Paternally expressed genes predominate in the placenta

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 26, 2013, Pages 10705-10710

  Wang, Xu ^a   Miller, Donald C ^a   Harman, Rebecca ^a   Antczak, Douglas F ^a   Clark, Andrew G ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Chorionic girdle; Hinny; Interspecific hybrid equids; Mule

Indexed keywords

HISTONE ACETYLTRANSFERASE; INSULIN RECEPTOR; LYMPHOCYTE ANTIGEN;

ALLELE; ARTICLE; CHROMATIN; DONKEY; EPIGENETICS; FATHER; GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE SILENCING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME IMPRINTING; GROWTH REGULATION; HORSE; HYBRID; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; NONHUMAN; PLACENTA; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA SEQUENCE; TROPHOBLAST; UTERUS;

CHORIONIC GIRDLE; HINNY; INTERSPECIFIC HYBRID EQUIDS; MULE;

ANIMALS; BASE SEQUENCE; EPIGENESIS, GENETIC; EQUIDAE; FEMALE; GENE EXPRESSION PROFILING; GENOMIC IMPRINTING; HORSES; HYBRIDIZATION, GENETIC; MALE; PLACENTA; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY;

EQUIDAE; EQUUS ASINUS;

EID: 84879526709     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1308998110     Document Type: Article

References (51)

1. Bartolomei MS, Ferguson-Smith AC (2011) Mammalian genomic imprinting. Cold Spring Harb Perspect Biol 3(7):a002592.
2. Fowden AL, Coan PM, Angiolini E, Burton GJ, Constancia M (2011) Imprinted genes and the epigenetic regulation of placental phenotype. Prog Biophys Mol Biol 106(1):281-288.
3. Frost JM, Moore GE (2010) The importance of imprinting in the human placenta. PLoS Genet 6(7):e1001015.
4. Eggermann T, Eggermann K, Schönherr N (2008) Growth retardation versus overgrowth: Silver-Russell syndrome is genetically opposite to Beckwith-Wiedemann syndrome. Trends Genet 24(4):195-204.
5. Feinberg AP (2004) The epigenetics of cancer etiology. Semin Cancer Biol 14(6):427-432.
6. Morison IM, Ramsay JP, Spencer HG (2005) A census of mammalian imprinting. Trends Genet 21(8):457-465.
7. Morison IM, Paton CJ, Cleverley SD (2001) The imprinted gene and parent-of-origin effect database. Nucleic Acids Res 29(1):275-276.
8. Barton SC, Surani MA, Norris ML (1984) Role of paternal and maternal genomes in mouse development. Nature 311(5984):374-376.
9. McGrath J, Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37(1):179-183.
10. Ferguson-Smith AC, Cattanach BM, Barton SC, Beechey CV, Surani MA (1991) Embryological and molecular investigations of parental imprinting on mouse chromosome 7. Nature 351(6328):667-670.
11. Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351(6322):153-155.
12. Bischoff SR, et al. (2009) Characterization of conserved and nonconserved imprinted genes in swine. Biol Reprod 81(5):906-920.
13. Zaitoun I, Khatib H (2006) Assessment of genomic imprinting of SLC38A4, NNAT, NAP1L5, and H19 in cattle. BMC Genet 7:49.
14. Markljung E, et al. (2009) ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 7(12):e1000256.
15. Takeda H, et al. (2006) The callipyge mutation enhances bidirectional long-range DLK1- GTL2 intergenic transcription in cis. Proc Natl Acad Sci USA 103(21):8119-8124.
16. Magee DA, et al. (2011) Single nucleotide polymorphisms within the bovine DLK1- DIO3 imprinted domain are associated with economically important production traits in cattle. J Hered 102(1):94-101.
17. Allen WR (1969) Factors influencing pregnant mare serum gonadotrophin production. Nature 223(5201):64-65.
18. McGrath J, Solter D (1986) Nucleocytoplasmic interactions in the mouse embryo. J Embryol Exp Morphol 97(Suppl):277-289.
19. SuraniMA, Barton SC, NorrisML (1984) Development of reconstitutedmouse eggs suggests imprinting of the genome during gametogenesis. Nature 308(5959):548-550.
20. Roemer I, et al. (1999) Genome evolution. Global methylation in eutherian hybrids. Nature 401(6749):131-132.
21. Gregg C, et al. (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329(5992):643-648.
22. Wang X, et al. (2008) Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3(12):e3839.
23. Wang X, Soloway PD, Clark AG (2011) A survey for novel imprinted genes in the mouse placenta by mRNA-seq. Genetics 189(1):109-122.
24. DeVeale B, van der Kooy D, Babak T (2012) Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective. PLoS Genet 8(3):e1002600.
25. Okae H, et al. (2012) Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. Hum Mol Genet 21(3):548-558.
26. Wade CM, et al.; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326(5954):865-867.
27. El Kharroubi A, Piras G, Stewart CL (2001) DNA demethylation reactivates a subset of imprinted genes in uniparental mouse embryonic fibroblasts. J Biol Chem 276(12):8674-8680.
28. Tremblay KD, Duran KL, Bartolomei MS (1997) A 5' 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol Cell Biol 17(8):4322-4329.
29. Orlando L, et al. (2009) Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci USA 106(51):21754-21759.
30. Verreault A, Kaufman PD, Kobayashi R, Stillman B (1998) Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr Biol 8(2):96-108.
31. Parthun MR (2012) Histone acetyltransferase 1: More than just an enzyme? Biochim Biophys Acta 1819(3-4):256-263.
32. Ge Z, Wang H, Parthun MR (2011) Nuclear Hat1p complex (NuB4) components participate in DNA repair-linked chromatin reassembly. J Biol Chem 286(19):16790-16799.
33. Ejlassi-Lassallette A, Mocquard E, Arnaud MC, Thiriet C (2011) H4 replicationdependent diacetylation and Hat1 promote S-phase chromatin assembly in vivo. Mol Biol Cell 22(2):245-255.
34. Barlow DP, Stöger R, Herrmann BG, Saito K, Schweifer N (1991) The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 349(6304):84-87.
35. DeChiara TM, Robertson EJ, Efstratiadis A (1991) Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64(4):849-859.
36. Killian JK, et al. (2000) M6P/IGF2R imprinting evolution in mammals. Mol Cell 5(4):707-716.
37. Miyoshi N, Barton SC, Kaneda M, Hajkova P, Surani MA (2006) The continuing quest to comprehend genomic imprinting. Cytogenet Genome Res 113(1-4):6-11.
38. Jacobs PA, Wilson CM, Sprenkle JA, Rosenshein NB, Migeon BR (1980) Mechanism of origin of complete hydatidiform moles. Nature 286(5774):714-716.
39. Wake N, Arima T, Matsuda T (1998) Involvement of IGF2 and H19 imprinting in choriocarcinoma development. Int J Gynaecol Obstet 60(Suppl 1):S1-S8.
40. AntczakDF, deMestre AM,Wilsher S,AllenWR (2013) The equine endometrial cup reaction: A fetomaternal signal of significance. Annual Review of Animal Biosciences 1(1):419-442.
41. Renfree MB, Suzuki S, Kaneko-Ishino T (2013) The origin and evolution of genomic imprinting and viviparity in mammals. Philos Trans R Soc Lond B Biol Sci 368(1609):20120151.
42. Mess A, Carter AM (2007) Evolution of the placenta during the early radiation of placental mammals. Comp Biochem Physiol A Mol Integr Physiol 148(4):769-779.
43. Wildman DE (2011) Review: Toward an integrated evolutionary understanding of the mammalian placenta. Placenta 32(Suppl 2):S142-S145.
44. Raudsepp T, Mariat D, Guérin G, Chowdhary BP (2001) Comparative FISH mapping of 32 loci reveals new homologous regions between donkey and horse karyotypes. Cytogenet Cell Genet 94(3-4):180-185.
45. Radford EJ, Ferrón SR, Ferguson-Smith AC (2011) Genomic imprinting as an adaptative model of developmental plasticity. FEBS Lett 585(13):2059-2066.
46. Antczak DF, et al. (1987) Differentiation molecules of the equine trophoblast. J Reprod Fertil Suppl 35:371-378.
47. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
48. Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079.
49. Storer BE, Kim C (1990) Exact Properties of Some Exact Test Statistics for Comparing 2 Binomial Proportions. J Am Stat Assoc 85(409):146-155.
50. Wang Y, Leung FC (2004) An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 20(7):1170-1177.
51. Li LC, Dahiya R (2002) MethPrimer: Designing primers for methylation PCRs. Bioinformatics 18(11):1427-1431.