Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes.
Imprinted genes are expressed from only one allele in a parent-of-origin-specific manner. We here describe a systematic approach to identify novel imprinted genes using quantification of allele-specific expression by Pyrosequencing, a highly accurate method to detect allele-specific expression differences. Sixty-eight candidate imprinted transcripts mapping to known imprinted chromosomal regions were selected from a recent expression profiling study of uniparental mouse embryos and analyzed. Three novel imprinted transcripts encoding putative non-protein-coding RNAs were identified on the basis of parent-of-origin-specific monoallelic expression in E11.5 (C57BL/6 x Cast/Ei)F1 and informative (C57BL/6 x Cast/Ei) x C57BL/6 backcross embryos. In addition, four transcripts with preferential expression of a strain-specific allele were found. Intriguingly, a vast majority of the analyzed transcripts showed no imprinting-associated expression in F1 embryos. These data strengthen the view that a large fraction of nonimprinted genes is differentially expressed between parthenogenetic and androgenetic embryos and question the efficiency of expression profiling of uniparental embryos to identify novel imprinted genes.
Ruf
Nico
N
Max-Delbrueck-Center for Molecular Medicine, Berlin-Buch, Germany.
Dünzinger
Ulrich
U
Brinckmann
Anja
A
Haaf
Thomas
T
Nürnberg
Peter
P
Zechner
Ulrich
U
D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes; D003433:Crosses, Genetic; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D004622:Embryo, Mammalian; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D014644:Genetic Variation; D018392:Genomic Imprinting; D051379:Mice; D008810:Mice, Inbred C57BL; D008815:Mice, Inbred Strains; D008957:Models, Genetic; D010312:Parthenogenesis; D020641:Polymorphism, Single Nucleotide; D011218:Prader-Willi Syndrome / Q000235:genetics; D011247:Pregnancy; D012313:RNA / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics; D012984:Software; D014158:Transcription, Genetic
D018076:DNA, Complementary; D012333:RNA, Messenger; D012313:RNA; D004247:DNA