A Silent Mutation With Unknown Mechanism Biology Essay
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Published: Mon, 5 Dec 2016
A silent mutation with unknown mechanism of C1311T in exon 11 combined with IVS11 T93C (G6PD 1311/93) has been reported in G6PD deficient individuals in many populations. In our previous study, G6PD 1311/93 was identified as the common G6PD variant in one of the Malaysian aboriginal groups. Here, we report the screening for this variant via PCR-RFLP method and then direct sequencing of the entire 3´UTR of the G6PD gene in 175 aboriginal volunteers and 45 non-aboriginals. In the aboriginal group, 72 individuals (41%) carried the G6PD 1311/93 while 6 individuals (13%) were identified in the non-aboriginal set. Three novel SNPs, ss218178027 (+272 G/A), ss218178028 (+304 T/C) and ss218178024 (+357 A/G) were discovered in 3´UTR. SNP ss218178024, which is located inside an AG-rich region, has shown a significant association with G6PD 1311/93 as it was observed solely in individuals with G6PD 1311/93. Computational analyses indicated that three miRNAs have potential to bind to the regions encompassing ss218178024. Whilst transitions of A to G dose not destroy these miRNA target sites, it extensively alters the mRNA secondary structure and creates a putative hsa-miR-877* binding site. Notably, ss218178027 and ss218178028 do not change mRNA secondary structure. It could be speculated that ss218178024 have a potential functional effect on the down-regulation of mRNA and consequently G6PD deficiency either by affecting mRNA secondary structure or mirRNA regulation process. This is the first report of clinical association of a SNP in 3´UTR of G6PD mRNA.
Genetic variations in the G6PD gene are responsible for G6PD deficiency in humans. More than 140 ethnic reliant nucleotide variations in the G6PD gene have been reported (Nkhoma et al 2009). Most of these variants are single missense mutations, with the rest being either double or triple missense mutations or small in frame deletions (Cappellini, G Fiorelli 2008). All these mutations alter the protein sequence of the G6PD enzyme by either amino acid substitution except for a silent mutation of C1311T in exon 11 combined with IVS11T93C (designated here as G6PD 1311/93). This genotype has been reported in G6PD deficient individuals in different ethnic populations with different frequency (Vulliamy et al. 1991; 2000; Jiang et al. 2006; Daoud et al. 2008; Jalloh et al. 2008; Wang et al. 2008; Moiz et al. 2009 ). This combination is a special G6PD variant where the carrier is deficient without any changes to the protein sequence of the G6PD enzyme. From previous studies, association of these two has been shown as significant in reducing G6PD enzyme activity in some individuals and hence has clinical implications (Yu et al 2004; Wang et al 2008; Jiang et al 2006). It is notable that some of the individuals with G6PD 1311/93 presented with normal G6PD activity (Jiang et al 2006). Bearing in mind, it is reasonable to postulate that other change(s) in the G6PD gene with potential linkage disequilibrium by this combination is responsible for the enzyme deficiency.
Importance of 3´UTR of human genes in the post-transcriptional regulation has been supported by finding of functional SNPs in the 3´UTR of a number of genes (ref). In the other word, genetic variations in the 3´UTR of some genes are associated with variety of human disease ( ref ). Cis-acting elements in the 3´UTR of human genes are key players in controlling of mRNA stability, localization and level of translation (ref). Conversely, according to a recent systematic search, 106 conserved motifs located in the 3´UTR of human gene are associated with post-transcriptional regulation which half of them likely are miRNA binding sites (Xie et al 2005). MicroRNAs (miRNAs) are a class of genes encoding short RNAs, which are known to inhibit gene expression by binding to the 3´UTR of the target transcript. Notably, miRNAs are predicted to regulate about 30% of all human genes by targeting sequences in their 3´UTR (ref) . Noteworthy, several SNPs inside the miRNA gene and the miRNA binding sites have been identified recently (ref). The associations of these SNPs with some disease like Parkinson and some kind of cancer have been documented (Sethupathy 2008; Shen 2008).
Given that, in the present study, we sought to determine if any SNP in the 3´UTR of G6PD gene in G6PD 1311/93 is involve in the regulation of mRNA processing.
Subjects and Methods
This study was approved by the University Kebangsaan Malaysia (UKM) hospital’s ethics committee. All subjects gave their written informed consent.
In our previous study, we attempted to identify the molecular basis of G6PD deficiency in 25 deficient individuals from one of the Malaysia aborigine group, namely, the Negrito (data in press). Our earlier results showed that G6PD 1311/93 is the commonest G6PD variant in Negrito. No other mutations were detected in the remaining exons or adjacent regions of the G6PD gene for subjects with G6PD 1311/93. In the present study, blood was collected from 175 consenting volunteers from four sub-ethnic groups of Negrito namely Kintak, Lanoh, Jahai, and Bateq. A series of 45 non-aboriginal volunteers were selected as the reference group. Genomic DNA was extracted by using the Salting Out method (ref). The oligonucleotides used as primers were either designed by online primer-BLAST program or obtained from published data (Kurdi-Haidar et al. 1990). The G6PD gene sequence was obtained from NCBI (reference sequence NC_000023.9). Sequence of each exon was obtained from ENSEMBL (Transcript ENST00000393562). Then two regions of the G6PD gene (region ab and cd in figure 1) were amplified using the PCR technique to detect variation in nt 1311 in exon 11and nt 93 in intron 11. A proportion of the PCR product from regions ab (207 bp) and cd (317 bp) were digested with the appropriate restriction enzyme according to the manufacturer’s instructions (New England Biolabs) and then run on 3% agarose gels, stained with ethidium bromide, and photographed under UV light. Region ab was digested with BclI and region cd was digested with NlaIII. For all samples, PCR direct sequencing was performed for 3´ UTR of G6PD gene by using 2 sets primer of ef (320 bp) and gh (397 bp).
Figure 1: Schematic map of part of G6PD gene (exon 10 to exon 13). The arrows point to the positions of each primer site. Oligonucleotides a: 5′ AAGACGTCCAGGATGAGGTGATC 3′ and b: 5′ TGTTCTTCAACCCCG AGGAGT 3′ are the primers used to detect 1311 C>T transition. Oligonucleotides c: 5′ TGGCATCAGCAAGACACTCTCTC 3′ and d: 5′ CCCTTTCCTCACCTG CCATAAA3′ are the primers used to detect IVS11 nt93 T>C. Oligonucleotides e: 5′ GAGCCCTGG GCACCCACCTC 3′ and f : 5′ TCTGTTGGGCTGGAGTGA 3′ were amplified part of 3’UTR and oligonucleotides g (5’TCACTCCAGCCCAACAGA3′) and h (5′ GGTCCTCAG GGAAGCAAA 3′) were amplified the rest of 3’UTR of G6PD gene for sequencing.
We used two computational tools for each section to confirm our results. F-SNP (http://compbio.cs. queensu.ca/F-SNP/) (Lee & Shatkay 2008) and FASTSNP (http://fastsnp.ibms.sinica.edu.tw) (Yuan et al. 2006) was used to find putative functional SNP in 3´UTR of G6PD gene. The RegRNA program (http://regrna.mbc.nctu.edu.tw/) (Huang et al. 2006) and MicroInspector (http://bioinfo. uni-plovdiv.bg/microinspector/) (Rusinov et al. 2005) was utilized to identify the miRNAs binding sites inside 3´UTR of G6PD gene. Secondary structures of the full-length of G6PD mRNA and as well, 3´UTR was predicted using GeneBee (http://www.genebee.msu.su/genebee.html) and mFold (http://mobyle.pasteur.fr/cgi-bin/portal.py) (Zuker et al. 1999). The program RNAhybrid (http://bibiserv. techfak.uni-bielefeld.de/cgi-bin/rnafold_submit) (Rehmsmeier et al. 2004) was implemented as a tool for finding the minimum free energy hybridisation of mRNA and miRNA.
DNA from 175 aboriginals and 45 non-aboriginals were screened for presence of G6PD 1311/93. In overall 72 aboriginal individuals (41%) and 6 non-aboriginal subjects (13%) carried this combination (table 1). Through direct sequencing of DNA fragments, three novel SNPs, of ss218178027 (+272 A/G), ss218178028 (+304 T/C) and ss218178024 (+357 A/G) was found (Figure 2). SNP ss218178027 was observed in 6 subjects in aboriginal group with G6PD 1311/93 (table 1) inside of an AG-rich region (AGAAGGAAGGAGGAGG). SNP ss218178028 was observed in 4 aboriginal individuals which 3 of them carried normal alleles in 1311 and 93. None of our non-aboriginal samples carried ss218178027 or ss218178028. SNP ss218178024 also surrounds by other 30 bp AG-rich sequence (gggagggagggacaag ggggaggaaagggg) and it was observed in all those G6PD deficient individuals who carried G6PD 1311/93. In the absence of G6PD 1311/93, ss218178024 was not found. Females who were heterozygote for the G6PD 1311/93 were also heterozygote for ss218178024.
Figure 2. Partial nucleotide sequence of normal, heterozygote and homozygote females respectively for forward strand of ss218178024 (a1, a2, a3), reverse strand of ss218178027 (b1, b2, b3) and reverse strand of ss218178028 (c1, c2,c3). Arrows show position of each SNP.
Individuals with G6PD 1311/93
individuals normal for G6PD 1311/93
Search for reported SNPs inside of 3´UTR of G6PD gene
By using F-SNP and FASTSNP programs, we found six SNPs have been reported inside of 3´UTR of G6PD gene including SNP ref ID: rs1050831, rs1050774, rs1050773, rs1050830, rs1063529, rs1050757. The last one is actually same with ss218178024. All of these known SNPs were
discovered via cDNA sequencing and to date no clinical associations have been reported for them.
Prediction of putative miRNA binding sites and mRNA secondary structure
The wild sequence of 3’UTR of G6PD was submitted to regRNA and MicroInspector programs to detect putative miRNAs target sites. The mutant variant of ss218178024, ss218178027 and ss218178028 was also submitted to evaluate effect of each SNP on creating or destroying the miRNAs target sites. However, in silico analysis indicated that three miRNAs have potential to bind to the regions encompassing ss218178024A. Of note, SNP ss218178024 is located inside seed region of these miRNAs which are hsa-mir-204, hsa-mir-211 and has-mir-1249 (figure 3). Moreover, further computational analyses reveal that transition of A to G in SNP ss218178024 creates additional miRNA target site for has- miR-877* which also is located inside seed region. Neither ss218178027 nor ss218178028 is targeted by any miRNA. The RNAhybrid program (Rehmsmeier et al. 2004) was implemented as a tool for finding the minimum free energy (MFE) hybridisation of mRNA and each miRNA.
Figure 3 The predicted binding site for hsa-mir-211(A), hsa-miR-1249 (B), hsa- mir-204 (C) and hsa-miR-877* (D) at 3´UTR of G6PD gene. Perfect Watson-Crick or wobble base pairings between the 5´ end of the miRNA and the 3â€² UTR target sites was observed. The minimum free energy (kcal/mol) of hybridization is shown in parentheses. Position of ss218178024G is indicated by arrows.
Using the program mFold and Genebee, we determined the potential effect of the SNP sequence alterations on RNA folding. As shown in figure 4, ss218178024G is predicted to alter the secondary structure of G6PD mRNA. Also, the free energy of full length mRNA and as well 3’UTR predicted to be affected by this substitution. The lower free energy in wild type indicates that mRNA might be more stable in wild type compare with the mutant. In the other word, it is suggesting that altered mRNA is capable to faster degradation. We also submitted the substituted nucleotide sequences of ss218178027A and ss218178028C to the GeenBee and mFold server. No change in the secondary structure of neither full length mRNA nor 3’UTR was observed. It might be assuming that ss218178027A and ss218178028C do not probably modify mRNA processing.
Consequently, secondary structure of 3´UTR of G6PD mRNA has been also checked for the accessibility of miRNA binding site. A stable base-paired duplex observe in the allele A (figure 4a2) and improper binding for allele G (figure 4b2) (arrows show position of changes). Then, it can be assume that miRNAs can be bind to the target site in mRNA due to the accessible site in the substitution of ss218178024G.
Genotype Change in secondary structure Change in secondary
of full length of mRNA structure of 3´UTR
1311T No –
ss218178024G Yes Yes
1311T+ ss218178024G Yes –
ss218178027A No No
1311T + ss218178027A No –
ss218178028T No No
1311T + ss218178028T No –
Figure 4 Predicted secondary structures of full length wild-type mRNA (A1) and 3´UTR (A2) compare with predicted secondary structures of full length mRNA relating to allele 1311T plus ss218178024G (B1) and 3’UTR relating to ss218178024G (B2). The free energy (kcal/mol) of the
full-length mRNA and 3’UTR is shown in parentheses.
A recent systematic study of G6PD deficiency indicated a global prevalence of 4.9% with varying frequencies among different ethnicities (Nkhoma et al. 2009). Although comprehensive studies have identified the molecular basis of G6PD deficiency worldwide, some pertinent questions remain to be addressed. For instance, several studies have reported deficient samples with unknown mutation(s) (Ara´mbula et al. 2000; Nuchprayoon et al. 2008; Barisic 2005; Laosombat 2005; Pietropertosa 2001; Jiang et al. 2006). Additionally, the silent mutation genotype of C1311T in exon 11 combined with IVS11T93C (G6PD 1311/93) does not explain the phenotype of G6PD deficiency in their carriers. Since there are appears to be no clear linkages to known sequence mutations with these examples, factors extrinsic to the G6PD gene sequence information need to be investigated. These factors may include the roles played by mRNA processing, the untranslated regions (UTRs) and regulatory function by miRNAs. To the best of our knowledge the importance of mRNA processing and regulation by miRNAs has not been extensively studies with regards to G6PD deficiency. The roles of the UTRs of the G6PD gene have also not received much attention. Our literature search revealed two reports which had evaluated the role of the 3´UTR of G6PD gene in their respective deficient population and these reports did not reveal any SNP in the 3´UTR for G6PD deficient individuals (Nguyen Thi Hue 2009; Karadsheh 2005). Our present study attempts to shed light on the possible role(s) of the 3’UTR of mRNA in G6PD deficiency, especially in the case of G6PD 1311/93.
The roles in disease phenotypes played by sequence polymorphisms of the 3´UTR have been reported (Lambert et al. 2003; Goto et al. 2001; Yang et al. 2007). Here, we present the possibility that the SNP ss218178024 which we have identified in an AG-rich region of the G6PD 3’UTR may participate in mRNA processing and can therefore be correlated with G6PD deficiency. There is, however, accumulating evidence on importance of some elements in the 3’UTR like AU-rich, C-rich, CU-rich and AG-rich elements relating to mRNA stability by affecting mRNA secondary structure (SS). For instance, functional SNPs were found to occur within AG-rich elements in some genes like Factor VII (Peyvandi et al. 2005), CYP2A6 gene (Wang et al. 2006), PTPN1 (Di Paola et al. 2002) and NPR1 (Knowles et al. 2003). Therefore, to gain further insights into the role of ss218178024 in G6PD deficiency, we have analyzed the SS of both full length mRNA and 3’UTR. Significant alteration was predicted in the SS of full length mRNA when we submitted the combination of 1311T and ss218178024G. Whilst in the SS of 3’UTR, we observed a possible standard Watson-Crick paired duplex in allele A whereas allele G has a reshuffling of the base pairings resulting in a differing SS prediction for the RNA sequence. The role of structure on RNA function is akin to that of protein. Interestingly, SS of the either full length of mRNA or 3’UTR including two substitutions of 1311T and ss218178027A or 1311T and ss218178028C was same with the SS of wild mRNA. This data is good in agree with Chen et al. (2006) which reported that non-functional SNPs in a gene usually have same secondary structure, but the functional SNPs usually change the mRNA secondary structure. Consequently, the free energy is affected by base substitution at ss218178024. In thermo stability point of view, the lower free energy (- 661.6 kcal/mol) in the SS of wild mRNA might be result in a more stable mRNA than mRNA with 1311T and ss218178024G. On the other view, SS contributes to interaction of regulatory elements with their target sequence in mRNA. In general, when target sequence is part of a stable base-paired with the other sequence of mRNA, the capacity of regulatory elements like miRNA to get involved in translational regulation could be diminished. Similarly, Hew et al. (2000) have been reported that an AG-rich region in elastin mRNA in chicken may affect mRNA stability and they proposed that alteration in SS in this region can affect the accessibility of endogenous RNse to the mRNA. Therefore, we postulated that miRNA binding site likely is not accessible in the wild mRNA due to its SS. When ss218178024G result in different mRNA SS the miRNA can access the target site as perfect complimentary of seed region is a key to the miRNA regulation. Nevertheless, recent evidence has discovered the significant miRNA expression in erythrocytes which dramatically altered in Sickle cell Disease (ref). Thus, our hypothesis in miRNA regulation of G6PD mRNA is reasonable.
While, SS is able to modify half life of mRNA, it is also capable to influence interaction of specific sequence of mRNA with regulatory proteins or miRNAs.
Site accessibility is thought to affect the activity of a miRNA binding site. If the secondary structure is such that a potential miRNA binding site is part of a stable base-paired duplex, these bonds will need to be broken before miRNA::mRNA interaction can take place, effectively decreasing the fraction of mRNA molecules of a particular gene which is regulated by a miRNA in question. This could be one of the reasons some of the computational-predicted binding sites are inactive.
Here, we demonstrate that a A357G mutation may potentially change the 3´UTR secondary structure and create a binding site for hsa-miR-877* affects G6PD expression by either inhibiting mRNA translation or inducing mRNA degradation (Can you explain this bit to me again when we meet).
However, we gave evidence for the relevance of the SNP rs3 in G6PD deficiency in G6PD 1311/93 and possible explanation is linkage disequilibrium between this SNP with combination of 1311/93 inside of G6PD gene that might be affect the mRNA translation or stability through miRNA function.
In conclusion, to the best of our knowledge, this study reports for the first time an association of a 3′ UTR variant of G6PD in a large populations of G6PD 13111/93. However, functional studies are necessary to test this hypothesis.
MicroInspector (http://www.imbb.forth.gr/microinspector) (Rusinov et al. 2005)
W696-W700 Nucleic Acids Research, 2005, Vol. 33, Web Server issue
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence
Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov and Martin Tabler
Typically, SNPs occurring in functional
genomic regions such as protein coding or regulatory
regions are more likely to cause functional distortion and,
as such, more likely to underlie disease-causing variations.
Current bioinformatics tools examine the functional
effects of SNPs only with respect to a single biological
function. Therefore, much time and effort is required from
researchers to separately use multiple tools and interpret
the (often conflicting) predictions. (F-SNP Lee at al)
The variant ESR1_rs2747648 affects the miRNA-binding site of
miR-453, miR-181(b/d) and miR-219. Due to in silico analysis using
miRanda (http://www.microrna.org/microrna/home.do), the variant
ESR1_rs2747648 does not significantly effect the binding capacity
of miR-219 and miR-181(b/d). However, the binding capacity of miR-
453 is stronger when the C variant allele is present, enabling to bind
the complementary G nucleotide of the miR-453 seed. In contrast, the
T allele attenuates the binding of miR-453, which we hypothesize to
lead to a reduced miRNA-mediated ESR1-repression, in consequence
higher ESR1 protein levels and an increased breast cancer risk. Therefore,
the breast cancer protective effect observed for the C allele is
biologically reasonable. However, functional studies are necessary to
test this hypothesis. Due to the fact that endogenous estrogen levels
are high premenopausal and drop down post-menopausal, it is plausible
that the risk effect of this variant can only be detected in
RNA secondary structure prediction was carried out
using the Vienna RNA Package 1.7.2. on the web
interface for online RNA folding on the Vienna RNA
WebServers.42 The target mRNA prediction was carried
out using ‘The microRNA.org’ resource
This is likely because miRNA-mRNA binding
is mediated by the RISC complex, and upstream and downstream
regions of miRNA binding site may interact with RISC, which
mediates miRNA-mRNA binding (26). A polymorphism in the
829C site (SNP-829C3T) is located near the miRNA binding site. 2007 Mishra mirna
SNP rs12720208 is located 166 bp downstream of the terminating
codon of FGF20 and lies within a predicted binding
site for microRNA (miRNA) miR-433.
(A) The predicted binding site for miR-433
at 30 UTR of FGF20 gene. At rs12720208,
allele C base paired with G in Watson-Crick
mode (as shown with a solid line), whereas
allele T wobble base paired with G (as shown
with a dashed line).
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Although the mechanism
by which interaction of proteins with the G3A sequence might
affect message stability remains a matter of speculation, the
fact that this sequence is located within a large region of stable
secondary structure in the 39-UTR of the elastin mRNA (4)
suggests the possibility that RNA/protein interactions at this
site may alter the stability of this secondary structure, perhaps
affecting the accessibility of endogenous RNases to the mRNA.
However, detailed understanding of the mechanism of this
process awaits further characterization of the nature of binding
protein and the consequences of its interaction with the G3A
motif in elastin mRNA.
GA rich Hew
From a physical point of view, we expect that the
interaction of a miRNA with its target will depend on the state of the target
region prior to interaction. In particular, if the target sequence is already bound
(by Watson-Crick base-pairing) to another section of the mRNA chain, this will
e_ectively pose a barrier to the base-pairing with the miRNA, and the capacity of
such target sequences to mediate translational repression could be diminished. If
we were able to predict the accessibility of a potential miRNA binding site, this
might improve our target predictions.
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It would be anticipated that increased DHFR reduces MTX
cytotoxicity in normal cells while conferring resistance in target
A comparison of the human and mouse DHFR 39-UTR sequences
revealed that only 100 nucleotides downstream from the
terminator codon were conserved between the two species (18).
studies have focused on the effects of coding region variants
on P-gp expression and function, whereas few noncoding
region variants have been investigated.
Mechanisms that alter mRNA levels can change mRNA expression
and potentially G6PD activity. Recent evidence has demonstrated
that the 3’UTR of mRNA is an important regulatory site controlling
interactions with mRNA degradation machinery (Hollams et al., 2002;
Tourriere et al., 2002; Mangus et al., 2003; Wilkie et al., 2003).
3’UTR RNA-binding proteins that recognize specific mRNA sequence
elements and secondary structure dictate the fate of mRNA
transcripts. Polymorphisms in the 3’UTR of G6PD could disrupt
RNA-protein interactions, resulting in altered mRNA stability. The stability of mRNA may be altered by 3’UTR polymorphisms if recognition of specific mRNA sequence and secondary structure by regulatory proteins is disrupted (Shen et al., 1999; Hollams et al.,
2002; Tourriere et al., 2002). A polymorphism in the 3’UTR of
human tumor necrosis factor-_ changes binding affinity for a multiprotein
complex that contains the HuR regulatory protein (Di Marco
et al., 2001). HuR binds AG-rich elements in the 3’UTR of certain
genes (Peng et al., 1998) and has been shown to stabilize mRNA
containing tumor necrosis factor-_ 3_-UTR sequence motifs (Dean et
al., 2001). There is one report that the 3435C_T synonymous variant
decreases mRNA stability (Wang et al., 2005), but to our knowledge
no pharmacogenetic research of this type has been conducted for
ABCB1 3_-UTR variants. Thus, our mRNA half-life data represent
novel findings as to the effects the _89A_T, _146G_A, and
_193A_G polymorphisms have on ABCB1 mRNA stability and
demonstrate the utility of using stable cell lines made with Flp-In
technology for these measurements. Similarly
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