|
|
|
|
|
|
|
||||
| Home Help Feedback Subscriptions Archive Search Table of Contents | ||||
doi: 10.1242/10.1242/dev.00302
1 Department of Molecular and Cellular Biology, Harvard University, Cambridge,
MA 02138, USA
2 Department of Genomics, Wyeth Research, Cambridge, MA 02140, USA
* Author for correspondence (e-mail: hunter{at}mcb.harvard.edu)
Accepted 18 November 2002
Temporal profiles of transcript abundance during embryonic development were obtained by whole-genome expression analysis from precisely staged C. elegans embryos. The result is a highly resolved time course that commences with the zygote and extends into mid-gastrulation, spanning the transition from maternal to embryonic control of development and including the presumptive specification of most major cell fates. Transcripts for nearly half (8890) of the predicted open reading frames are detected and expression levels for the majority of them (>70%) change over time. The transcriptome is stable up to the four-cell stage where it begins rapidly changing until the rate of change plateaus before gastrulation. At gastrulation temporal patterns of maternal degradation and embryonic expression intersect indicating a mid-blastula transition from maternal to embryonic control of development. In addition, we find that embryonic genes tend to be expressed transiently on a time scale consistent with developmental decisions being made with each cell cycle. Furthermore, overall rates of synthesis and degradation are matched such that the transcriptome maintains a steady-state frequency distribution. Finally, a versatile analytical platform based on cluster analysis and developmental classification of genes is provided.
Key words: Genomics, Time series, Embryogenesis, mRNA amplification, Mid-blastula transition, Zygotic transcription, Microarray, C. elegans
This article has been cited by other articles:
|
|
 |
|
  P. R. Boag, A. Atalay, S. Robida, V. Reinke, and T. K. Blackwell Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis J. Cell Biol., August 11, 2008; 182(3): 543 - 557. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. A. Spike, J. Bader, V. Reinke, and S. Strome DEPS-1 promotes P-granule assembly and RNA interference in C. elegans germ cells Development, March 1, 2008; 135(5): 983 - 993. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. C. Dunty Jr, K. K. Biris, R. B. Chalamalasetty, M. M. Taketo, M. Lewandoski, and T. P. Yamaguchi Wnt3a/ -catenin signaling controls posterior body development by coordinating mesoderm formation and segmentation Development, January 1, 2008; 135(1): 85 - 94. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Eki, T. Ishihara, I. Katsura, and F. Hanaoka A Genome-wide Survey and Systematic RNAi-based Characterization of Helicase-like Genes in Caenorhabditis elegans DNA Res, October 6, 2007; (2007) dsm016v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Fukushige, T. M. Brodigan, L. A. Schriefer, R. H. Waterston, and M. Krause Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development Genes & Dev., December 15, 2006; 20(24): 3395 - 3406. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. B. Bender, J. Suh, C. R. Carroll, Y. Fong, I. M. Fingerman, S. D. Briggs, R. Cao, Y. Zhang, V. Reinke, and S. Strome MES-4: an autosome-associated histone methyltransferase that participates in silencing the X chromosomes in the C. elegans germ line. Development, October 1, 2006; 133(19): 3907 - 3917. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Qu and S. Xu Quantitative Trait Associated Microarray Gene Expression Data Analysis Mol. Biol. Evol., August 1, 2006; 23(8): 1558 - 1573. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Dejima, A. Seko, K. Yamashita, K. Gengyo-Ando, S. Mitani, T. Izumikawa, H. Kitagawa, K. Sugahara, S. Mizuguchi, and K. Nomura Essential Roles of 3'-Phosphoadenosine 5'-Phoshosulfate Synthase in Embryonic and Larval Development of the Nematode Caenorhabditis elegans J. Biol. Chem., April 21, 2006; 281(16): 11431 - 11440. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Cheung, M. Schertzer, A. Rose, and P. M. Lansdorp High incidence of rapid telomere loss in telomerase-deficient Caenorhabditis elegans Nucleic Acids Res., January 10, 2006; 34(1): 96 - 103. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. W. Hillier, A. Coulson, J. I. Murray, Z. Bao, J. E. Sulston, and R. H. Waterston Genomics in C. elegans: So many genes, such a little worm Genome Res., December 1, 2005; 15(12): 1651 - 1660. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Goszczynski and J. D. McGhee Reevaluation of the Role of the med-1 and med-2 Genes in Specifying the Caenorhabditis elegans Endoderm Genetics, October 1, 2005; 171(2): 545 - 555. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Lu and P. E. Mains Mutations of a Redundant {alpha}-Tubulin Gene Affect Caenorhabditis elegans Early Embryonic Cleavage via MEI-1/Katanin-Dependent and -Independent Pathways Genetics, May 1, 2005; 170(1): 115 - 126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. R. Baugh, A. A. Hill, J. M. Claggett, K. Hill-Harfe, J. C. Wen, D. K. Slonim, E. L. Brown, and C. P. Hunter The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo Development, April 15, 2005; 132(8): 1843 - 1854. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Fernandez, K. C. Gunsalus, J. Huang, L.-S. Chuang, N. Ying, H.-l. Liang, C. Tang, A. J. Schetter, C. Zegar, J.-F. Rual, et al. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones Genome Res., February 1, 2005; 15(2): 250 - 259. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Cutter and S. Ward Sexual and Temporal Dynamics of Molecular Evolution in C. elegans Development Mol. Biol. Evol., January 1, 2005; 22(1): 178 - 188. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Walker, Y. Shi, and T. K. Blackwell An Extensive Requirement for Transcription Factor IID-specific TAF-1 in Caenorhabditis elegans Embryonic Transcription J. Biol. Chem., April 9, 2004; 279(15): 15339 - 15347. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. C. Ellis, J. B. Phillips, S. O'Rourke, R. Lyczak, and B. Bowerman Maternally expressed and partially redundant {beta}-tubulins in Caenorhabditis elegans are autoregulated J. Cell Sci., January 22, 2004; 117(3): 457 - 464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Reinke, I. S. Gil, S. Ward, and K. Kazmer Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans Development, January 15, 2004; 131(2): 311 - 323. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. C. Gunsalus, W.-C. Yueh, P. MacMenamin, and F. Piano RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects Nucleic Acids Res., January 1, 2004; 32(90001): D406 - 410. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Lu, M. Srayko, and P. E. Mains The Caenorhabditis elegans Microtubule-severing Complex MEI-1/MEI-2 Katanin Interacts Differently with Two Superficially Redundant {beta}-Tubulin Isotypes Mol. Biol. Cell, January 1, 2004; 15(1): 142 - 150. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Petalidis, S. Bhattacharyya, G. A. Morris, V. P. Collins, T. C. Freeman, and P. A. Lyons Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis Nucleic Acids Res., November 15, 2003; 31(22): e142 - e142. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Wright and C. P. Hunter Mutations in a {beta}-Tubulin Disrupt Spindle Orientation and Microtubule Dynamics in the Early Caenorhabditis elegans Embryo Mol. Biol. Cell, November 1, 2003; 14(11): 4512 - 4525. [Abstract] [Full Text] [PDF]
|
|
