Nucleic Acids Research, 2001, Vol. 29, No. 1 275-276
© 2001 Oxford University Press
The imprinted gene and parent-of-origin effect database
Cancer Genetics Laboratory, University of Otago, PO Box 56, Dunedin, New Zealand
Received August 28, 2000; Revised and Accepted October 11, 2000.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONTHE DATABASEREFERENCES |
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The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC ) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals. In addition a wide variety of other parent-of-origin effects, such as transmission of human disease phenotypes, transmission of QTLs, uniparental disomies and interspecies crosses are recorded. Data are accessed through a search engine and references are hyperlinked to PubMed.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONTHE DATABASEREFERENCES |
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Imprinting describes those genes for which the transcriptional activity is dependent on the parent-of-origin of the allele. In addition to genomic imprinting, numerous other parent-of-origin effects have been documented, the mechanisms for which may include undiscovered gene imprinting, parental-specific mutation or other mechanisms.
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THE DATABASE |
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TOPABSTRACTINTRODUCTIONTHE DATABASEREFERENCES |
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In 1998 we published a catalogue of imprinted genes and parent-of-origin effects (1) which formed the basis of an online database which is larger, more comprehensive and regularly updated. The database is publicly available and provides a searchable compilation of parent-of-origin effects, most of which have been extracted from the biomedical literature. For each gene or phenotype entry, a brief summary of the parent-of-origin effect is provided, along with relevant references hyperlinked to PubMed. Searchable fields include species, chromosome, gene or phenotype name, text within the description and the date on which the entry was last modified. The database is maintained by the corresponding author, who welcomes submissions and comments.
At the time of submission, 41 genes were reported to be imprinted in human and mouse (Table 1) with 12 new imprinted genes having been reported in the first 9 months of 2000. These 41 genes are equally divided between those which show preferential or exclusive expression from the maternally-versus the paternally-derived allele. Enumeration of the actual number of imprinted genes depends on the definition of a ‘gene’. Some of the imprinted genes express multiple sense and/or antisense transcripts, while several imprinted transcripts of undefined function have been reported, especially in the Prader–Willi and Angelman syndromes locus on human chromosome 15 (2). Excluding variably spliced isoforms, but including antisense transcripts and non-coding transcripts of unknown function, approximately 60 imprinted transcripts have been reported. There are some differences between the reported imprinting status of genes in mouse and human which largely reflect the lack of comparative data, but documented examples of discordance exist; for example IGF2R which is imprinted in mouse but not humans.
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The discovery of increasing numbers of imprinted antisense or adjacent RNA transcripts parallels the earlier observations of IGF2 and H19 which are coordinately and oppositely imprinted, and has provided further evidence for the involvement of non-coding RNA transcripts in mechanisms to establish or maintain imprinted gene expression (3). Genomic imprinting was formally demonstrated for the first time in 1991, but parent-of-origin effects have been recorded for millennia among animal breeders (4). Ironically, historical interpretations of Mendel’s work and the emphasis on the equality of alleles may have impeded the discovery of imprinted phenomena, but recently parent-of-origin effects have been reported for quantitative-trait loci (QTLs) such as back fat thickness, muscle depth and intramuscular fat content in pigs (5) and for birth weight, weaning weight, hot carcass weight and gestation in cattle (I.G.Imumorin, personal communication).
Several other parent-of-origin effects have been reported, with varying qualities of supporting evidence. For example the phenotypes associated with uniparental disomies such as Prader–Willi and Angelman syndromes (human 15q), Beckwith–Wiedemann syndrome (11p), Russell–Silver syndrome (7p) and transient neonatal diabetes (6q) indicate the presence of imprinted genes and strong candidate genes now exist for each of these syndromes. The influence of parental origin on the transmission of human disease phenotypes has been demonstrated for conditions such as hereditary paragangliomas and diabetes susceptibility, and more recently has been suggested for a wide range of phenotypes such as premature ovarian failure (6) and male transsexuality (7).
The database also records genes for which there is a parent-of-origin effect on mutation rates: for example de novo mutations of RET, FGFR2, FGFR3 and RB preferentially occur during male gametogenesis. It also records parental effects on the direction of interspecies crosses, such as lion–tiger crosses (ligers and tigons), horse–donkey crosses (mules and hinnies) mink frog–bull frog crosses and others.
Although the database attempts to include as many reports and hypotheses as possible, it cannot always judge the accuracy of these claims. Apparent imprinted gene expression can simply reflect the technical problems of allelic drop-out during RT–PCR when transcript frequency is rare, while some of the reported imprinted inheritance patterns might reflect chance skewing or biases within the families studied. Conversely, apparent absence of imprinting can merely indicate the absence of data from specific tissues at specific developmental time periods.
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ACKNOWLEDGEMENTS |
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This work was supported by the Health Research Council of New Zealand and the Cancer Society of New Zealand.
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FOOTNOTES |
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* To whom correspondence should be addressed. Tel: +64 3 479 5391; Fax +64 3 479 7738; Email: ian.morison{at}otago.ac.nz
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REFERENCES |
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TOPABSTRACTINTRODUCTIONTHE DATABASEREFERENCES |
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1 Morison,I.M. and Reeve,A.E. (1998) A catalogue of imprinted genes and parent-of-origin effects in humans and animals. Hum. Mol. Genet., 7, 1599–1609.
2 Lee,S. and Wevrick,R. (2000) Identification of novel imprinted transcripts in the Prader-Willi syndrome and Angelman syndrome deletion region: further evidence for regional imprinting control. Adv. Hum. Genet., 66, 848–858.
3 Sleutels,F., Barlow,D.P. and Lyle,R. (2000) The uniqueness of the imprinting mechanism. Curr. Opin. Genet. Dev., 10, 229–233.[Web of Science][Medline]
4 Savory,T.H. (1970) The mule. Sci. Am., 223(6), 102–109.[Web of Science][Medline]
5 de Koning,D.J., Rattink,A.P., Harlizius,B., van Arendonk,J.A., Brascamp,E.W. and Groenen,M.A. (2000) Genome-wide scan for body composition in pigs reveals important role of imprinting. Proc. Natl Acad. Sci. USA, 97, 7947–7950.
6 Hundscheid,R.D., Sistermans,E.A., Thomas,C.M., Braat,D.D., Straatman,H., Kiemeney,L.A., Oostra,B.A. and Smits,A.P. (2000) Imprinting effect in premature ovarian failure confined to paternally inherited fragile X premutations. Am. J. Hum. Genet., 66, 413–418.[Web of Science][Medline]
7 Green,R. and Keverne,E.B. (2000) The disparate maternal aunt-uncle ratio in male transsexuals: an explanation invoking genomic imprinting. J. Theor. Biol., 202, 55–63.[Web of Science][Medline]
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