A synonymous change, p.Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett syndrome patient

Orphanet Journal of Rare Diseases

John B Vincent⁴  Mary J Willis²  Kirti Mittal¹  Taimoor I Sheikh³ 

[1] Molecular Neuropsychiatry & Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction & Mental Health, Toronto, Canada;Clinical Genetics, Naval Medical Center, San Diego, USA;Institute of Medical Science, University of Toronto, Toronto, Canada;Department of Psychiatry, University of Toronto, Toronto, Canada

关键词: Frame-shift mutation;    Silent mutation;    Rett syndrome;    MECP2, exon 1;    Synonymous mutation;    Cryptic splice site;   

Others  :  863645
DOI  :  10.1186/1750-1172-8-108

 received in 2013-04-30, accepted in 2013-07-12,  发布年份 2013

【 摘 要 】

Background

Mutations in MECP2 are the main cause of Rett Syndrome. To date, no pathogenic synonymous MECP2 mutation has yet been identified. Here, we investigated a de novo synonymous variant c.48C>T (p.Gly16Gly) identified in a girl presenting with a typical RTT phenotype.

Methods

In silico analyses to predict the effects of sequence variation on mRNA splicing were employed, followed by sequencing and quantification of lymphocyte mRNAs from the subject for splice variants MECP2_E1 and MECP2_E2.

Results

Analysis of mRNA confirmed predictions that this synonymous mutation activates a splice-donor site at an early position in exon 1, leading to a deletion (r.[=, 48_63del]), codon frameshift and premature stop codon (p.Glu17Lysfs*16) for MECP2_E1. For MECP2_E2, the same premature splice site is used, but as this is located in the 5′untranslated region, no effect on the amino acid sequence is predicted. Quantitative analysis that specifically measured this cryptic splice variant also revealed a significant decrease in the quantity of the correct MECP2_E1 transcript, which indicates that this is the etiologically significant mutation in this patient.

Conclusion

These findings suggest that synonymous variants of MECP2 as well as other known disease genes—and de novo variants in particular— should be re-evaluated for potential effects on splicing.

【 授权许可】

   
2013 Sheikh et al.; licensee BioMed Central Ltd.

【 图 表 】

【 参考文献 】

• [1]Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A: Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 1992, 69(6):905-914.
• [2]Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY: Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nature Genet 1999, 23(2):185-188.
• [3]Nan X, Meehan RR, Bird A: Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 1993, 21(21):4886-4892.
• [4]Nan X, Campoy FJ, Bird A: MeCP2 Is a Transcriptional Repressor with Abundant Binding Sites in Genomic Chromatin. Cell 1997, 88(4):471-481.
• [5]Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A: Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393(6683):386-389.
• [6]Nikitina T, Ghosh RP, Horowitz-Scherer RA, Hansen JC, Grigoryev SA, Woodcock CL: MeCP2-chromatin interactions include the formation of chromatosome-like structures and are altered in mutations causing Rett syndrome. J Biol Chem 2007, 282(38):28237-28245.
• [7]Ghosh RP, Horowitz-Scherer RA, Nikitina T, Shlyakhtenko LS, Woodcock CL: MeCP2 Binds Cooperatively to Its Substrate and Competes with Histone H1 for Chromatin Binding Sites. Mol Cell Biol 2010, 30(19):4656-4670.
• [8]Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K: Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2–nucleosome complexes. Nucleic Acids Res 2011, 39(10):4122-4135.
• [9]Mnatzakanian GN, Lohi H, Munteanu I, Alfred SE, Yamada T, MacLeod PJ, Jones JR, Scherer SW, Schanen NC, Friez MJ, Vincent JB, Minassian BA: A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome. Nat Genet 2004, 36:339-341.
• [10]Kriaucionis S, Bird A: The major form of MeCP2 has a novel N terminus generated by alternative splicing. Nucleic Acids Res 2004, 32(5):1818-1823.
• [11]Harvey C, Menon SD, Stachowiak B, Noor A, Proctor A, Mensah AK, Mnatzakanian GN, Alfred SE, Guo R, Scherer SW, Kennedy JL, Roberts W, Srivastava AK, Minassian BA, Vincent JB: Sequence Variants Within Exon 1 of MECP2 Occur In Females With Mental Retardation. Am J Med Genet Part B 2007, 144:355-360.
• [12]Calfa G, Percy AK, Pozzo-Miller L: Experimental models of Rett syndrome based on Mecp2 dysfunction. Exp Biol Med 2011, 236(1):3-19.
• [13]Saunders CJ, Minassian BE, Chow EW, Zhao W, Vincent JB: Novel exon 1 mutations in MECP2 implicate isoform MeCP2_e1 in classical Rett syndrome. Am J Med Genet A 2009, 149A:1019-1023.
• [14]Fichou Y, Nectoux J, Bahi-Buisson N, Rosas-Vargas H, Girard B, Chelly J, Bienvenu T: The first missense mutation causing Rett syndrome specifically affecting the MeCP2_e1 isoform. Neurogenet 2009, 10(2):127-133.
• [15]Itoh M, Tahimic CG, Ide S, Otsuki A, Sasaoka T, Noguchi S, Oshimura M, Goto Y, Kurimasa A: Methyl CpG-binding protein isoform MeCP2_e2 is dispensable for Rett syndrome phenotypes but essential for embryo viability and placenta development. J Biol Chem 2012, 287(17):13859-13867.
• [16]Gianakopoulos PJ, Zhang Y, Pencea N, Orlic-Milacic M, Mittal K, Windpassinger C, White SJ, Kroisel PM, Chow EW, Saunders CJ, Minassian BA, Vincent JB: Mutations in MECP2 exon 1 in classical Rett patients disrupt MECP2_e1 transcription, but not transcription of MECP2_e2. Am J Med Genet B Neuropsychiatr Genet 2012, 159B(2):210-216.
• [17]Sheikh TI, Qadri I: Expression of EBV Encoded viral RNA 1, 2 and anti-inflammatory Cytokine (interleukin-10) in FFPE lymphoma specimens: a preliminary study for diagnostic implication in Pakistan. Diag Pathol 2011, 6:1-8. BioMed Central Full Text
• [18]Livak KJ, Schmittgen TD: Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-ΔΔCT Method. Methods 2001, 25(4):402-408.
• [19]Neul JL, Kaufmann WE, Glaze DG, Christodoulou J, Clarke AJ, Bahi-Buisson N, Leonard H, Bailey ME, Schanen NC, Zappella M, Renieri A, Huppke P: Percy AK; RettSearch Consortium. Rett syndrome: revised diagnostic criteria and nomenclature. Ann Neurol 2010, 68(6):944-950.
• [20]Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM: A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 2007, 315(5811):525-528.
• [21]Edwards NC, Hing ZA, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CE SG, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Przytycka TM, Sauna ZE, Salari R, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C: Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches. PLoS One 2012, 7(6):e38864.
• [22]Cartegni L, Chew SL, Krainer AR: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002, 3:285-298.
• [23]Squillaroa T, Alessioc N, Cipollaroa M, Melone MA, Hayek G, Renieri A, Giordano A, Galderisi U: Reduced expression of MECP2 affects cell commitment and maintenance in neurons by triggering senescence: new perspective for Rett syndrome. Mol Biol Cell 2012, 23(8):1435-1445.
• [24]Reese MG, Eeckman FH, Kulp D, Haussler D: Improved Splice Site Detection in Genie. J Comp Biol 1997, 4(3):311-323.
• [25]Desmet FO, Hamroun D, Lalande M, Collod-Beroud G, Claustres M, Beroud C: Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acid Research 2009, 37:1-14.
• [26]Dogan RI, Getoor LM, Wilbur WJ, Mount SM: SplicePort—An interactive splice-site analysis tool. Nucleic Acids Research 2007, 35:W285-W291.
• [27]Yeo G, Burge CB: Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004, 11(2–3):377-394.