Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon.

BACKGROUND: The disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a new 140bp exon from the intron 9 of human FMR1 gene. In this study, we further examined the biological functions of this new exon and its underlying signaling pathways. RESULTS: qRT-PCR results showed that this novel exon is commonly expressed in the peripheral blood of normal individuals. Comparative genomics showed that sequences paralogous to the 140 bp sequence only exist in the genomes of primates. To explore the biological functions of the new transcript, we constructed recombinant eukaryotic expression vectors and lentiviral overexpression vectors. Results showed that the spliced transcript encoded a truncated protein which was expressed mainly in the cell nucleus. Additionally, several genes, including the BEX1 gene involved in mGluR-LTP or mGluR-LTD signaling pathways were significantly influenced when the truncated FMRP was overexpressed. CONCLUSIONS: our work identified a new exon from amid intron 9 of human FMR1 gene with wide expression in normal healthy individuals, which emphasizes the notion that the AS of FMR1 gene is complex and may in a large part account for the multiple functions of FMRP.

Splicing of exon 9a in FMR1 transcripts results in a truncated FMRP with altered subcellular distribution.

FMRP is an RNA-binding protein, loss of which causes fragile X syndrome (FXS). FMRP has several isoforms resulted from alternative splicing (AS) of fragile X mental retardation 1 (FMR1) gene, but their biological functions are still poorly understood. In the analysis of alternatively spliced FMR1 transcripts in the blood cells from a patient with FXS-like phenotypes (normal CGG repeats and no mutation in coding sequence of FMR1), we identified three novel FMR1 transcripts that include a previously unidentified microexon (46 bp), terming the exon 9a. This microexon exists widely in unaffected individuals, inclusion of which introduces an in-frame termination codon. To address whether these exon 9a-containing transcripts could produce protein by evading nonsense-mediated decay (NMD), Western blot was used to analysis blood cell lysate from unaffected individuals and a 34 kDa protein that consistent in size with the molecular weight of the predicted truncated protein produced from mRNA with this microexon was found. Meanwhile, treatment of peripheral blood mononuclear cells with an inhibitor of NMD (Cycloheximide) did not result in significant increase in exon 9a-containing transcripts. Using confocal immunofluorescence, we found the truncated protein displayed both nuclear and cytoplasmic localization in HEK293T and HeLa cells due to lacking C-terminal domains including KH2, NES, and RGG, while the full-length FMRP protein mainly localized in the cytoplasm. Therefore, we hypothesize that the inclusion of this microexon to generate exon 9a-containing transcripts may regulate the normal functionality of FMRP, and the dysregulation of normal FMRP due to increased exon 9a-containing alternatively spliced transcripts in that patient may be associated with the manifestation of FXS phenotype.

[Analysis of small supernumerary marker chromosome 15q11 in four infertile males].

OBJECTIVE: To delineate the origins of small supernumerary marker chromosomes (sSMCs) identified in 4 infertile males. METHODS: The sSMCs were analyzed with combined G-banding, N-banding, multiplex ligation-dependent probe amplification (MLPA), fluorescence in situ hybridization (FISH) and single nucleotide polymorphisms array (SNP-array) techniques. RESULTS: G-banding analysis has suggested a 46,X,-Y,+mar karyotype in all of the 4 cases. N-banding revealed that all of the sSMCs have possessed two satellites located on both sides. By MLPA, 1 patient showed copy number gains for 15q11.2 region. SNP-array analysis suggested that all had duplication for 15q11.1-q11.2 region, spanning 3.06 Mb, 0.9118 Mb, 1.728 Mb and 0.287 Mb, respectively. By FISH analysis, all of the sSMCs showed two hybridization signals, indicating that they were dicentric chromosomes. CONCLUSION: In all of the four cases, the marker chromosomes have derived from chromosome 15 and were bisatellited and dicentric, which gave rise to a karyotype of 47,XY,+ish,inv dup(15)(q11)(D15Z4++). sSMC 15q11 therefore may be a major cause for male infertility.

[Delineation of three structural Y chromosome aberrations combined molecular techniques].

OBJECTIVE: To delineate the structure of Y chromosome aberrations and recombinant mechanisms for three patients. METHODS: Karyotype analysis, multiplex ligation dependent probe amplification (MLPA), fluorescence in situ hybridization (FISH), Y chromosome sequence tagged sites (STS) analysis, human whole genome-wide SNP array were used. RESULTS: The karyotypes of the three patients were 46, X, +mar. As suggested by MLPA analysis, case 1 has increased copy numbers of SRY, ZFY and UTY genes, case 2 had increased copies of SRY and ZFY genes, and deletion of UTY gene, and case 3 had decreased copies for subtelomeric regions of X/Yp and X/Yq. By STSs analysis, case 1 has retained SRY, sY84 and sY86 in the AZFa region, sY1227 in the AZFb region, whilst lost sY1228 in the AZFb region and other STSs in the AZFc region. Its breakpoint was thereby mapped between sY1227 and sY1228. Case 2 has retained SRY and sY1200 in the centromeric region, whilst has deletion of other STSs. Case 3 has retained SRY and STSs in the AZF regions. By SNP array, case 1 had duplicated Yp11.31-p11.2 and deletion of Yq11.22-q11.23 (approximately 5.18 Mb). Case 2 had duplicated Yp11.31-p11.2 and deletion of Yq11.21-q11.23 (approximately 14.644 Mb). Case 3 had single copy number deletion of p22.33 and q28 in the subtelomeric region of X/Yp and X/Yq. By FISH, cases 1 and 2 showed two signals for SRY and DYZ3 but no signal for DYZ1 on their marker chromosomes. Combining above results, the karyotypes of cases 1, 2 and 3 were determined as 46, X, idic(Y) (q11.23), 46, X, idic(Y) (q10) and 46, X, r(Y) (p11q12), respectively. CONCLUSION: Y chromosome aberrations are variable. Combined use of MLPA, STSs, FISH and SNP array is effective for revealing the breakpoints and recombinant mechanisms.

[Partial AZfc region deletions of the Y chromosome in spermatogenic dysfunction patients].

OBJECTIVE: To investigate the influence of partial deletions in the AZFc region of the Y chromosome on spermatogenesis. METHODS: We selected 9 sequence tagged sites (sY1258, sY1291, sY254, sY255, sY1201, sY1206, sY1161, sY1197 and sY1191) in the AZFc region of the Y chromosome, with ZFX/ZFY and SRY (sY14) as the interior control. We amplified by multiplex PCR the DNA of 160 patients with azoospermia or severe oligozoospermia that showed no microdeletion of the Y chromosome (the case group) and another 76 males with normal fertility (the control group). For the individuals suspected of DAZ gene deletion, we detected the single nucleotide polymorphism sites (SNPs) in the four copies of the DAZ gene by single nucleotide variation (SNV) analysis to determine the types of DAZ copy deletion. RESULTS: In the case group, there were 10 cases of gr/gr (sY1291) deletion (6.3%), 14 b2/b3 (sY1191) deletion (8.8%), 1 sY1291,sY1197 deletion (0.6%), 1 b1/b2 deletion (0.6%) and 1 b1/b3 deletion (0.6%), while in the control group, there were 4 cases of gr/gr deletion (5.3%) and 4 b2/b3 deletion (5.3%). SNV analysis showed DAZ1/DAZ2 deletion in all those with gr/gr and those with b1/b3 deletion, DAZ3/DAZ4 deletion in those with b2/b3 deletion, and DAZ-SNV sY587 deletion in 1 case of sY1291, sY1197 deletion, but no DAZ deletion was found in 1 case of b1/b2 deletion. CONCLUSION: B2/b3 (sY1191) and gr/gr (sY1291) deletions are genomic polymorphisms and quite common in the normal Chinese population; while b1/b2, b1/b3, and sY1291, sY1197 deletions may be high risk factors of dyszoospermia.

[Mutation analysis of SMN gene in a patient and his family with spinal muscular atrophy].

OBJECTIVE: To perform mutation analysis and describe the genotype of the SMN gene in a patient with spinal muscular atrophy (SMA) and his family. METHODS: Deletion analysis of the SMN1 exon 7 by conventional PCR-restriction fragment length polymorphism (RFLP) and allele-specific PCR, and gene dosage of SMN1 and SMN2 by multiplex ligation-dependent probe amplification (MLPA) were performed for the patient and his parents; reverse transcriptase (RT)-PCR and sequencing were performed for the patient. To determine whether the SMN variant was exclusive to transcripts derived from SMN1, the RT-PCR product of the patient was subcloned and multiple clones were sequenced directly; PCR of SMN exon 5 from the genomic DNA of the parents and direct sequencing were performed to confirm the mutation. RESULTS: In SMN1 exon 7 deletion analysis, no homozygous deletion of the SMN1 was observed in the family; the gene dosage analysis by MLPA showed that the patient had 1 copy of SMN1 and 1 copy of SMN2 his father had 2 copies of SMN1 and 2 copies of SMN2, and his mother had 1 copy of SMN1 and no SMN2. A previously unreported missense mutation of S230L was identified from the patient and this mutation was also found in his father. CONCLUSION: A novel missense mutation of S230L was identified in the SMA family and the genotype of the family members were investigated.

[Molecular diagnosis of a Chinese pedigree with osteogenesis imperfecta type I].

OBJECTIVE: To perform molecular diagnosis for a Chinese pedigree with osteogenesis imperfecta type I. METHODS: Thirty pairs of primers were designed to amplify all the 52 exons, exon boundaries and promoter region of the COL1A1 gene from genomic DNA of peripheral blood cells of the family members. The PCR products were purified and directly sequenced. To check the mutation in normal controls, the genomic DNA from peripheral blood cells of the index patient, his mother and 60 normal controls were analyzed by amplification refractory mutation system. RESULTS: A missense mutation of GAT>CAT was identified at codon 1441 of the COL1A1 gene from the family, which resulted in the replacement of aspartic acid by histidine (D1441H). This mutation was not found in a group of 60 normal controls. CONCLUSION: The method for molecular diagnosis of osteogenesis imperfecta was established and a novel COL1A1 gene mutation, D1441H, was identified in the Chinese pedigree with osteogenesis imperfecta type I.