Polymorphisms within the PHF11 gene at chromosome 13q14 are associated with childhood atopic dermatitis

Jang, Na Young; Stewart, Graeme J.; Jones, Graham

doi:10.1038/sj.gene.6364169

Cited by 45 publications

(35 citation statements)

References 15 publications

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“…The strong association of H3 K9 3m with the S regions after stimulation suggests that it may have a role in the regulation of CSR. This proposition is supported by recent reports linking two H3 K9 methyltransferase enzymes with switching to specific isotypes or Ig serum levels and human disease: Suv39h1 is linked to switching to IgA (56), whereas SETDB2 is linked to serum IgE levels and atopic dermatitis (57,58).…”

Section: Discussionsupporting

confidence: 71%

Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus

Chowdhury

Forouhi

Dayal

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Ig class switch recombination (CSR) is initiated by activationinduced cytidine deaminase (AID) mediated deamination of the switch (S) regions; the resultant mismatch is processed to yield the DNA breaks required for recombination. Whereas many of the pathways involved in the mechanism of recombination have been identified, little is known about how CSR is regulated. AID action is known to require transcription of the Ig heavy-chain genes. However, it is not understood how AID is restricted to the Ig genes. Many aspects of gene expression are known to be regulated by modification of chromatin structure. In turn, chromatin is known to be regulated by several RNA-dependent activities. We have mapped the transcriptional and chromatin landscape of the human Ig heavy-chain locus to investigate the effect these activities have on CSR. We demonstrate that the Ig heavy-chain constant genes and 3-regulatory regions are in an active chromatin conformation in unstimulated total human B cells: the locus undergoes both genic and intergenic transcription and possesses histone modifications associated with ''active'' chromatin (acetylated H3 and H4 and lysine 4 trimethylated H3). However, on cytokine stimulation, these modifications spread into the S regions, demonstrating a chromatin remodeling activity associated with switching. Surprisingly, after stimulation, the S regions also accumulate lysine 9 trimethylated H3, a modification previously associated with gene silencing. These data demonstrates that the Ig locus is maintained with a complex pattern of both positive and negative histone marks and suggest that some of these marks may have dual functions.human B cells ͉ immunoglobulin class switching ͉ chromatin

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Section: Discussionsupporting

confidence: 71%

Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus

Chowdhury

Forouhi

Dayal

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…For the genotyping of the samples, we acknowledge the University of Eastern Finland and the Mutation Analysis Core Facility at Karolinska Institutet. Thomas Dahllund, 11 Johanna Granvik, 12 Maarit Haapalehto-Ikonen, 13 AnuMaaria Hämäläinen, 14 Hanna Huopio, 15 Christian Johansson, 16 Anne Kinnala, 17 Jussi Korhonen, 18 Paavo Korpela, 19 Maarit Korteniemi, 20 Pentti Lautala, 21 Kaija Lindströ m, 22 Päivi Miettinen, 1 Taina Mustila, 23 Anja Nuuja, 24 Päivi Nykänen, 25 Jussi Ojanperä, 26 Anne Putto-Laurila, 5 Marja-Terttu Saha, 4 Juhani Sankila, 27 Anne-Maarit Suomi, 6 Sirpa Tenhola, 28 Pentti Varimo, 29 Riitta Veijola, 8 Ritva Virransalo, 30 Pentti Vuolukka, 31 …”

Section: Acknowledgmentsunclassified

“…We have recently shown that human GIMAP4 plays a role in Th cell secretory processes (27). Both GIMAP4 and GIMAP5 have been shown to be regulated by plant homeodomain finger protein 11 (28), polymorphisms of which affect total IgE, allergic asthma, and eczema (29,30). Moreover, most of the GIMAP family proteins are downregulated in the Tregs of T1D patients, possibly because of IL-2 deprivation (31).…”

mentioning

confidence: 99%

GIMAP GTPase Family Genes: Potential Modifiers in Autoimmune Diabetes, Asthma, and Allergy

Heinonen¹,

Laine

Söderhäll

et al. 2015

The Journal of Immunology

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GTPase of the immunity-associated protein (GIMAP) family members are differentially regulated during human Th cell differentiation and have been previously connected to immune-mediated disorders in animal studies. GIMAP4 is believed to contribute to the Th cell subtype–driven immunological balance via its role in T cell survival. GIMAP5 has a key role in BB-DR rat and NOD mouse lymphopenia. To elucidate GIMAP4 and GIMAP5 function and role in human immunity, we conducted a study combining genetic association in different immunological diseases and complementing functional analyses. Single nucleotide polymorphisms tagging the GIMAP haplotype variation were genotyped in Finnish type 1 diabetes (T1D) families and in a prospective Swedish asthma and allergic sensitization birth cohort. Initially, GIMAP5 rs6965571 was associated with risk for asthma and allergic sensitization (odds ratio [OR] 3.74, p = 0.00072, and OR 2.70, p = 0.0063, respectively) and protection from T1D (OR 0.64, p = 0.0058); GIMAP4 rs13222905 was associated with asthma (OR 1.28, p = 0.035) and allergic sensitization (OR 1.27, p = 0.0068). However, after false discovery rate correction for multiple testing, only the associations of GIMAP4 with allergic sensitization and GIMAP5 with asthma remained significant. In addition, transcription factor binding sites surrounding the associated loci were predicted. A gene–gene interaction in the T1D data were observed between the IL2RA rs2104286 and GIMAP4 rs9640279 (OR 1.52, p = 0.0064) and indicated between INS rs689 and GIMAP5 rs2286899. The follow-up functional analyses revealed lower IL-2RA expression upon GIMAP4 knockdown and an effect of GIMAP5 rs2286899 genotype on protein expression. Thus, the potential role of GIMAP4 and GIMAP5 as modifiers of immune-mediated diseases cannot be discarded.

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“…All of the regions have been previously found to be linked to asthma/atopic disease or related phenotypes, such as IgE titres (Iyengar et al, 2001;Jang et al, 2005;Kurz et al, 2006;Xu et al, 2001;Zhang et al, 2003). The novel regions of linkage were chromosome 5p15-p13 and 13q13-q22 linked with the number of P. falciparum clinical malaria attacks in Dielmo, and chromosome 12q21-q23 with the maximum parasite density during asymptomatic carriage in Ndiop.…”

Section: Genome Wide Linkage Analysis Of P Falciparum In Senegalmentioning

confidence: 99%

Human Genetic Contribution to the Outcome of Infection with Malaria Parasites

Machado¹,

Loucoubar²,

Grange³

et al. 2012

Malaria Parasites

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Polymorphisms within the PHF11 gene at chromosome 13q14 are associated with childhood atopic dermatitis

Cited by 45 publications

References 15 publications

Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus

Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus

GIMAP GTPase Family Genes: Potential Modifiers in Autoimmune Diabetes, Asthma, and Allergy

Human Genetic Contribution to the Outcome of Infection with Malaria Parasites

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