High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.
BACKGROUND
Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue.


RESULTS
Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%).


CONCLUSIONS
Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. ASE was common in human term placenta.
Daelemans
Caroline
C
Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1 SA, UK.
Ritchie
Matthew E
ME
Smits
Guillaume
G
Abu-Amero
Sayeda
S
Sudbery
Ian M
IM
Forrest
Matthew S
MS
Campino
Susana
S
Clark
Taane G
TG
Stanier
Philip
P
Kwiatkowski
Dominic
D
Deloukas
Panos
P
Dermitzakis
Emmanouil T
ET
Tavaré
Simon
S
Moore
Gudrun E
GE
Dunham
Ian
I
D000483:Alleles; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D015870:Gene Expression; D018392:Genomic Imprinting; D006801:Humans; D008840:Microfilament Proteins / Q000235:genetics; D009363:Neoplasm Proteins / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010920:Placenta / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D012680:Sensitivity and Specificity
D004268:DNA-Binding Proteins; D008840:Microfilament Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; C543104:PHACTR2 protein, human; C403666:ZNF331 protein, human
Dev Cell. 2007 Jul;13(1):87-102
17609112
Nat Genet. 2006 Dec;38(12):1375-7
17072315
Nat Genet. 2005 Jul;37(7):766-70
15965474
Science. 2002 Aug 16;297(5584):1143
12183620
Genome Res. 2003 Aug;13(8):1855-62
12902379
PLoS Genet. 2008 Feb 29;4(2):e1000006
18454203
Stat Appl Genet Mol Biol. 2004;3:Article3
16646809
PLoS One. 2009;4(1):e4247
19158953
Genome Res. 2004 Jan;14(1):126-33
14707174
Bioinformatics. 2002 Nov;18(11):1427-31
12424112
J Biol Chem. 2003 Nov 14;278(46):45611-9
12925532
Nucleic Acids Res. 2008 Mar;36(5):e34
18296484
Nat Genet. 2003 Apr;33(4):469-75
12627232
Nat Genet. 2005 May;37(5):549-54
15838508
J Clin Invest. 2004 Aug;114(3):339-48
15286800
Trends Genet. 2005 Aug;21(8):457-65
15990197
PLoS Genet. 2008 Jun 06;4(6):e1000091
18535661
Hum Mol Genet. 2007 Nov 1;16(21):2591-9
17704508
Science. 1996 Jul 12;273(5272):236-8
8662506
Hum Mol Genet. 2000 Mar 1;9(4):589-96
10699182
Epigenetics. 2009 Nov 16;4(8):587-92
19923923
Genome Res. 2007 Dec;17(12):1723-30
18055845
Cancer J. 2007 Jan-Feb;13(1):70-4
17464249
Cell. 1994 Sep 9;78(5):823-34
8087849
Methods Enzymol. 2006;410:57-73
16938546
Nat Genet. 2007 Oct;39(10):1217-24
17873874
J Exp Med. 1965 Nov 1;122(5):853-76
4159057
J Mol Biol. 2008 Mar 28;377(3):605-8
18295233
Science. 2007 Feb 9;315(5813):848-53
17289997
Science. 2007 Nov 16;318(5853):1136-40
18006746
J Cell Physiol. 2002 Sep;192(3):245-58
12124770
Mol Biol Evol. 2008 Jul;25(7):1493-502
18417486
Genome Res. 2006 Mar;16(3):331-9
16467561
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5478-83
16567644
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6623-8
16614068
Bioinformatics. 2006 Dec 15;22(24):3032-9
17038342
Bioinformatics. 2007 Aug 15;23(16):2183-4
17586828
Nat Rev Genet. 2001 Jan;2(1):21-32
11253064
Biochem Biophys Res Commun. 2001 May 25;283(5):1124-30
11355889
Nat Genet. 1996 Sep;14(1):106-9
8782830
Hum Genet. 2008 Jan;122(6):625-34
17955261
Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4253-8
18337500
Placenta. 2005 Apr;26 Suppl A:S10-20
15837057
Science. 2009 Sep 4;325(5945):1246-50
19644074
Epigenetics. 2008 Sep;3(5):261-9
18769151
Proc Natl Acad Sci U S A. 2004 May 4;101(18):7187-92
15107502
Genome Res. 2008 May;18(5):771-9
18369178
Hum Mol Genet. 1998;7(10):1599-609
9735381
Genome Res. 2005 Jun;15(6):875-84
15930497