SNP-specific array-based allele-specific expression analysis.
We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39-49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples.
Bjornsson
Hans T
HT
Department of Medicine and Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Albert
Thomas J
TJ
Ladd-Acosta
Christine M
CM
Green
Roland D
RD
Rongione
Michael A
MA
Middle
Christina M
CM
Irizarry
Rafael A
RA
Broman
Karl W
KW
Feinberg
Andrew P
AP
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D000483:Alleles; D000626:Aminopeptidases / Q000235:genetics; D051017:Apoptosis Regulatory Proteins; D002352:Carrier Proteins / Q000235:genetics; D002460:Cell Line; D018392:Genomic Imprinting; D006579:Heterozygote; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011987:Receptors, Steroid; D015203:Reproducibility of Results; D000098825:Oxysterol Binding Proteins
D048868:Adaptor Proteins, Signal Transducing; D051017:Apoptosis Regulatory Proteins; D002352:Carrier Proteins; C495732:NLRP2 protein, human; D011987:Receptors, Steroid; D000098825:Oxysterol Binding Proteins; D000626:Aminopeptidases; C503944:ERAP2 protein, human