Only a very few origins have been mapped in different multicellular organisms, and they do not share detectable consensus sequence elements. Moreover, it is not clear if origins are localized at similar positions in the corresponding locus in genomes of different organisms. Here, we have mapped DNA replication origins in the c-myc locus both in Xenopus and mouse, allowing a comparison of the co...

Understanding the relationship between variations in DNA methylation and gene expression has been challenging. Evidence suggests the function of DNA methylation may vary with genomic context, and few consistent rules linking methylation to expression have been noted. For array-based studies, the content of current DNA methylation array platforms provide broad coverage of the genome but target o...

Regulated on activation, normal T-cell expressed and secreted (RANTES) and stromal cell-derived factor 1 (SDF-1) are members of the CC- and CXC-chemokine families, respectively. Both genes have been postulated to be involved in the pathogenesis of systemic lupus erythematosus (SLE). We analyzed position 28 of the RANTES gene promoter region, as well as the SNP observed in the 3' UTR of the...

MCL1 expression has been found to be up-regulated during infection with virulent Mycobacterium tuberculosis. We investigated the genetic polymorphisms in MCL1 as potential candidate gene for a host genetic study of clinical TB infection. We have sequenced exons and their boundaries of MCL1, including the 1.5 kb promoter region, to identify polymorphisms, and eight polymorphisms were identified....

RNA activation has been reported to be induced by small interfering RNAs (siRNAs) that act on the promoters of several genes containing E-cadherin. In this study, we present an alternative mechanism of E-cadherin activation in human PC-3 cells by siRNAs previously reported to possess perfect-complementary sequences to E-cadherin promoter. We found that activation of E-cadherin can be also induc...

background & objective: interleukin (il)-10 is an important anti-inflammatory and immunomodulatory cytokine. some authors believe that single nucleotide polymorphisms (snp) in the promoter region of the il-10 gene have been associated with susceptibility to hiv infection and progression to aids, but its role is not clearly defined yet. the present study was undertaken to evaluate the associ...

Background and objectives: Rheumatoid arthritis (RA) is a complex and systemic inflammatory disease in which the immune response is disturbed. Single nucleotide polymorphisms (SNPs) in the promoter regions of regulatory cytokines including interleukin-10 (IL-10) may lead to exacerbated immune response and increased risk of RA. Here, we aimed to assess the association of IL-10 -1082 (G/A) (rs180...

This communication proposes a simple algorithm with high specificity and sensitivity for determining promoter regions in human genomic sequences. This method relies upon non-redundant and experimentally verified promoter data sets form Eukaryotic Promoter Database (EPD) as training parameters. This technique predicts and computationally satisfies the promoter regions in the NCBI annotated datab...

Supporting analysis of “active promoter” and “enhancer” region properties We compared a number of properties of “promoter” and “enhancer” regions as defined in the main paper. We observed that both clusters contained high levels of PU.1 and C/EBPβ ChIP-seq tags, but Pol2 binding was restricted mainly to the “promoter” cluster (Supplementary Fig. 1B). CpG scores and GC content (not shown) were m...

In mice and humans, IGF2 has multiple promoters to maintain its complex tissue- and developmental stage-specific imprinting and expression. IGF2 is also imprinted in marsupials, but little is known about its promoter region. In this study, three IGF2 transcripts were isolated from placental and liver samples of the tammar wallaby, Macropus eugenii. Each transcript contained a unique 5' untransl...