RESUMO
We analyzed the publicly available ChromHMM BED files of the ENCODE project and tested the Markov properties of the different chromatin states in the human genome. Nucleotide frequency profiles of regional chromatin segmentations were analyzed, and Markov chains were built to detect Markov properties in the chromatin states of different ChromHMM regions. By estimating the transition probabilities of 200-base pair nucleotide sequences of the human genome, we constructed a nucleotide-sequence-based Markovian chromatin map called SeqChromMM.
Assuntos
Cromatina/genética , Cromossomos Humanos/genética , Mapeamento Cromossômico , Epigênese Genética , Genoma Humano , Humanos , Cadeias de Markov , Análise de Sequência de DNARESUMO
Recent advances in computational epigenetics have provided new opportunities to evaluate n-gram probabilistic language models. In this paper, we describe a systematic genome-wide approach for predicting functional roles in inactive chromatin regions by using a sequence-based Markovian chromatin map of the human genome. We demonstrate that Markov chains of sequences can be used as a precursor to predict functional roles in heterochromatin regions and provide an example comparing two publicly available chromatin annotations of large-scale epigenomics projects: ENCODE project consortium and Roadmap Epigenomics consortium.
Assuntos
Cromatina/genética , Sequência de Bases , Linhagem Celular , Mapeamento Cromossômico , Biologia Computacional , Epigênese Genética , Genoma Humano , Humanos , Modelos Genéticos , Modelos Estatísticos , Anotação de Sequência Molecular , Análise de Sequência de DNA , SoftwareRESUMO
COL6A1 and BMP-2 genes have been implicated in ossification of the posterior longitudinal ligament (OPLL) susceptibility in Japanese and Chinese Han populations. However, no study has yet investigated the DNA of unaffected family members of patients with OPLL. This study investigated differences in genetic polymorphisms of BMP-2 and COL6A1 between Korean patients with OPLL and their family members (with and without OPLL). A total of 321 subjects (110 patients with OPLL and 211 family members) were enrolled in the study. Associations between two single nucleotide polymorphisms (SNPs) of the BMP-2 gene (Ser37Ala and Ser87Ser) and two SNPs of COL6A1 [promoter (-572) and intron 33 (+20)] with susceptibility to OPLL of the cervical spine were investigated between the two groups (OPLL+ and OPLL-). Of the 321 subjects, 162 had cervical OPLL (50.4%; 110 patients, 52 family members). There was a familial tendency of OPLL in 34 of the 110 families (30.9%). Allele and haplotype frequencies of the four SNPs in the BMP-2 and COL6A1 genes did not differ significantly between the OPLL+ and OPLL- groups, even when excluding participants over 50 years of age. This is the first report identifying SNPs of COL6A1 and BMP-2 in Korean patients and family members with OPLL. Although allele and haplotype frequencies were similar with those of a previous study in Japanese and Chinese patients, unaffected family members also showed similar rates of these SNPs in the present study. These results suggest that these SNPs may not directly influence the expression of OPLL.
Assuntos
Povo Asiático/genética , Proteína Morfogenética Óssea 2/genética , Colágeno Tipo VI/genética , Predisposição Genética para Doença , Ossificação do Ligamento Longitudinal Posterior/genética , Polimorfismo Genético , Adolescente , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Alelos , Feminino , Frequência do Gene , Estudos de Associação Genética , Genótipo , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , República da Coreia , Adulto JovemRESUMO
Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding.
Assuntos
Chrysanthemum/classificação , Chrysanthemum/genética , DNA de Plantas , Repetições de Microssatélites , Filogenia , Alelos , Cruzamento , Análise por Conglomerados , Frequência do Gene , Genética Populacional , Genótipo , Polimorfismo Genético , República da CoreiaRESUMO
We investigated the molecular response of degenerated human cervical and lumbar nucleus pulposus (NP) cells following cytokine treatment. Degenerated cervical and lumbar discs (8 each) were obtained from patients who underwent discectomy for degenerative disc disease; NP cells were isolated and cultured. The mRNA expressions of aggrecan, alkaline phosphatase, type I collagen, type II collagen, osteocalcin, and Sox9 in the 2 groups were compared by real-time PCR, before and following treatment with rhBMP-2 and TGF-ß1. Immunoreactivity was analyzed to check protein activity. Type I collagen expression was significantly higher in cervical compared with that in lumbar disc cells. The mRNA expression was significantly increased after rhBMP-2 and TGF-ß1 treatment. After rhBMP-2 treatment, mRNA expression of type I and II collagens increased significantly more in cervical than in lumbar NP cells. Following TGF-ß1 treatment, the increase in mRNA expression was not significantly different between cervical and lumbar disc cells. Protein immunoreactivity, before and after cytokine treatment was similar to mRNA expression data. The matrix-related gene expression of cervical and lumbar NP after rhBMP-2 and TGF-ß1 treatment increased similarly, with the exception of collagen expression.
Assuntos
Citocinas/farmacologia , Degeneração do Disco Intervertebral/genética , Disco Intervertebral/efeitos dos fármacos , Disco Intervertebral/metabolismo , Adulto , Idoso , Agrecanas/genética , Agrecanas/metabolismo , Fosfatase Alcalina/genética , Fosfatase Alcalina/metabolismo , Proteína Morfogenética Óssea 2/farmacologia , Células Cultivadas , Vértebras Cervicais , Colágeno Tipo I/genética , Colágeno Tipo I/metabolismo , Colágeno Tipo II/genética , Colágeno Tipo II/metabolismo , Imunofluorescência , Regulação da Expressão Gênica/efeitos dos fármacos , Humanos , Disco Intervertebral/patologia , Degeneração do Disco Intervertebral/patologia , Vértebras Lombares , Microscopia de Fluorescência , Pessoa de Meia-Idade , Osteocalcina/genética , Osteocalcina/metabolismo , Proteínas Recombinantes/farmacologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Transcrição SOX9/genética , Fatores de Transcrição SOX9/metabolismo , Fator de Crescimento Transformador beta/farmacologia , Fator de Crescimento Transformador beta1/farmacologiaRESUMO
Ossification of the posterior longitudinal ligaments (OPLL) has been considered to be associated with abnormalities of bone metabolism, and transforming growth factor-ß1 (TGF-ß1) has been demonstrated to affect the bone remodeling process. We investigated two SNPs of the TGF-ß1 promoter (-509C>T; rs1800469) and exon 1 (869T>C; rs1982073) in 298 Koreans (98 patients with OPLL and 200 control subjects). The promoter SNP -509C>T was determined by PCR and RFLP, and the TaqMan probe assay was used to determine 869T>C polymorphism genotypes. The subjects were divided into OPLL continuous group (continuous type plus mixed type) and OPLL segmental group (segmental and localized type). We also separately analyzed this association according to gender difference. There was no significant difference in genotype distributions of -509C>T and 869T>C polymorphisms of the TGF-ß1 gene between OPLL patients and controls. A combined analysis of TGF-ß1 -509C>T and 869T>C polymorphisms showed no significant association with OPLL, and a subgroup analysis did not show any significant correlation between the SNP -509C>T or SNP 869T>C and OPLL subgroups. Stratification by gender demonstrated no significant effect. We conclude that promoter region (-509C>T) and exon 1 (869T>C) polymorphisms are not associated with OPLL in the Korean population.
Assuntos
Predisposição Genética para Doença , Ossificação do Ligamento Longitudinal Posterior/genética , Polimorfismo Genético , Fator de Crescimento Transformador beta1/genética , Adulto , Alelos , Estudos de Casos e Controles , Feminino , Frequência do Gene , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , República da CoreiaRESUMO
We used an enzyme-linked immunosorbent assay system to compare prevalence and levels of systemic and local antibody to Giardia lamblia in different populations. Serial blood and milk samples were collected simultaneously from lactating women in Texas and Mexico. IgG antibody to G. lamblia was present in 118 (77%) of 153 sera from 27 Mexican mothers but in only 51 (24%) of 214 sera obtained from 28 Texan mothers (P less than .001). Sera positive for IgG antibody to G. lamblia revealed antibody levels that were significantly higher in Mexico than in Texas (0.325 +/- 0.076 vs. 0.219 +/- 0.079 optical density units). Secretory IgA antibody to G. lamblia was found in 121 (79%) of 153 milk samples in the Mexican population, but in only 33 (15%) of 214 samples in the Texan population (P less than .001). The levels of secretory antibody to G. lamblia also were higher in the Mexican population. The study documents a widely different antibody response to G. lamblia in individuals living in different areas. As antibodies to G. lamblia can be acquired by infants transplacentally or through breast-feeding, this difference might be important in the relative protection against giardial infection.