Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

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

Volumn 111, Issue 21, 2014, Pages 7582-7587

  Li, Guosheng ^a   Wang, Dongfang ^a,e   Yang, Ruolin ^a   Logan, Kyle ^b   Chen, Hao ^a,f   Zhang, Shanshan ^a   Skaggs, Megan I ^a   Lloyd, Alan ^b   Burnett, William J ^b   Laurie, John D ^a,g   Hunter, Brenda G ^a   Dannenhoffer, Joanne M ^c   Larkins, Brian A ^a,d   Drews, Gary N ^b   Wang, Xiangfeng ^a   Yadegari, Ramin ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c CENTRAL MICHIGAN UNIVERSITY   (United States)

^d UNIVERSITY OF NEBRASKA   (United States)

^e SPELMAN COLLEGE   (United States)

^f BOSTON UNIVERSITY   (United States)

^g UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

MRNA localization; Time series

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; ENDOSPERM; GENE EXPRESSION; GENE EXPRESSION PROFILING; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLLINATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; TRANSPOSON; UPREGULATION;

MRNA LOCALIZATION; TIME SERIES;

COMPUTATIONAL BIOLOGY; ENDOSPERM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; TIME FACTORS; ZEA MAYS;

EID: 84901649762     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1406383111     Document Type: Article

References (45)

1. Lopes MA, Larkins BA (1993) Endosperm origin, development, and function. Plant Cell 5(10):1383-1399. (Pubitemid 2001816)
2. Olsen OA (2001) Endosperm development: Cellularization and cell fate specification. Annu Rev Plant Physiol Plant Mol Biol 52:233-267.
3. Olsen OA (2004) Nuclear endosperm development in cereals and Arabidopsis thaliana. Plant Cell 16(Suppl):S214-S227.
4. Sabelli PA, Larkins BA (2009) The development of endosperm in grasses. Plant Physiol 149(1):14-26.
5. Lending CR, Larkins BA (1989) Changes in the zein composition of protein bodies during maize endosperm development. Plant Cell 1(10):1011-1023.
6. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25.
7. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105-1111.
8. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1): 139-140.
9. Rodrigues JA, et al. (2013) Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proc Natl Acad Sci USA 110(19):7934-7939.
10. Hsieh TF, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324(5933):1451-1454.
11. Sahoo D, Dill DL, Tibshirani R, Plevritis SK (2007) Extracting binary signals from mi-croarray time-course data. Nucleic Acids Res 35(11):3705-3712. (Pubitemid 47244663)
12. Kiesselbach TA, Walker ER (1952) Structure of certain specialized tissues in the kernel of corn. Am J Bot 39(8):561-569.
13. Schel JHN, Kieft H, Vanlammeren AAM (1984) Interactions between embryo and endosperm during early developmental stages of maize caryopses (Zea mays). Can J Bot 62(12):2842-2853.
14. Kiesselbach TA (1949) The Structure and Reproduction of Corn (University of Nebraska College of Agriculture, Agricultural Experiment Station, Lincoln, NE), 96 pp.
15. Gómez E, Royo J, Guo Y, Thompson R, Hueros G (2002) Establishment of cereal endosperm expression domains: Identification and properties of a maize transfer cell-specific transcription factor, ZmMRP-1. Plant Cell 14(3):599-610. (Pubitemid 34299666)
16. 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(5):1288-1301. (Pubitemid 38641521)
17. Hueros G, Varotto S, Salamini F, Thompson RD (1995) Molecular characterization of BET1, a gene expressed in the endosperm transfer cells of maize. Plant Cell 7(6):747-757.
18. Serna A, et al. (2001) Maize endosperm secretes a novel antifungal protein into adjacent maternal tissue. Plant J 25(6):687-698. (Pubitemid 32406382)
19. Opsahl-Ferstad HG, Le Deunff E, Dumas C, Rogowsky PM (1997) ZmEsr, a novel endosperm-specific gene expressed in a restricted region around the maize embryo. Plant J 12(1):235-246. (Pubitemid 27312780)
20. Bonello JF, et al. (2002) Esr proteins are secreted by the cells of the embryo surrounding region. J Exp Bot 53(374):1559-1568.
21. Woo YM, Hu DWN, Larkins BA, Jung R (2001) Genomics analysis of genes expressed in maize endosperm identifies novel seed proteins and clarifies patterns of zein gene expression. Plant Cell 13(10):2297-2317. (Pubitemid 33044953)
22. Wittich PE, Vreugdenhil D (1998) Localization of sucrose synthase activity in developing maize kernels by in situ enzyme histochemistry. J Exp Bot 49(324):1163-1171. (Pubitemid 28336142)
23. Schmidt RJ, Burr FA, Aukerman MJ, Burr B (1990) Maize regulatory gene opaque-2 encodes a protein with a "leucine-zipper" motif that binds to zein DNA. Proc Natl Acad Sci USA 87(1):46-50.
24. Vicente-Carbajosa J, Moose SP, Parsons RL, Schmidt RJ (1997) A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2. Proc Natl Acad Sci USA 94(14): 7685-7690. (Pubitemid 27345377)
25. Pedersen K, Devereux J, Wilson DR, Sheldon E, Larkins BA (1982) Cloning and sequence analysis reveal structural variation among related zein genes in maize. Cell 29(3):1015-1026. (Pubitemid 12027923)
26. Pedersen K, Argos P, Naravana SVL, Larkins BA (1986) Sequence analysis and characterization of a maize gene encoding a high-sulfur zein protein of Mr 15, 000. J Biol Chem 261(14):6279-6284. (Pubitemid 17204133)
27. Prat S, Pérez-Grau L, Puigdomènech P (1987) Multiple variability in the sequence of a family of maize endosperm proteins. Gene 52(1):41-49.
28. Kirihara JA, Petri JB, Messing J (1988) Isolation and sequence of a gene encoding a methionine-rich 10-kDa zein protein from maize. Gene 71(2):359-370.
29. Du Z, Zhou X, Ling Y, Zhang ZH, Su Z (2010) agriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Res 38(Web Server issue):W64-W70.
30. Becraft PW (2001) Cell fate specification in the cereal endosperm. Semin Cell Dev Biol 12(5):387-394.
31. Charlton WL, et al. (1995) Endosperm development in Zea mays: Implication of gametic imprinting and paternal excess in regulation of transfer layer development. Development 121(9):3089-3097.
32. Cooper DC (1951) Caryopsis development following matings between diploid and tetraploid strains of Zea Mays. Am J Bot 38(9):702-708.
33. Gao Y, Xu H, Shen YY, Wang JB (2013) Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique. Plant Mol Biol 81(4-5):363-378.
34. Gillies SA, Futardo A, Henry RJ (2012) Gene expression in the developing aleuroneand starchy endosperm of wheat. Plant Biotechnol J 10(6):668-679.
35. Gutierrez-Gonzalez JJ, Tu ZJ, Garvin DF (2013) Analysis and annotation of the hexa-ploid oat seed transcriptome. BMC Genomics 14:471.
36. Lu XD, et al. (2013) The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol 162(1):440-455.
37. Pellny TK, et al. (2012) Cell walls of developing wheat starchy endosperm: Comparison of composition and RNA-Seq transcriptome. Plant Physiol 158(2):612-627.
38. Jones RJ, Schreiber BMN, Roessler JA (1996) Kernel sink capacity in maize: Genotypic and maternal regulation. Crop Sci 36(2):301-306. (Pubitemid 126541182)
39. Reddy VM, Daynard TB (1983) Endosperm characteristics associated with rate of grain filling and kernel size in corn. Maydica 28(4):339-355.
40. Capitanio R, Gentinetta E, Motto M (1983) Grain weight and its components in maize inbred lines. Maydica 28(4):365-379.
41. Sekhon RS, et al. (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS ONE 8(4):e61005.
42. Le BH, et al. (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci USA 107(18):8063-8070.
43. Walley JW, et al. (2013) Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc Natl Acad Sci USA 110(49):E4808-E4817.
44. Kodrzycki R, Boston RS, Larkins BA (1989) The opaque-2 mutation of maize differentially reduces zein gene transcription. Plant Cell 1(1):105-114.
45. Schmidt RJ, Ketudat M, Aukerman MJ, Hoschek G (1992) Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. Plant Cell 4(6):689-700.