expressing PMCHL RNA failed to reveal any protein corresponding to VMCH-p8 and protein variants encoded by spliced transcripts.
Our present results improve our knowledge of the gene structure and the evolutionary history of the primate-specific chimeric PMCHL genes. These genes produce multiple spliced transcripts, bearing short, non-conserved and apparently non-translated ORFs that may function as mRNA-like non-coding RNAs.
- Fetal Brain
- Segmental Duplication
- Splice Acceptor Site
- Small ncRNAs
There is an ancient  but still active debate in the molecular biologist community about the relative contribution of structural genomic modifications  that could account for the phenotypic differences observed between primate species, particularly in the emergence of new brain structure and functions [3, 4]. Very debated results were found when determining the Ka/Ks ratio, a tentative indicator of positive Darwinian selection, in the coding region of genes expressed in the mammalian brain [5–7]. However, genome-wide comparative studies of mammalian promoters suggested an accelerated evolution of primate promoters during the last 25 million years [8–10]. Recently, divergence between human and chimpanzee sequences have been re-evaluated to almost 5%, resulting mainly from indel events [2, 11–13] and copy number variants (CNVs) that strongly contributed in shaping primate genomes , offering therefore a wide variety of sites at which primate lineage-specific genetic novelty could happen. Indeed, recent segmental duplications are particularly enriched in genes that display expression differences between humans and chimpanzees . In addition, an accelerated rate of contraction or expansion in gene families, including brain-expressed genes, operated in primates when compared with other mammals . On a larger scale, CNVs contributed significantly to diverse expression phenotypes in primates  and to emergence of complex or sporadic diseases in humans . To reconcile apparently conflicting data, we previously proposed that, in parallel to single nucleotide mutations that confer alterations in the gene expression patterns or amino acids sequences, genomic rearrangements may have played an important role during primate evolution, providing creation of novel but rare regulatory modules as well as protein coding and/or non-coding genes [19–21]. Indeed, combination of exon shuffling, retrotransposition and gene promoter fusion have led to genes harbouring completely new structures and expression patterns selectively in the primate lineage (reviewed in [22, 23]). These rare events would have been nevertheless particularly important in shaping human genes found expressed in reproductive organs, as exemplified by the chimeric POTE-actin genes , or involved in hominoid brain neurotransmission, as exemplified by the GLUD2 gene .
The study of primate-specific gene creation and early evolution requires the discovery of genes that have retained characteristic features of their youth . The PMCHL system, which combines the retroposition/exon shuffling and the segmental duplication models, has been one of the first hominoid-specific gene creation model described [19–21, 27, 28]. We have shown that these genes have been created in the hominoid lineage through i) retroposition at the ancestral chromosome 5p14 locus in catarrhini of an antisense pro-melanin-concentrating hormone (PMCH) gene transcript, ii) local rearrangement leading to a truncated version of the retrogene, iii) sequence remodelling (indel and mutation accumulation that allowed creation of exons) and iv) final duplication at the ancestral 5q13 locus in hominids. Furthermore, processed and unprocessed transcripts were characterized in a human fetal brain library  as well as in developing human brain . These mRNAs were found to encode a putative nuclear protein of 8 kD, named VMCH-p8, that was only identified using in vitro translation systems or transfected cell models . However, many questions remained unsolved regarding the region and time of insertion of the retrogene, the fine structure of both genes (complete exon/intron structure), their expression patterns (in particular the relative abundance and tissue-specificity of processed transcripts) and their protein coding potential in human cells.
In this paper, we established the structure of PMCHL1/PMCHL2 genes and demonstrated that alternatively spliced transcripts encompassing exons 1 to 6 are mostly expressed in human testis. We established further the evolutionary history and regional organization of PMCHL genes at both loci on human chromosome 5 and proposed that a single retroposition event followed by point mutations provided novel exonic sequences in transcriptional sense direction. Several short open reading frames (ORFs) were found encoded within the spliced PMCHL RNAs but most of them were not conserved in the primate lineage. This suggests a lack of overt functionality of these ORFs, even though the existence of a small species-specific protein cannot be ruled out. Finally, we attempted to identify proteins generated from PMCHL genes in macaque and human tissues with an antiserum directed against VMCH-p8 and its variants but we failed to detect them. Therefore, spliced transcripts from the primate-specific PMCHL1/PMCHL2 genes would likely represent mRNA-like non-protein coding RNAs (ncRNAs).
1. Structure and distribution of spliced PMCHLtranscripts in human brain and testis
We identified six PMCHL1 spliced variants in adult testicular Marathon cDNA library (Figure 1B), two of which [GenBank:EU921424, GenBank:EU921428] had already been identified in the same cDNA library [GenBank:AY008408, GenBank:AY008410, respectively]. However, transcript [GenBank:EU921424] bears one A to G mutation within exon 1, resulting in an arginine to glycine mutation in ORF1. Noteworthy, transcript [GenBank:EU921428] corresponds also to two testis ESTs (IMAGE clone 1753807 [GenBank:AI203691; EMBL:BX091674] and IMAGE clone 1326573 [GenBank:AA724728]), and was also found in a human fetal brain Marathon cDNA library in our previous study . This apparently abundant transcript harbours exons 1-2b and 6a, like most spliced transcripts in testis which were obtained in a single round of PCR. In contrast, transcripts harbouring exon 6b were identified after two rounds of PCR and never contained exon 6a. Transcripts containing exon 2a were never observed in the present study.
We further identified one novel PMCHL1 splice variant in a fetal prefrontal cortex sample (Figure 1B). This transcript was the only one to harbour an alternative splice donor in exon 4, which was never observed in testis RNAs.
In our previous study , we reported two alternative acceptor sites in exon 5b (previously named exon 4b) separated by only four nucleotides and with apparent testis- and brain-specificities (indicated by superscript t/b in Figure 1). Our present results show that most testis transcripts use the exon 5a splice acceptor site, and two use the alternative 5bt site. However, the PMCHL1 transcripts identified in fetal brain also use the alternative 5bt site indicating that it could not be considered anymore as a testis-specific splice acceptor site. The alternative 5bb site, previously reported in a fetal brain transcript was not found in our present study.
In contrast to human testis and fetal brain, we could not detect any spliced PMCHL RNA harbouring exons 1 and 6a in the human adult cortex Marathon cDNA library using the 3–7/3–30 primer pair. This primer pair was further used in RT-PCR experiments combined with Southern blot to determine the tissue distribution of the spliced transcripts in testis, prefrontal cortex and cerebellum in adult human and macaque (Figure 1C). In agreement with our results using the Marathon cDNA libraries, we detected spliced PMCHL RNA harbouring exons 1 and 6a in human adult testis, but not in adult prefrontal cortex and cerebellum. Thus, PMCHL1 transcripts are found in testis and fetal brain and are more abundant than PMCHL2 transcripts that are observed only in testis. In addition, PMCHL2 gene expression was reported in HT1080 cells subjected to RAGE (random activation of gene expression), in which an EST [GenBank:BG184695] encompassing exons 2a and 3 of PMCHL2 has been identified.
In macaque, no spliced transcripts were identified by Southern blot (Figure 1C) in agreement with our sequence analysis indicating that the macaque PMCHL1 gene lacks the exon 6a acceptor splice site (see below).
Taken together, our findings indicate that PMCHL1 and PMCHL2 genes: i) give rise to a complex pattern of alternative splicings, ii) are subject to distinct tissue-specific expressions and iii) are developmentally regulated (i.e. expressed in fetal but not adult cortex).
The finding that a rather high diversity of spliced transcripts are present in testis is not surprising, because of the permissive chromatin environment present in gonads, allowing high transcriptional activity even from weak tissue-specific promoters . Thus, most retroposons evolve into non-functional pseudogenes that are transcribed only in the testis . However, the abrupt emergence of a new chimeric gene in primates could potentially contribute to reproductive barriers and thus play a role in speciation . In this regard the hominoid-specific oncogene Tre2 appears expressed only in testis while the two parental genes USP32 and TBC1D3, that fused to generate the Tre2 gene, are expressed in a broad range of human tissues . In addition, the presence of spliced PMCHL transcripts in fetal brain, is rather suggestive of a functional role during human brain development. This would imply that the retroposon acquired an active promoter and has been subjected to selection pressure. Whether these spliced PMCHL transcripts actually play a functional role in testis and fetal brain is an obvious question, which we further addressed below.
2. Evolutionary history of the PMCHLgenes
Retroposition-driven creation of PMCHL1 gene occurred 30–35 Mya in primate lineage
Sequences of oligonucleotides used for PCR
We first carried out the phylogenetic analysis of the exon/intron boundaries of the PMCHL genes (Figure 2A, B). Consensus gt/ag splice donor and acceptor sites are present in all species bearing the retroposon, i.e. all catarrhines of this study, with the exception of the splice acceptor site of exon 6a which is present only in hominoids. Moreover, the exon 5c donor site and the 6a and 6b splice acceptor sites were not consensual in the platyrrhines analysed here, i. e. before the retroposition event, suggesting that canonical splicing could not occur in this ancestral region before the arrival of the retroposed sequence. Our sequence analysis showed that these splice sites were created de novo through single nucleotide mutations. Thus, the splicing between exons 5 and 6 corresponds to de novo exonisation and not to an Alu-driven exonisation mechanism , exon 6 being absent in platyrrhines and then conserved through selection pressure. In contrast, splice sites of exons 3 and 4 pre-dated the retroposition event, indicating that a fusion of the PMCH-derived exons with pre-existing exons is likely to have occurred. Whether these exons were expressed before the retroposition remains to be determined, but no expressed sequence tag corresponding to exons 3 and 4 alone could be identified in mammalian EST databases. Furthermore, chimeric transcripts formed by transcription of two consecutive genes into a single RNA can occur quite frequently in human cells . A similar mechanism may be involved in the production of fused transcripts encompassing either exon 3 or 4 of PMCHL1/PMCHL2 genes. However, further characterization of putative promoters inside the PMCHL genes needs to be done before involving such RNA domain accretion process on regulation of these genes.
When focusing on the PMCHL genes, in the regions encompassing exons 1-2b (Figure 3B) and exons 5–6 (Figure 3C) the nucleotidic phylogenetic trees fully correspond to accepted species trees, indicating that no particular and global (since here the entire gene sequences were used) evolutionary event interfered. However, we observed a difference in the Pan troglodytes/Pan paniscus/Homo sapiens positioning between the two phylogenetic trees. This simply corresponds to an inherent irresolution in the hominidae speciation, which could be inferred (or not) from a complex speciation with interbreeding before final separation of chimpanzees, gorillas and humans [37–39]. All three species should probably be grouped under the Pan or Homo clade as previously suggested [35, 40, 41].
We previously reported the presence of a complete Alu-Sq sequence element within PMCHL exon 2 , but the insertion event into PMCHL1 could not be dated precisely. It is worth noting that this sequence appears to be an AluSg, and not an Alu Sq element. Our present sequence analysis reveals that all primate species carrying the PMCHL1 exon 2 harbour the AluSg sequence (Figure 2B). Thus, the insertion was likely concomitant to the retroposition, occurring after the divergence of Cebus species (C. apella and C. capucinus), and before the divergence of the cercopithecoids, approximately between 30–35 Mya.
A 92 kb element encompassing PMCHL1 and adjacent intronic/exonic sequence of CDH12 on 5p14 duplicated to create PMCHL2 on 5q13 at the time of hominid divergence
We have therefore precisely mapped the limits of the PMCHL1/PMCHL2 duplicon. A question concerning the creation of novel genes, particularly in the case of segmental duplication, is relative to the acceptor sites. Which kind of sequences allows invasion by foreign sequences? Which kind of sequences can we find at the segmental duplication boundaries? No clear boundaries specificities are described for segmental duplication except for a significant enrichment in short interspersed elements (SINEs) such as young Alu Y and Alu S sequences and other repeats similar to these involved in Ig heavy chain recombination in pericentromeric and interstitial segmental duplications [2, 13, 43]. Alu mediated DNA duplications have exceptionally been reported in eukaryotes . These duplications appeared however to affect mainly hyper-recombinogenic chromosomal regions, and particularly for secondary duplications . Long interspersed elements (LINEs) like Line 1 elements were also directly (i.e. not only favouring Alu sequences duplication) implicated in exon recombination and have been proposed to mediate exon shuffling , but none of the previously described human chimeric genes  harbour this kind of element at its boundaries. In the case of PMCHL1/L2, no particular SINEs or LINEs sequences could be found at the boundaries, neither at the first insertion site of the PMCH antisense retroposon (in an intron of the Brain Cadherin (CDH12) gene at the 5p14 locus), nor at the 5q13 locus when creating PMCHL2. Recently, a duplication-driven model for DNA transposition has been put forth by Eichler's group  suggesting that the probability for a DNA element to be duplicated correlated with the degree of proximity to so-called core duplicons. In this context, a core duplicon named Glu5–10 and corresponding to a truncated version of the GUSB gene, has been found in close vicinity to PMCHL1 and PMCHL2 genes on 5p14 and 5q13 respectively . Whether the proximity with this duplicon was determinant for emergence of the PMCHL2 gene remains at this stage a matter of speculation but the timing of both Glu5–10 duplicon expansion and intrachromosomal duplication of PMCHL1 in primates fits very well. These duplication events are also congruent with the global surge in intrachromosomal duplications at the time of hominid divergence, as previously predicted  and experimentally proven .
3. Analysis of the protein coding potential of PMCHLtranscripts
The longest ORF identified on PMCHL transcripts is 294 bp (98 amino acids) long and locates within the Alu sequence in exon 2a. Four transcripts harbouring exon 2a were identified in testis in our previous study . However, the corresponding putative protein is not conserved due to a single nucleotide insertion in the human PMCHL1 sequence causing a frameshift in the middle of the ORF. Therefore, this ORF is also spurious according to the criteria of Clamp and colleagues .
What might be the role(s) of the large variety of spliced PMCHL mRNAs in human testis and fetal brain? It is tempting to propose that these PMCHL transcripts work mainly as an mRNA-like non-protein coding RNA (ncRNA). Since the realization that 98% of the transcriptional output in mammals consists of ncRNAs, the enthusiasm for this class of RNAs has grown tremendously [53–55] and has been granted its own NONCODE database . Numerous classes of ncRNAs have been reported, most of which are small ncRNAs (including miRNAs, siRNAs and snoRNAs), but also long ncRNAs (ranging from 1 to more than 100kb) such as Xist and the antisense Tsix transcripts involved in × inactivation in mammals [57, 58], or the Air RNA that appears to be responsible for imprinted repression of nearby genes (including Igf2r gene) through an antisense-mediated mechanism . Several mRNA-like ncRNAs that are transcribed by RNA polymerase II, spliced and polyadenylated have also been reported [60–62], including in human [63, 64]. Interestingly, many small ncRNAs are located in introns of coding or non-coding mRNAs [54, 65]. The functional roles of ncRNA are diverse, corresponding mainly to adaptor functions targeting nucleic acids to various enzymatic complexes (involved in RNA processing, splicing, transcription...) and gene expression regulation/silencing (involved in virtually all cellular functions).
Do the PMCHL transcripts host small ncRNAs in their introns, and/or do the PMCHL transcripts control the expression of neighbouring genes in cis (an obvious candidate is the CDH12 gene) or in trans through RNA-RNA duplexes (obvious candidates are the PMCH and Antisense RNA Overlapping MCH (AROM) genes)? We are now addressing these intriguing questions.
We provide here new data concerning spliced PMCHL transcripts, further precising the PMCHL gene structure. Sequencing data of the PMCHL genes in several non-human primates offered a substantial improvement of the creation model proposed previously . In particular, we proposed that the initial retroposition occurred within an intron of the CDH12 gene soon after platyrrhine/catarrhine divergence and was concomitant with the insertion of an Alu Sg element. Our sequence analysis further points to the presence of short ORFs that present little or no evolutionary conservation, suggesting that spliced PMCHL transcripts are non-protein coding RNAs. This proposal is further supported by our expression analysis of the most relevant PMCHL ORFs in human and macaque tissues, which failed to detect any corresponding protein.
Human prefrontal cortex and cerebellum from adults were provided by the National Neurological Research Specimen Bank (Los Angeles, CA, USA) and by the GIE Neuro-CEB (Hôpital de la Pitié-Salpétrière, Paris, France), which collect tissues with the full authorization of the respective local ethical committees. Human adult testis RNA was purchased from BioChain/Cliniscience (France). Dr. A. Coquerel (CHU Rouen, France) provided human prefrontal cortex and hippocampus tissues from a newborn. Dr. D. Jordan (Faculté de médecine, Lyon, France) provided human prefrontal cortex and hippocampus tissues from a foetus. Collection of human new-born and foetal tissues was according to the french legislation of parental consent and with the approval of local ethical committees. Human adult testis total proteins were purchased from BioChain/Cliniscience (France). Testis, prefrontal cortex, cerebellum, visual area, and supplementary motor area samples from three adult macaques (Macaca fascicularis) were obtained from Dr. E. Bezard at the Biothèque Primate/Primatech (CNRS, Bordeaux, France), where tissue collection is carried out in agreement with the European Communities Council Directive of November 24, 1986 (86/609/EEC).
Genomic DNAs were collected from Cebus capucinus (gift from B. Dutrillaux, cytogénétique moléculaire et oncologie, CNRS, Institut Curie, Paris, France), Tarsius syrichta, Saguinus oedipus, Cebus apella, Chlorocebus aethiops, Hylobates lar, Pan paniscus and Pan troglodytes (gift from Dr P. Dijan, CEREMOD, Meudon, France) and were already used in previous studies . Other genomic samples were kindly provided by San Diego Zoo/CRES (Pan paniscus, Gorilla g.g., Pongo pygmaeus, Pongo p.abelii, Hylobates lar, Macaca silenus) and by Prof A. Blancher (Rangueil Hospital, Toulouse, France) (Cebus appella, Pan troglodytes). Genomic DNA was isolated from the occipital cortex of a Macaca fascicularis (provided by Dr. E. Bezard (Biothèque Primate/Primatech, CNRS, Bordeaux, France) according to the Blin and Stafford's method .
RNA extraction and reverse-transcription
Total RNAs were extracted from human and macaque tissues according to standard guanidium phenol method  and using a FastPrep apparatus (FP220A Thermo instrument, Qbiogene, France). Contaminating genomic DNA was removed from RNA preparation by RQ1 RNase-free DNase treatment (Promega) according to the manufacturer's protocol. cDNAs were synthesized by reverse-transcription (RT) of 2 μg of total DNase-treated RNAs using the SuperScript TM II Reverse Transcriptase (Invitrogen) and oligo dT according to the manufacturer's protocol.
Oligonucleotides (list provided in Table 1) were purchased from Eurogentec (Belgium).
For genomic DNA, 100–200 ng were PCR-amplified using the oligonucleotide couples indicated in Table 1 and the LA Taq polymerase (Takara) following the supplier's protocol. Thirty-five cycles of amplification were carried out as follows: 30 s at 94°C (denaturation), 30 s at annealing temperature (indicated in Table 1), 1 to 10 min at 72°C (extension). A final extension step of 7 min at 72°C was performed. PCR products were purified using the NucleoSpin kit (Machery Nagel) and sequenced.
For RT samples and Marathon cDNA libraries, 2 μl were PCR-amplified using the indicated primer pairs and the HotMaster Taq DNA polymerase (Eppendorf) following the supplier's protocol. Thirty-eight cycles of amplification were carried out as follows: 30 s at 94°C (denaturation), 30 s at annealing temperature (indicated in Table 1), 2 min at 65°C (extension). A final extension step of 7 min at 72°C was performed. When necessary, nested PCR was performed with internal primers using 2 μl of a 1:20 dilution of the first round products. PCR-amplified fragments were subcloned into the pGEM-T Easy vector (Promega) and transfected into TOP10 thermocompetent cells (Invitrogen) according to the manufacturer's instructions, followed by plasmid DNA preparation using a Qiaprep Spin Miniprep kit (Qiagen) and sequencing.
PCR products obtained with primer pair 3–7/3–30 (thirty-five cycles) were electrophoresed on a 1% agarose gel containing ethidium bromide and were visualized under UV. The gel was then denatured 15 min in 500 mM NaOH, 1.5 M NaCl solution, neutralized 15 min in 500 mM Tris, 1.5 M NaCl, and soaked 5 min in 2 × SCC solution (300 mM NaCl, 30 mM sodium citrate). The DNA was transferred overnight as a gravity-dry blot onto a cellulose membrane (Biodyne B, Pall Corporation, FL, USA). The membrane was prehybridized for 4 h at 65°C in Church solution (500 mM Na2HPO4, pH 6.8, 5% SDS), hybridized overnight at 65°C in fresh Church solution containing previously prepared 32P-labeled PMCHL-specific probe 1 corresponding to the fragment amplified with primer pair 3–25/3–30 (see Table 1) at 5.105 dpm.ml-1. 32P-labeled probes were prepared using the Prime-a-gene labelling system (Promega) according to the manufacturer's protocol. After hybridization, the membrane was washed twice 15 min in 2 × SSPE and twice 10 min in 1 × SSPE. Hybridized radioactive probes were detected with a Fujifilm phosphoimager (FLA-5100).
DNA sequencing and alignment
Sequencing of PCR-amplified fragments was carried out on both DNA strands using the Ampli Taq Polymerase FS, the Big Dye Terminator 1.1 sequencing kit (Applera), and a ABI PRISM 3100 sequencer (Perkin Elmer). Sequences obtained from the public databases (EMBL/GenBank/DDBJ) and fragments sequenced by PCR were aligned manually using SEAVIEW . Species are: Homo sapiens (HSA), Pan paniscus (PPA), Pan troglodytes (PTR), Pongo pygmaeus (PPY), Hylobates lar (HLA), Macaca mulatta (MML), Macaca fascicularis (MFA), Cercopithecus hamlyni (CHA), Chlorocebus aethiops (CAE), Cebus capucinus (CCA), Cebus apella (CAP), Saginus oedipus (SOE), Tarsius syrichta (TSY).
Phylogenetic dendrograms were reconstructed according to three different methods: Neighbour Joining (BIONJ), Maximum Likelihood (ML, using the Global option), and Maximum Parsimony (MP). For the Neighbour Joining (NJ) analysis, a distance matrix was calculated by DNADIST according to the Kimura two parameters correction. Bootstraps were done using 1,000 replications, BIONJ and Kimura two parameters correction. BIONJ was according to Gascuel , ML and MP were from PHYLIP (Phylogeny Inference Package, version 3.573c, distributed by J. Felsenstein, Department of Genetics, UW, Seattle, WA, USA). Phylogenetic analyses were done excluding domains that were not common to every sequence as well as low complexity domains that could not be properly aligned. The phylogenetic dendrograms were drawn using NJPLOT .
Preparation of proteins
Human and macaque tissues were homogenized in RIPA buffer (20 mM Tris HCl, pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholic acid, 0.1% SDS, 2 mM EDTA, protease inhibitor cocktail Complete (Roche)) using a FastPrep apparatus (FP220A Thermo instrument, Qbiogene, France), incubated on ice for 30 min, and centrifuged at 20000 × g for 15 min at 4°C. Proteins in the supernatants were quantitated using a commercial Bradford reagent (BioRad).
Production of recombinant GST-VMCHp8 protein
PMCHL1 ORF1 encoding the putative VMCH-p8 protein was sub-cloned into the BamH1/EcoR1 sites of the pGEX-3X vector, in frame with GST (Amersham Biosciences). The construct was used to transform thermocompetent Rosetta cells (Novagen) and the recombinant GST-VMCH-p8 protein was produced and purified using glutathione-sepharose (Amersham Biosciences) beads according to the manufacturer's instructions.
Polyclonal antibodies were raised against the putative VMCH-p8 protein encoded by PMCHL1 ORF1. A peptide comprising the thirteen N-terminal amino acids of the sequence (MLSQKPKKKHNFL) was designed by Dr B. Cardinaud (IPMC, Valbonne, France), synthesized and coupled to keyhole limpet haemocyanin (KLH) before rabbit immunization (Genaxis, Nîmes, France). Anti-VMCH-p8 antiserum was used at a final dilution of 1:1,000. Secondary HRP-coupled goat anti-rabbit antibodies (Jackson ImmunoResearch) were used at a 1:10,000 dilution.
Proteins were separated on 12% Tris-glycine or 16.5% Tris-tricine gels under reducing conditions and transferred to nitrocellulose membranes (Schleicher & Schuell, Germany) using a wet tank transfer system (BioRad). Membranes were blocked 1 h in TBS-T (137 mM NaCl, 2.7 mM KCl, 2.5 mM Tris, pH 7.4, 0.1% Tween-20) containing 5% fetal calf serum, incubated for 2 h at room temperature with primary antibodies (1:1000 dilution), followed by 1 h incubation with secondary antibodies, and revealed with the SuperSignal West Pico (Pierce) chemiluminescence detection system.
We thank very much Drs F. Presse and E. Lalli (IPMC, Valbonne, France) for helpful advice and critical reading of the manuscript. We are grateful to Dr B. Cardinaud (IPMC, Valbonne, France) for developing the anti-VMCH-p8 antiserum, and C. Payré for excellent technical assistance. We are grateful to Dr A. Coquerel (CHU Rouen, France), Dr D. Jordan (Faculté de médecine, Lyon, France), Dr E. Bezard (Biothèque Primate/Primatech, CNRS, Bordeaux, France), the National Neurological Research Specimen Bank (Los Angeles, CA, USA) and the GIE Neuro-CEB (Hôpital de la Pitié-Salpétrière, Paris, France) for generously providing human and macaque tissues. Genomic DNAs were kindly provided by Dr B. Dutrillaux (CNRS, Institut Curie, Paris, France), by Dr P. Dijan (CEREMOD, Meudon, France), by Prof A. Blancher (Hôpital Rangeuil, Toulouse, France) and by Dr L. Chemnick (San Diego Zoo/CRES, San Diego, Ca, USA). This work was supported by the Centre National de la Recherche Scientifique (CNRS programme OHLL 2002–2004; crédits exceptionnels Biothèque Primate), by a 6th FP EU STREPS/NEST (APES project n° 28594), and by the Agence Nationale de la Recherche (ANR MNP-2008). SS is presently supported by the APES project. FDT was a recipient of a fellowship from the French Education Ministry (Allocation couplée MENRS/ENS). ADA and MJA were supported by the CNRS (crédits exceptionnels Biothèque Primate). MJA was also supported by the MJ Fox Foundation.
- King MC, Wilson AC: Evolution at two levels in humans and chimpanzees. Science. 1975, 188: 107-16. 10.1126/science.1090005.View ArticlePubMedGoogle Scholar
- Bailey JA, Eichler EE: Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006, 7: 552-64. 10.1038/nrg1895.View ArticlePubMedGoogle Scholar
- Khaitovich P, Enard W, Lachmann M, Paabo S: Evolution of primate gene expression. Nat Rev Genet. 2006, 7: 693-702. 10.1038/nrg1940.View ArticlePubMedGoogle Scholar
- Sikela JM: The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain. PLoS Genet. 2006, 2: e80-10.1371/journal.pgen.0020080.PubMed CentralView ArticlePubMedGoogle Scholar
- Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, et al: Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science. 2003, 302: 1960-3. 10.1126/science.1088821.View ArticlePubMedGoogle Scholar
- Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M, Wyckoff GJ, Malcom CM, Lahn BT: Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell. 2004, 119: 1027-40. 10.1016/j.cell.2004.11.040.View ArticlePubMedGoogle Scholar
- Shi P, Bakewell MA, Zhang J: Did brain-specific genes evolve faster in humans than in chimpanzees?. Trends Genet. 2006, 22: 608-13. 10.1016/j.tig.2006.09.001.View ArticlePubMedGoogle Scholar
- Keightley PD, Lercher MJ, Eyre-Walker A: Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 2005, 3: e42-10.1371/journal.pbio.0030042.PubMed CentralView ArticlePubMedGoogle Scholar
- Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA: Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet. 2007, 8: 424-36. 10.1038/nrg2026.View ArticlePubMedGoogle Scholar
- Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA: Heterotachy in mammalian promoter evolution. PLoS Genet. 2006, 2: e30-10.1371/journal.pgen.0020030.PubMed CentralView ArticlePubMedGoogle Scholar
- Britten RJ: Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci USA. 2002, 99: 13633-5. 10.1073/pnas.172510699.PubMed CentralView ArticlePubMedGoogle Scholar
- Britten RJ, Rowen L, Williams J, Cameron RA: Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA. 2003, 100: 4661-5. 10.1073/pnas.0330964100.PubMed CentralView ArticlePubMedGoogle Scholar
- Frazer KA, Chen X, Hinds DA, Pant PV, Patil N, Cox DR: Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003, 13: 341-6. 10.1101/gr.554603.PubMed CentralView ArticlePubMedGoogle Scholar
- Cooper GM, Nickerson DA, Eichler EE: Mutational and selective effects on copy-number variants in the human genome. Nat Genet. 2007, 39: S22-9. 10.1038/ng2054.View ArticlePubMedGoogle Scholar
- Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, et al: Regional patterns of gene expression in human and chimpanzee brains. Genome Res. 2004, 14: 1462-73. 10.1101/gr.2538704.PubMed CentralView ArticlePubMedGoogle Scholar
- Hahn MW, Demuth JP, Han SG: Accelerated rate of gene gain and loss in primates. Genetics. 2007, 177: 1941-9. 10.1534/genetics.107.080077.PubMed CentralView ArticlePubMedGoogle Scholar
- Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315: 848-53. 10.1126/science.1136678.PubMed CentralView ArticlePubMedGoogle Scholar
- Sebat J: Major changes in our DNA lead to major changes in our thinking. Nat Genet. 2007, 39: S3-5. 10.1038/ng2095.View ArticlePubMedGoogle Scholar
- Courseaux A, Nahon JL: Birth of two chimeric genes in the Hominidae lineage. Science. 2001, 291: 1293-7. 10.1126/science.1057284.View ArticlePubMedGoogle Scholar
- Courseaux A, Richard F, Grosgeorge J, Ortola C, Viale A, Turc-Carel C, Dutrillaux B, Gaudray P, Nahon JL: Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation. Genome Res. 2003, 13: 369-81. 10.1101/gr.490303.PubMed CentralView ArticlePubMedGoogle Scholar
- Nahon JL: Birth of 'human-specific' genes during primate evolution. Genetica. 2003, 118: 193-208. 10.1023/A:1024157714736.View ArticlePubMedGoogle Scholar
- Long M: Evolution of novel genes. Curr Opin Genet Dev. 2001, 11: 673-80. 10.1016/S0959-437X(00)00252-5.View ArticlePubMedGoogle Scholar
- Long M, Betran E, Thornton K, Wang W: The origin of new genes: glimpses from the young and old. Nat Rev Genet. 2003, 4: 865-75. 10.1038/nrg1204.View ArticlePubMedGoogle Scholar
- Lee Y, Ise T, Ha D, Saint Fleur A, Hahn Y, Liu XF, Nagata S, Lee B, Bera TK, Pastan I: Evolution and expression of chimeric POTE-actin genes in the human genome. Proc Natl Acad Sci USA. 2006, 103: 17885-90. 10.1073/pnas.0608344103.PubMed CentralView ArticlePubMedGoogle Scholar
- Burki F, Kaessmann H: Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat Genet. 2004, 36: 1061-3. 10.1038/ng1431.View ArticlePubMedGoogle Scholar
- Long M, Deutsch M, Wang W, Betran E, Brunet FG, Zhang J: Origin of new genes: evidence from experimental and computational analyses. Genetica. 2003, 118: 171-82. 10.1023/A:1024153609285.View ArticlePubMedGoogle Scholar
- Viale A, Courseaux A, Presse F, Ortola C, Breton C, Jordan D, Nahon JL: Structure and expression of the variant melanin-concentrating hormone genes: only PMCHL1 is transcribed in the developing human brain and encodes a putative protein. Mol Biol Evol. 2000, 17: 1626-40.View ArticlePubMedGoogle Scholar
- Viale A, Ortola C, Richard F, Vernier P, Presse F, Schilling S, Dutrillaux B, Nahon JL: Emergence of a brain-expressed variant melanin-concentrating hormone gene during higher primate evolution: a gene "in search of a function". Mol Biol Evol. 1998, 15: 196-214.View ArticlePubMedGoogle Scholar
- Schmidt EE: Transcriptional promiscuity in testes. Curr Biol. 1996, 6: 768-9. 10.1016/S0960-9822(02)00589-4.View ArticlePubMedGoogle Scholar
- Kleene KC, Mulligan E, Steiger D, Donohue K, Mastrangelo MA: The mouse gene encoding the testis-specific isoform of Poly(A) binding protein (Pabp2) is an expressed retroposon: intimations that gene expression in spermatogenic cells facilitates the creation of new genes. J Mol Evol. 1998, 47: 275-81. 10.1007/PL00006385.View ArticlePubMedGoogle Scholar
- Vinckenbosch N, Dupanloup I, Kaessmann H: Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA. 2006, 103: 3220-5. 10.1073/pnas.0511307103.PubMed CentralView ArticlePubMedGoogle Scholar
- Paulding CA, Ruvolo M, Haber DA: The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc Natl Acad Sci USA. 2003, 100: 2507-11. 10.1073/pnas.0437015100.PubMed CentralView ArticlePubMedGoogle Scholar
- Sorek R: The birth of new exons: mechanisms and evolutionary consequences. Rna. 2007, 13: 1603-8. 10.1261/rna.682507.PubMed CentralView ArticlePubMedGoogle Scholar
- Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R: Transcription-mediated gene fusion in the human genome. Genome Res. 2006, 16: 30-6. 10.1101/gr.4137606.PubMed CentralView ArticlePubMedGoogle Scholar
- Enard W, Paabo S: Comparative primate genomics. Annu Rev Genomics Hum Genet. 2004, 5: 351-78. 10.1146/annurev.genom.5.061903.180040.View ArticlePubMedGoogle Scholar
- Glazko GV, Nei M: Estimation of divergence times for major lineages of primate species. Mol Biol Evol. 2003, 20: 424-34. 10.1093/molbev/msg050.View ArticlePubMedGoogle Scholar
- Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D: Genetic evidence for complex speciation of humans and chimpanzees. Nature. 2006, 441: 1103-8. 10.1038/nature04789.View ArticlePubMedGoogle Scholar
- Wakeley J: Complex speciation of humans and chimpanzees. Nature. 2008, 452: E3-4. 10.1038/nature06805. discussion E4View ArticlePubMedGoogle Scholar
- Wall JD: Estimating ancestral population sizes and divergence times. Genetics. 2003, 163: 395-404.PubMed CentralPubMedGoogle Scholar
- Goodman M: The genomic record of Humankind's evolutionary roots. Am J Hum Genet. 1999, 64: 31-9. 10.1086/302218.PubMed CentralView ArticlePubMedGoogle Scholar
- Wildman DE, Uddin M, Liu G, Grossman LI, Goodman M: Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proc Natl Acad Sci USA. 2003, 100: 7181-8. 10.1073/pnas.1232172100.PubMed CentralView ArticlePubMedGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-10.View ArticlePubMedGoogle Scholar
- Samonte RV, Eichler EE: Segmental duplications and the evolution of the primate genome. Nat Rev Genet. 2002, 3: 65-72. 10.1038/nrg705.View ArticlePubMedGoogle Scholar
- Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV: Duplication, coclustering, and selection of human Alu retrotransposons. Proc Natl Acad Sci USA. 2004, 101: 1268-72. 10.1073/pnas.0308084100.PubMed CentralView ArticlePubMedGoogle Scholar
- Eichler EE, Johnson ME, Alkan C, Tuzun E, Sahinalp C, Misceo D, Archidiacono N, Rocchi M: Divergent origins and concerted expansion of two segmental duplications on chromosome 16. J Hered. 2001, 92: 462-8. 10.1093/jhered/92.6.462.View ArticlePubMedGoogle Scholar
- Johnson ME, Cheng Z, Morrison VA, Scherer S, Ventura M, Gibbs RA, Green ED, Eichler EE: Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci USA. 2006, 103: 17626-31. 10.1073/pnas.0605426103.PubMed CentralView ArticlePubMedGoogle Scholar
- She X, Liu G, Ventura M, Zhao S, Misceo D, Roberto R, Cardone MF, Rocchi M, Green ED, Archidiacano N, et al: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 2006, 16: 576-83. 10.1101/gr.4949406.PubMed CentralView ArticlePubMedGoogle Scholar
- Basu S, Schaefer TM, Ghosh M, Fuller CL, Reinhart TA: Molecular cloning and sequencing of 25 different rhesus macaque chemokine cDNAs reveals evolutionary conservation among C, CC, CXC, AND CX3C families of chemokines. Cytokine. 2002, 18: 140-8. 10.1006/cyto.2002.0875.View ArticlePubMedGoogle Scholar
- Luenser K, Ludwig A: Variability and evolution of bovine beta-defensin genes. Genes Immun. 2005, 6: 115-22. 10.1038/sj.gene.6364153.View ArticlePubMedGoogle Scholar
- Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM: The abundance of short proteins in the mammalian proteome. PLoS Genet. 2006, 2: e52-10.1371/journal.pgen.0020052.PubMed CentralView ArticlePubMedGoogle Scholar
- Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES: Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA. 2007, 104: 19428-33. 10.1073/pnas.0709013104.PubMed CentralView ArticlePubMedGoogle Scholar
- Kozak M: Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984, 12: 857-72. 10.1093/nar/12.2.857.PubMed CentralView ArticlePubMedGoogle Scholar
- Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, et al: Hidden layers of human small RNAs. BMC Genomics. 2008, 9: 157-10.1186/1471-2164-9-157.PubMed CentralView ArticlePubMedGoogle Scholar
- Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet. 2006, 15 (Spec No 1): R17-29. 10.1093/hmg/ddl046.View ArticlePubMedGoogle Scholar
- Storz G: An expanding universe of noncoding RNAs. Science. 2002, 296: 1260-3. 10.1126/science.1072249.View ArticlePubMedGoogle Scholar
- He S, Liu C, Skogerbo G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R: NONCODE v2.0: decoding the non-coding. Nucleic Acids Res. 2008, 36: D170-2. 10.1093/nar/gkm1011.PubMed CentralView ArticlePubMedGoogle Scholar
- Johnston CM, Nesterova TB, Formstone EJ, Newall AE, Duthie SM, Sheardown SA, Brockdorff N: Developmentally regulated Xist promoter switch mediates initiation of × inactivation. Cell. 1998, 94: 809-17. 10.1016/S0092-8674(00)81739-0.View ArticlePubMedGoogle Scholar
- Panning B, Dausman J, Jaenisch R: X chromosome inactivation is mediated by Xist RNA stabilization. Cell. 1997, 90: 907-16. 10.1016/S0092-8674(00)80355-4.View ArticlePubMedGoogle Scholar
- Sleutels F, Zwart R, Barlow DP: The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature. 2002, 415: 810-3.View ArticlePubMedGoogle Scholar
- Kim M, Patel B, Schroeder KE, Raza A, Dejong J: Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10. Rna. 2008, 14: 1005-11. 10.1261/rna.974608.PubMed CentralView ArticlePubMedGoogle Scholar
- Raho G, Barone V, Rossi D, Philipson L, Sorrentino V: The gas 5 gene shows four alternative splicing patterns without coding for a protein. Gene. 2000, 256: 13-7. 10.1016/S0378-1119(00)00363-2.View ArticlePubMedGoogle Scholar
- Tycowski KT, Shu MD, Steitz JA: A mammalian gene with introns instead of exons generating stable RNA products. Nature. 1996, 379: 464-6. 10.1038/379464a0.View ArticlePubMedGoogle Scholar
- Lottin S, Vercoutter-Edouart AS, Adriaenssens E, Czeszak X, Lemoine J, Roudbaraki M, Coll J, Hondermarck H, Dugimont T, Curgy JJ: Thioredoxin post-transcriptional regulation by H19 provides a new function to mRNA-like non-coding RNA. Oncogene. 2002, 21: 1625-31. 10.1038/sj.onc.1205233.View ArticlePubMedGoogle Scholar
- Szell M, Bata-Csorgo Z, Kemeny L: The enigmatic world of mRNA-like ncRNAs: their role in human evolution and in human diseases. Semin Cancer Biol. 2008, 18: 141-8. 10.1016/j.semcancer.2008.01.007.View ArticlePubMedGoogle Scholar
- Matera AG, Terns RM, Terns MP: Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007, 8: 209-20. 10.1038/nrm2124.View ArticlePubMedGoogle Scholar
- Blin N, Stafford DW: A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976, 3: 2303-8.PubMed CentralView ArticlePubMedGoogle Scholar
- Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987, 162: 156-9. 10.1016/0003-2697(87)90021-2.View ArticlePubMedGoogle Scholar
- Galtier N, Gouy M, Gautier C: SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci. 1996, 12: 543-8.PubMedGoogle Scholar
- Gascuel O: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997, 14: 685-95.View ArticlePubMedGoogle Scholar
- Perriere G, Gouy M: WWW-query: an on-line retrieval system for biological sequence banks. Biochimie. 1996, 78: 364-9. 10.1016/0300-9084(96)84768-7.View ArticlePubMedGoogle Scholar
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 (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.