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Development of a robust and efficient approach for extracting useful information from microarray data continues to be a significant and challenging task. Microarray data are characterized by a high dimension, high signal-to-noise ratio, and high correlations between genes, but with a relatively small sample size. Current methods for dimensional reduction can further be improved for the scenario of...
Members of the Pumilio and DAZL family of RNA binding proteins are required for germ cell development in Drosophila, Xenopus, and Caenorhabditis elegans. Here, we report identification and characterization of RNA sequences to which PUM2 and DAZL bind. We established that human PUM2 specifically recognized the Drosophila Pumilio RNA target (the NRE or Nanos regulator element sequence); single nucleotide...
Polymorphic minisatellites, also known as variable number of tandem repeats (VNTRs), are tandem repeat regions that show variation in the number of repeat units among chromosomes in a population. Currently, there are no general methods for predicting which minisatellites have a high probability of being polymorphic, given their sequence characteristics. An earlier approach has focused on potentially...
Angelman syndrome (AS) is a neurodevelopmental disorder due to a functional deficit, usually a deletion, of the UBE3A gene located in the 15q11–q13 chromosome region. We report the first microarray analysis of gene expression in AS using a custom cDNA microarray to compare expression patterns from lymphoblastoid cell lines from control males and AS subjects with a 15q deletion or uniparental paternal...
Fluorescence in situ hybridization mapping of fully integrated human BAC clones to primate chromosomes, combined with precise breakpoint localization by PCR analysis of flow-sorted chromosomes, was used to analyze the evolutionary rearrangements of the human 3q21.3-syntenic region in orangutan, siamang gibbon, and silvered-leaf monkey. Three independent evolutionary breakpoints were localized within...
The domestic dog, Canis familiaris, is an excellent model species in which to study complex inherited diseases, having over 200 recognized breeds, each of which represents a closed gene pool. Overlapping canine genomic BAC clones were sequenced to obtain 711,521 bp of the canine classical and extended MHC class II regions. Analysis and annotation of this sequence reveals that it contains 45 loci,...
The BALB/cGa mouse strain and its descendants, now called the SELH/Bc strain, have produced two waves of high frequency of spontaneous heritable mutations. One of these, the recessive lidgap-Gates (lg Ga ) mutation, causes the same open-eyelids-at-birth phenotype as the gene knockout mutations of Map3k1 and co-maps to distal Chr 13. The lg Ga mutation is demonstrated to be a 27.5-kb...
We report the molecular cloning of SLC35D2, a novel member of the SLC35 nucleotide sugar transporter family. The gene SLC35D2 maps to chromosome 9q22.33. SLC35D2 cDNA codes for a hydrophobic protein consisting of 337 amino acid residues with 10 putative transmembrane helices. Northern blot analysis revealed the SLC35D2 mRNA as a single major band corresponding to 2.0 kb in length. SLC35D2 was localized...
DNA microarrays are a well-established technology for measuring gene expression levels. Microarrays designed for this purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide-based whole-genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential...
DYRKs are an emerging family of dual-specificity kinases that play key roles in cell proliferation, survival, and development. Up to seven mammalian DYRK isoforms have been reported, but only the DYRK1A gene (and its products) has been well characterized. Defined here are the genomic structures (and phylogenetics) of DYRK3, four additional murine and/or human DYRKs, and two related HIPK genes. For...
Tgfbm1 (chromosome 5, P = 8 × 10 −5 ) and Tgfbm3 (chromosome 12, P = 6 × 10 −11 ) were identified as loci that modify developmental angiogenesis of Tgfb1−/− mice. Congenic mice validated these loci and demonstrated epistatic interaction between them. The novel locus, Tgfbm3, encompasses ∼22 genes, colocalizes with both tumor susceptibility and atherosclerosis susceptibility loci, and...
The mammalian gene (ACACA) encoding acetyl-CoA carboxylase-α, a key regulatory enzyme of fatty acid synthesis, is transcribed from multiple promoters. We have delineated the 5′ boundary of ACACA in four species (human, mouse, rat, and ovine). The 5′ end of ACACA is located within a 600- to 700-bp CpG island encompassing a bidirectional promoter shared with the divergently oriented TADA2L, which encodes...
We recently identified optineurin (OPTN) as a novel gene for glaucoma and determined its mRNA and protein expression patterns in different human tissues. Herein, we describe the cloning, mapping, genomic organization, and mRNA and protein expression patterns for murine optineurin (Optn). We mapped Optn to chromosome 2, within a region that is syntenic to human 10p14. Optn has 13 coding exons and its...
We have analyzed the organization of the chicken α-globin gene domain using DNA miniarrays and have found two novel chromatin loop attachment regions. We have found a 40-kb loop domain that includes all the α-globin genes in cells of erythroid origin. One of the domain borders colocalizes almost exactly with a strong MAR element and with a block of enhancer-blocking elements found earlier at the upstream...
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