EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes

Nikaido, Itoshi; Saito, Chika; Wakamoto, Akiko; Tomaru, Yuji; Arakawa, Takahiro; Hayashizaki, Yoshihide; Okazaki, Yasushi

doi:10.1093/nar/gkh093

Cited by 18 publications

(15 citation statements)

References 17 publications

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“…To explore links between dynamic TSS usage and imprinting, we used candidate imprinted transcripts stored in the EICO database [29], which were identified by differential expression dependent upon chromosomal parent of origin using cDNA microarrays [30]. The sensitivity of the method was demonstrated by identification of previously reported imprinted genes [30].…”

Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2006

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This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Dynamic usage of transcription start sites

An exploration of the internal dynamics of mammalian promoters demonstrates that start site selection within mouse core promoters varies amongst tissues.

Abstract Background: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends.

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Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2006

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An exploration of the internal dynamics of mammalian promoters demonstrates that start site selection within mouse core promoters varies amongst tissues.

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“…The exceptions, with a relatively high degree of methylation despite relatively strong insulator activity and in vivo binding to CTCF, could be explained by invoking the possibility that these clones reside in imprinting control regions in which one of the alleles is methylated, while the unmethylated allele is binding CTCF, as in the case of the H19 ICR (Kanduri et al 2000a,b). Indeed, two of the library CTCF target sites mapped within known imprinted domains (Grb10 and Snrpn), whereas five other members of the CTCF target-site library could be identified in the EICO library of candidate imprinted genes (Nikaido et al 2004), strengthening a link between CTCF and genomic imprinting.…”

Section: Discussionmentioning

confidence: 96%

The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

Mukhopadhyay

Yu²,

Whitehead³

et al. 2004

Genome Res.

126

109

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All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states.

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“…FTO is indeed listed as a candidate maternally imprinted gene in mice in the Expression‐based Imprint Candidate Organizer (http://fantom2.gsc.riken.jp/EICODB/). This database contains candidate imprinted genes identified by the RIKEN full‐length mouse cDNA microarray study [Nikaido et al, 2004]. In this study, genes were identified as potentially imprinted by comparing mRNA expression profiles between parthenogenetic and androgenetic embryos [Mizuno et al, 2002].…”

Section: Discussionmentioning

confidence: 99%

Investigation of a patient with a partial trisomy 16q including the fat mass and obesity associated gene (FTO): Fine mapping and FTO gene expression study

Berg

Waal

Han

et al. 2010

American J of Med Genetics Pt A

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A female patient with a partial trisomy 16q was described previously. Her clinical characteristics included obesity, severe anisomastia, moderate to severe mental retardation, attention deficit hyperactivity disorder, dysmorphic facies, and contractions of the small joints. In this paper, we describe a more detailed analysis of the genetic anomaly in this patient. We were particularly interested in the involvement of the fat mass and obesity associated gene (FTO) in her duplication. Single nucleotide polymorphisms in FTO have recently been associated with obesity. The breakpoints of the duplication were precisely mapped using high resolution oligonucleotide array comparative genomic hybridization (CGH). We found that the duplication spans 11.45 Mb on 16q11.2 to 16q13 and it includes FTO. The increased copy number of FTO was confirmed with a qPCR on genomic DNA of the patient. We investigated the influence of the increased FTO copy number on FTO gene expression in immortalized lymphocytes from the patient using qPCR. No evidence of increased FTO expression was detected in the patient's lymphocytes. We discuss these findings and shared phenotypic features of patients with overlapping 16q duplications, as well as candidate genes for some of the clinical manifestations.

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EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes

Cited by 18 publications

References 17 publications

Untitled

Untitled

The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

Investigation of a patient with a partial trisomy 16q including the fat mass and obesity associated gene (FTO): Fine mapping and FTO gene expression study

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