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In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.
Subject(s)
Alleles , Binding Sites , Chromatin , Epigenomics , Gene Expression , Gene Frequency , Histone Code , Introns , Polymorphism, Single Nucleotide , Transcription FactorsABSTRACT
[Objective]To study the rare alleles frequencies and sequences of Expressmarker 22 kit in Guangdong Han Population.[Methods]3495 Samples from unrelated individuals in Guangdong Han Population were screened by using AGCU Expressmarker 22 kit(EX22)and ABI 3100 Genetic Analyzer. Then analyzed the frequencies of the off-ladder(OL)alleles and sequenced the rare alleles obtained based on comparison with the STRBase database and litera-ture.[Results]33 off-ladder alleles with 25 rare alleles were found in 10 STR loci,and allele frequencies ranged from 0.0003~0.0046. Sequencing of the11unreported rare OL alleles showed that most of them have incomplete repeats.[Conclusion]Off-ladder alleles especially the rare alleles are helpful to improve the power of discrimination and the power of exclusion and to provide samples which will be added its allele into ladders These OL-alleles will supplement forensic DNA database.
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Objective@#To explore the mutations of vitamin D receptor (VDR) gene in patients with multiple myeloma (MM).@*Methods@#Polymerase chain reaction (PCR) and direct DNA sequencing were used to detect the mutations of VDR gene(loci Fok Ⅰ, Bsm Ⅰ, Apa Ⅰ, Taq Ⅰ) in forty MM cases and 84 healthy control subjects.@*Results@#A synonymous mutation (ATC→ATA , both encode isoleucine) at cDNA codon1421 of VDR gene was found in one MM patients, which correlated to a better therapeutic response. Rare Bsm Ⅰ AA genotype and Taq Ⅰ CC genotype were detected in a MM patient, which might be related to the relapsing and refracfory disease. Meanwhile, a rare allele(rs201747972, global MAF: A=0.0005/1), was found in another MM patient, which might be related to MM cell lines of two origins. rs11574113 G>C, rs2229829 C>A and rs201747972 C>T polymorphic loci(the same as Fok Ⅰ, Bsm Ⅰ, Apa Ⅰ and Taq Ⅰ) were found in a MM patient, which were associated with nonsense-mediated mRNA decay(NMD), contributing to the onset of MM.@*Conclusions@#A new synonymous mutation, rare genotype, rare allele and new SNP are found in this study. These data enrich the genetic information of MM in China, and are helpful for the further research on MM pathogenesis.
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Objective To investigate the relationship between the apolipoprotein B (ApoB) gene Xba Ⅰ and EcoR Ⅰ polymorphisms and cholelithiasis in Han and Mongolian population in the Midwest Area of Inner Mongolia.Methods The clinical data of 100 patients with cholelithiasis and 115 healthy individuals at the First Affiliated Hospital of Medical College of Baotou from April to October in 2010 were collected.A case-control study which detected ApoB alleles of patients with cholelithiasis (cholelithiasis group) and healthy individuals (control group) in Han nationality and Mongolian nationality in the Midwest Area of Inner Mongolia was conducted by polymerase chain reaction-restriction fragment length polymorphism,which included Xba Ⅰ (X + X +,X + X-,X-X-,X +,X-) and EcoR Ⅰ (E + E +,E-E-,E + E-,E +,E-).The serum lipid (including triglyceride,total cholesterol,high density lipoprotein and low density lipoprotein) levels in different groups were detected.The count data and the measurement data were analyzed using the chi-square test and t test,respectively.Results Genotype X + X + was not found in the Han and Mongolian population,and Xba Ⅰ (X +) or EcoR Ⅰ (E-) alleles was not found in the Mongolian population.The levels of low density lipoprotein were (2.8 ± 0.9)mmol/L in the cholelithiasis group,which was significantly higher than (1.9 ± 0.8) mmol/L of the control group in the Han population (t =2.800,P ＜ 0.05).The levels of high density lipoprotein and low density lipoprotein were (1.7 ± 0.3) mmol/L and (3.5 ± 0.8) mmol/L of the cholelithiasis group,which were significantly higher than (1.2 ± 0.3) mmol/L and (2.8 ± 0.9) mmol/L of the control group in the Mongolian population (t =7.596,2.549,P ＜ 0.05).The levels of triglyceride,total cholesterol,high density lipoprotein and low density lipoprotein of the cholelithiasis group in the Mongolian population were (3.1 ± 1.6) mmol/L,(5.6 ± 1.0) mmol/L,(1.7 ± 0.3) mmol/L and (3.5 ± 0.8) mmol/L,which were significantly higher than (1.2 ± 0.6) mmol/L,(4.4 ± 1.2) mmol/L,(1.3 ± 0.3) mmol/L and (2.8 ± 0.9) mmol/L of the cholelithiasis group in the Han population (t =5.501,3.667,4.448,3.430,P ＜ 0.05).The levels of triglyceride,total cholesterol,low density lipoprotein were (2.6 ± 1.7) mmol/L,(5.1 ± 1.1) mmol/L and (2.8 ± 0.9) mmol/L of the control group in the Mongolian population,which were significantly higher than (1.3 ±0.7)mmol/L,(3.9 ±0.9) mmol/L and (1.9 ±0.8) mmol/L of the control group in the Han population (t =4.298,4.772,3.888,P ＜ 0.05),while the level of high density lipoprotein was significantly higher of the control group in the Han nationality than the control group in the Mongolian population (t =1.997,P ＜ 0.05).The levels of low density lipoprotein in patients with genotypes X + X-,X-X-of the cholelithiasis group in the Han population were (2.7 ± 0.1) mmol/L and (2.6 ± 1.0) mmol/L,and the levels of low density lipoprotein in patients with genoeypes E + E ±,E + E-/E-E-were (2.6 ± 1.0) mmol/L and (2.5±0.4)mmol/L,with no significant difference (t=0.225,0.124,P＞0.05).Conclusion In the Midwest area of Inner Mongolia,the Mongolian population might be more susceptible to cholelithiasis than the Han population.No relationship between the rare alleles X +,E-and the increase of blood lipids,which indicates that X + and E-of ApoB may not be a risk factor of cholelithiasis.
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Objective To study the genetic polymorphism and frequencies of 15 STR loci in 10071 unrelated individuals of Han nationality, which are compared with the data reported previously. Methods 15 STR loci were amplified in DNA samples from 10071 unrelated individuals in Guangdong Han population using PowerPlex~(TM) 16 system, which were genotyped with ABI 377 or 3100 Genetic Analyzer. Frequencies for 15 STR loci were obtained. Results Except D8S1179 locus, rare alleles were found in the other 14 STR loci. The number of rare alleles ranged froml to 7 in the 14 STR loci ,which increased up to 34 rare alleles, including D21 S11 (32.1 and 36.2), D18S51 (15.2 and 17.2), Penta E (15.2, 17.4, 18.4, 19.4, 26 and 27), D7S820 (9.2, 10.1, 11.1 and 15), Penta D (18, 19 and 20), TPOX (14) and FGA (13) which were detected the first time and D21S11 (30.3), D7S820(9.1 and 9.2) which were frequently seen in the population although infrequent in European population. Conclusion More rare alleles can be detected with genetic polymorphism data from a lager number of individuals and more credible frequencies of alleles be obtained.