Asb4, Ata3, and Dcn Are Novel Imprinted Genes Identified by High-Throughput Screening Using RIKEN cDNA Microarray

Mizuno, Yosuke; Sotomaru, Yusuke; Katsuzawa, Yukiko; Kono, Toru; Meguro, Mitsue; Oshimura, Mitsuo; Kawai, Jun; Tomaru, Yuji; Kiyosawa, Hidenori; Nikaido, Itoshi; Arima, Hiroshi; Hayashizaki, Yoshihide; Okazaki, Yasushi

doi:10.1006/bbrc.2002.6370

Cited by 124 publications

(102 citation statements)

References 34 publications

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“…Four imprinted genes have previously been isolated from this region in human and mouse (Piras et al 2000;Ono et al 2001;Mizuno et al 2002;Okita et al 2003). Calcr was localized close to these genes, indicating that it was a new member of this imprinted cluster (Fig.…”

Section: Resultsmentioning

confidence: 91%

Calcr, a brain-specific imprinted mouse calcitonin receptor gene in the imprinted cluster of the proximal region of chromosome 6

et al. 2003

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Expressed sequence tags (ESTs) in the human chromosome 7q21-q31 region were recently used to screen for allelic expression bias in monochromosomal hybrids retaining a paternal or maternal human chromosome 7. Six candidate imprinted genes were identified. In this study, we investigated parent-of-originspecific expression profiles of their mouse homologues in the proximal region of chromosome 6. An imprinting analysis, using F1 mice from reciprocal crosses between the B6 and JF strains, demonstrated that the mouse calcitonin receptor gene (Calcr) was expressed preferentially from the maternal allele in brain, whereas no allelic bias was detected in other tissues. Our results indicate that Calcr is imprinted in a tissue-specific manner, with a predominant expression from the maternal allele in the brain.

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Section: Resultsmentioning

confidence: 91%

Calcr, a brain-specific imprinted mouse calcitonin receptor gene in the imprinted cluster of the proximal region of chromosome 6

et al. 2003

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“…19 We investigated additional genes in 7q21.3 but could not find them imprinted. ASB4, which has been shown to be paternally imprinted in mice, 17 could not be amplified from lymphoblastoid cell lines with one round of RT -PCR.…”

Section: Discussionmentioning

confidence: 98%

The epsilon-sarcoglycan gene (SGCE), mutated in myoclonus-dystonia syndrome, is maternally imprinted

Grabowski¹,

et al. 2003

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Myoclonus-dystonia syndrome (MDS) is a non-degenerative neurological disorder that has been described to be inherited in an autosomal dominant mode with incomplete penetrance. MDS is caused by loss of function mutations in the epsilon-sarcoglycan gene. Reinvestigation of MDS pedigrees provided evidence for a maternal imprinting mechanism. As differential methylated regions (DMRs) are a characteristic feature of imprinted genes, we studied the methylation pattern of CpG dinucleotides within the CpG island containing the promoter region and the first exon of the SGCE gene by bisulphite genomic sequencing. Our findings revealed that in peripheral blood leukocytes the maternal allele is methylated, while the paternal allele is unmethylated. We also showed that most likely the maternal allele is completely methylated in brain tissue. Furthermore, CpG dinucleotides in maternal and paternal uniparental disomy 7 (UPD7) lymphoblastoid cell lines show a corresponding parent-of-origin specific methylation pattern. The effect of differential methylation on the expression of the SGCE gene was tested in UPD7 cell lines with only a weak RT -PCR signal observed in matUPD7 and a strong signal in patUPD7. These results provide strong evidence for a maternal imprinting of the SGCE gene. The inheritance pattern in MDS families is in agreement with such an imprinting mechanism with the exception of a few cases. We investigated one affected female that inherited the mutated allele from her mother. Surprisingly, we found the paternal wild type allele expressed whereas the mutated maternal allele was not detectable in peripheral blood cDNA.

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“…To date, about 120 imprinted genes have been identified and successfully validated in humans and mice (Morison et al, 2001(Morison et al, , 2005Prickett and Oakey, 2012), and we know this list is not complete. Genomewide and transcriptome-wide approaches have been applied to detect genomic imprinting (Maeda and Hayashizaki, 2006;Henckel and Arnaud, 2010), including microarray expression profiling of parthenogenote and androgenote embryos (Mizuno et al, 2002;Nikaido et al, 2003;Kuzmin et al, 2008;Sritanaudomchai et al, 2010) and uniparental disomic mice (Choi et al, 2001(Choi et al, , 2005Schulz et al, 2006), expression profiling using allele-specific single-nucleotide polymorphism (SNP) arrays (Pollard et al, 2008;Serre et al, 2008;Brideau et al, 2010;Morcos et al, 2011) and computational prediction methods (Ke et al, 2002;Yang et al, 2003;Luedi et al, 2005Luedi et al, , 2007Brideau et al, 2010). Recently, RNA-seq has become the method of choice for in-depth analysis of the whole transcriptome of an organism (Ozsolak and Milos, 2011).…”

Section: Introductionmentioning

confidence: 99%

Using next-generation RNA sequencing to identify imprinted genes

2014

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Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.

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Asb4, Ata3, and Dcn Are Novel Imprinted Genes Identified by High-Throughput Screening Using RIKEN cDNA Microarray

Cited by 124 publications

References 34 publications

Calcr, a brain-specific imprinted mouse calcitonin receptor gene in the imprinted cluster of the proximal region of chromosome 6

Calcr, a brain-specific imprinted mouse calcitonin receptor gene in the imprinted cluster of the proximal region of chromosome 6

The epsilon-sarcoglycan gene (SGCE), mutated in myoclonus-dystonia syndrome, is maternally imprinted

Using next-generation RNA sequencing to identify imprinted genes

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