Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

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

Volumn 108, Issue 50, 2011, Pages 20042-20047

  Zhang, Mei ^a   Zhao, Hainan ^a   Xie, Shaojun ^a   Chen, Jian ^a   Xu, Yuanyuan ^a   Wang, Keke ^a   Zhao, Haiming ^a   Guan, Haiying ^a   Hu, Xiaojiao ^a   Jiao, Yinping ^a   Song, Weibin ^a   Lai, Jinsheng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ALLELE; ARTICLE; BASE PAIRING; ENDOSPERM; GENE EXPRESSION; GENOME IMPRINTING; INTRON; MAIZE; METHYLATION; NONHUMAN; PRIORITY JOURNAL;

ALLELES; CLUSTER ANALYSIS; DNA METHYLATION; ENDOSPERM; GENOME, PLANT; GENOMIC IMPRINTING; INTRONS; OPEN READING FRAMES; REPRODUCIBILITY OF RESULTS; RNA, UNTRANSLATED; ZEA MAYS;

EID: 84055178968     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1112186108     Document Type: Article

References (46)

1. Huh JH, Bauer MJ, Hsieh T-F, Fischer RL (2008) Cellular programming of plant gene imprinting. Cell 132:735-744. (Pubitemid 351312806)
2. Luo M, Bilodeau P, Dennis ES, Peacock WJ, Chaudhury A (2000) Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci USA 97:10637-10642.
3. Grossniklaus U, Vielle-Calzada JP, Hoeppner MA, Gagliano WB (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280:446-450. (Pubitemid 28208169)
4. Vielle-Calzada J-P, et al. (1999) Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev 13:2971-2982.
5. Kinoshita T, Yadegari R, Harada JJ, Goldberg RB, Fischer RL (1999) Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11:1945-1952.
6. Guitton A-E, et al. (2004) Identification of new members of Fertilisation Independent Seed Polycomb Group pathway involved in the control of seed development in Arabidopsis thaliana. Development 131:2971-2981. (Pubitemid 38997284)
7. Kiyosue T, et al. (1999) Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci USA 96:4186-4191. (Pubitemid 29169058)
8. Berger F, Chaudhury A (2009) Parental memories shape seeds. Trends Plant Sci 14:550-556.
9. Raissig MT, Baroux C, Grossniklaus U (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23:16-26.
10. Gregg C, et al. (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329:643-648.
11. Weaver JR, Susiarjo M, Bartolomei MS (2009) Imprinting and epigenetic changes in the early embryo. Mamm Genome 20:532-543.
12. Pandey RR, et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232-246.
13. Nagano T, et al. (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717-1720.
14. Hsieh T-F, et al. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci USA 108:1755-1762.
15. Wolff P, et al. (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet 7:e1002126.
16. Gehring M, Missirian V, Henikoff S (2011) Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS ONE 6:e23687.
17. Luo M, et al. (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7:e1002125.
18. Kermicle JL (1970) Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 66:69-85.
19. Gutierrez-Marcos JF, Pennington PD, Costa LM, Dickinson HG (2003) Imprinting in the endosperm: A possible role in preventing wide hybridization. Philos Trans R Soc Lond B Biol Sci 358:1105-1111. (Pubitemid 36774904)
20. Gutiérrez-Marcos JF, et al. (2004) Maternally expressed gene1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. Plant Cell 16:1288-1301. (Pubitemid 38641521)
21. Jahnke S, Scholten S (2009) Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 19:1677-1681.
22. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447-1451.
23. Gutiérrez-Marcos JF, et al. (2006) Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet 38:876-878. (Pubitemid 44141654)
24. Haun WJ, et al. (2007) Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs. Plant J 49:325-337. (Pubitemid 46058957)
25. Hsieh T-F, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324:1451-1454.
26. Schnable PS, et al. (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science 326:1112-1115.
27. Lai J, et al. (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027-1030.
28. Danilevskaya ON, et al. (2003) Duplicated fie genes in maize: Expression pattern and imprinting suggest distinct functions. Plant Cell 15:425-438. (Pubitemid 36234078)
29. Royo H, Cavaille J (2008) Non-coding RNAs in imprinted gene clusters. Biol Cell 100: 149-166. (Pubitemid 351372674)
30. Gambetta MC, Oktaba K, Müller J (2009) Essential role of the glycosyltransferase sxc/Ogt in polycomb repression. Science 325:93-96.
31. Brannan CI, Bartolomei MS (1999) Mechanisms of genomic imprinting. Curr Opin Genet Dev 9:164-170.
32. Guo M, Rupe MA, Danilevskaya ON, Yang X, Hu Z (2003) Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J 36:30-44. (Pubitemid 37231655)
33. Springer NM, et al. (2002) Sequence relationships, conserved domains, and expression patterns for maize homologs of the polycomb group genes E(z), esc, and E(Pc). Plant Physiol 128:1332-1345. (Pubitemid 34315677)
34. Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351:153-155. (Pubitemid 21896555)
35. Mitsuya K, et al. (1999) LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids. Hum Mol Genet 8:1209-1217. (Pubitemid 29328989)
36. Santoro F, Barlow DP (2011) Developmental control of imprinted expression by macro non-coding RNAs. Semin Cell Dev Biol 22:328-335.
37. Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76-79.
38. Pauler FM, Koerner MV, Barlow DP (2007) Silencing by imprinted noncoding RNAs: Is transcription the answer? Trends Genet 23:284-292. (Pubitemid 46783843)
39. Tiwari S, et al. (2010) Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. BMC Plant Biol 10:72.
40. Birchler JA, Bhadra U, Bhadra MP, Auger DL (2001) Dosage-dependent gene regulation in multicellular eukaryotes: Implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev Biol 234:275-288. (Pubitemid 32552658)
41. Birchler JA, Riddle NC, Auger DL, Veitia RA (2005) Dosage balance in gene regulation: Biological implications. Trends Genet 21:219-226. (Pubitemid 40387899)
42. Zemach A, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA 107:18729-18734.
43. Köhler C, Page DR, Gagliardini V, Grossniklaus U (2005) The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37:28-30. (Pubitemid 40070936)
44. Köhler C, et al. (2003) The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 17:1540-1553. (Pubitemid 36734710)
45. Makarevich G, Villar CBR, Erilova A, Köhler C (2008) Mechanism of PHERES1 imprinting in Arabidopsis. J Cell Sci 121:906-912. (Pubitemid 351578126)
46. Lister R, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.