Binding of octamer factors to a novel 3'-positive regulatory element in the mouse interleukin-5 gene

Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data

Polyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism such as mRNA stability, translocation, and translation. However, polyadenylation has been rarely studied in teleosts. Here we conducted polyadenylation analysis in channel catfish, a commercially important aquaculture species around the world. Using RNA-Seq data, we identified 20,320 PASs which were classified into 14,500 clusters by merging adjacent PASs. Most of the PASs were found in 3' UTRs, followed by intron regions based on the annotation of channel catfish reference genome. No apparent difference in PAS distribution was observed between the sense and antisense strand of the channel catfish genome. The sequence analysis of nucleotide composition and motif around PASs yielded a highly similar profile among various organisms, suggesting the conservation and importance of polyadenylation in evolution. Using APA genes with more than two PASs, gene ontology enrichment revealed genes particularly involved in RNA binding. Reactome pathway analysis showed the enrichment of the innate immune system, especially neutrophil degranulation.

Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)

BACKGROUND

Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.

OBJECTIVE

Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels--rs3765526, rs9526569, and rs1046295--for a role in transcription factor binding.

METHODS

We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.

RESULTS

Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10(-16)), preferential expression of the A allele consistent with a functional role for rs1046295.

CONCLUSION

These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.

Genetic association of neurotrophic tyrosine kinase receptor type 2 (NTRK2) With Alzheimer's disease

Brain-derived neurotrophic factor (BDNF)/tyrosine receptor kinase (TRK) signaling pathway activates a wide range of downstream intracellular cascades, regulating neuronal development and plasticity, long-term potentiation, and apoptosis. The NTRK family encodes the receptors TRKA, TRKB, and TRKC, to which the neurotrophins, nerve growth factor (NGF), BDNF and neurotrophin-3 (NT-3) bind, respectively, with high affinity. Signaling through these receptors appears to be compromised in Alzheimer's disease (AD). This study is the most comprehensive investigation of genetic variants of NTRK2, and the first to show significant association between NTRK2 with AD. Fourteen single nucleotide polymorphisms (SNPs), located in 8 of 18 linkage disequilibrium (LD) blocks, were genotyped in 203 families with at least two AD affected siblings with mean age of onset (MAO) of 70.9 +/- 7.4 years and one unaffected sibling from the NIMH-ADGJ dataset. Family based association testing found no single SNP association, however, significant associations were found for two and three locus haplotypes (P = 0.012, P = 0.009, respectively) containing SNPs rsl624327, rsl443445, and rs378645. These SNPs are located in areas of the gene containing sequences that could be involved in alternative splicing and/or regulation of NTRK2. Our results suggest that NTRK2 may be a genetic susceptibility gene contributing to AD pathology.

Binding of octamer factors to the murine IL-5 CLE0 in primary T-cells and a T-cell line

Interleukin-5 (IL-5) is an inducible T-cell derived cytokine with remarkable specificity for the eosinophil lineage. It is controlled at the level of transcription and regulation of the gene is an obvious target for therapy of eosinophil-dependent allergic disorders such as asthma, eczema and rhinitis. Using a T-cell line and primary T-cells we have shown for the first time that the Oct1 and Oct2 transcription factors combine to form a complex with the functionally critical murine IL-5 cis-regulatory element, conserved lymphokine element 0 (CLE0), and contribute to positive regulation of the gene. These results show the increasingly important role of octamer factors in regulation of the IL-5 gene.