Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Science Careers Booklet

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 22 October 2004:
Vol. 306. no. 5696, pp. 655 - 660
DOI: 10.1126/science.1101312
Prev | Table of Contents | Next

Research Articles

A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

Viktor Stolc,1,5* Zareen Gauhar,1,2* Christopher Mason,2* Gabor Halasz,7 Marinus F. van Batenburg,7,9 Scott A. Rifkin,2,3 Sujun Hua,2 Tine Herreman,2 Waraporn Tongprasit,6 Paolo Emilio Barbano,2,4 Harmen J. Bussemaker,7,8 Kevin P. White2,3{dagger}

We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult males and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.

1 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
2 Department of Genetics, Yale University, New Haven, CT 06520, USA.
3 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
4 Department of Mathematics, Yale University, New Haven, CT 06520, USA.
5 Genome Research Facility, NASA Ames Research Center, Mail Stop 239-11, Moffett Field, CA 94035, USA.
6 Eloret Corporation, Sunnyvale, CA 94087, USA.
7 Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
8 Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10027, USA.
9 Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, 1100 DE Amsterdam, Netherlands.


* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: kevin.white{at}yale.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Effects of X-Linkage and Sex-Biased Gene Expression on the Rate of Adaptive Protein Evolution in Drosophila.
J. F. Baines, S. A. Sawyer, D. L. Hartl, and J. Parsch (2008)
Mol. Biol. Evol. 25, 1639-1650
   Abstract »    Full Text »    PDF »
Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes.
A. Bhutkar, S. W. Schaeffer, S. M. Russo, M. Xu, T. F. Smith, and W. M. Gelbart (2008)
Genetics 179, 1657-1680
   Abstract »    Full Text »    PDF »
Genome-wide Analysis of Alternative Pre-mRNA Splicing.
C. Ben-Dov, B. Hartmann, J. Lundgren, and J. Valcarcel (2008)
J. Biol. Chem. 283, 1229-1233
   Abstract »    Full Text »    PDF »
Genomic regulatory blocks underlie extensive microsynteny conservation in insects.
P. G. Engstrom, S. J. Ho Sui, O. Drivenes, T. S. Becker, and B. Lenhard (2007)
Genome Res. 17, 1898-1908
   Abstract »    Full Text »    PDF »
Adaptive Protein Evolution of X-linked and Autosomal Genes in Drosophila: Implications for Faster-X Hypotheses.
T. Connallon (2007)
Mol. Biol. Evol. 24, 2566-2572
   Abstract »    Full Text »    PDF »
Developmental genomics of the most dangerous animal.
M. P. Scott (2007)
PNAS 104, 11865-11866
   Full Text »    PDF »
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci.
J. S. Rozowsky, D. Newburger, F. Sayward, J. Wu, G. Jordan, J. O. Korbel, U. Nagalakshmi, J. Yang, D. Zheng, R. Guigo, et al. (2007)
Genome Res. 17, 732-745
   Abstract »    Full Text »    PDF »
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.
K. Hanada, X. Zhang, J. O. Borevitz, W.-H. Li, and S.-H. Shiu (2007)
Genome Res. 17, 632-640
   Abstract »    Full Text »    PDF »
The SR Family Proteins B52 and dASF/SF2 Modulate Development of the Drosophila Visual System by Regulating Specific RNA Targets.
M. Gabut, J. Dejardin, J. Tazi, and J. Soret (2007)
Mol. Cell. Biol. 27, 3087-3097
   Abstract »    Full Text »    PDF »
A core transcriptional network for early mesoderm development in Drosophila melanogaster.
T. Sandmann, C. Girardot, M. Brehme, W. Tongprasit, V. Stolc, and E. E.M. Furlong (2007)
Genes & Dev. 21, 436-449
   Abstract »    Full Text »    PDF »
Applications of High-Throughput RNA Interference Screens to Problems in Cell and Developmental Biology.
N. Perrimon and B. Mathey-Prevot (2007)
Genetics 175, 7-16
   Abstract »    Full Text »    PDF »
ATM and ATR Pathways Signal Alternative Splicing of Drosophila TAF1 Pre-mRNA in Response to DNA Damage.
R. J. Katzenberger, M. S. Marengo, and D. A. Wassarman (2006)
Mol. Cell. Biol. 26, 9256-9267
   Abstract »    Full Text »    PDF »
The transcriptome of the sea urchin embryo..
M. P. Samanta, W. Tongprasit, S. Istrail, R. A. Cameron, Q. Tu, E. H. Davidson, and V. Stolc (2006)
Science 314, 960-962
   Abstract »    Full Text »    PDF »
RNA editing in Drosophila melanogaster: New targets and functional consequences.
M. Stapleton, J. W. Carlson, and S. E. Celniker (2006)
RNA 12, 1922-1932
   Abstract »    Full Text »    PDF »
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.
F. Gnad and J. Parsch (2006)
Bioinformatics 22, 2577-2579
   Abstract »    Full Text »    PDF »
Widespread Adaptive Evolution of Drosophila Genes With Sex-Biased Expression.
M. Proschel, Z. Zhang, and J. Parsch (2006)
Genetics 174, 893-900
   Abstract »    Full Text »    PDF »
Transcript mapping with high-density oligonucleotide tiling arrays.
W. Huber, J. Toedling, and L. M. Steinmetz (2006)
Bioinformatics 22, 1963-1970
   Abstract »    Full Text »    PDF »
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.
C. Moorman, L. V. Sun, J. Wang, E. de Wit, W. Talhout, L. D. Ward, F. Greil, X.-J. Lu, K. P. White, H. J. Bussemaker, et al. (2006)
PNAS 103, 12027-12032
   Abstract »    Full Text »    PDF »
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison.
D. L. Halligan and P. D. Keightley (2006)
Genome Res. 16, 875-884
   Abstract »    Full Text »    PDF »
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.
M. T. Levine, C. D. Jones, A. D. Kern, H. A. Lindfors, and D. J. Begun (2006)
PNAS 103, 9935-9939
   Abstract »    Full Text »    PDF »
Identification of the Major Spliceosomal RNAs in Dictyostelium discoideum Reveals Developmentally Regulated U2 Variants and Polyadenylated snRNAs.
A. Hinas, P. Larsson, L. Avesson, L. A. Kirsebom, A. Virtanen, and F. Soderbom (2006)
Eukaryot. Cell 5, 924-934
   Abstract »    Full Text »    PDF »
Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway..
M. P. Samanta, W. Tongprasit, H. Sethi, C.-S. Chin, and V. Stolc (2006)
PNAS 103, 4192-4197
   Abstract »    Full Text »    PDF »
Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags.
D. J. Begun, H. A. Lindfors, M. E. Thompson, and A. K. Holloway (2006)
Genetics 172, 1675-1681
   Abstract »    Full Text »    PDF »
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae.
C. A. Davis and M. Ares Jr. (2006)
PNAS 103, 3262-3267
   Abstract »    Full Text »    PDF »
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations..
X. Wu, L. Zhu, J. Guo, D.-Y. Zhang, and K. Lin (2006)
Nucleic Acids Res. 34, 2137-2150
   Abstract »    Full Text »    PDF »
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.
T. Ravasi, H. Suzuki, K. C. Pang, S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M. C. Frith, M. M. Gongora, et al. (2006)
Genome Res. 16, 11-19
   Abstract »    Full Text »    PDF »
Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).
R. A. Hoskins, M. Stapleton, R. A. George, C. Yu, K. H. Wan, J. W. Carlson, and S. E. Celniker (2005)
Nucleic Acids Res. 33, e185
   Abstract »    Full Text »    PDF »
Drosophila melanogaster: A case study of a model genomic sequence and its consequences.
M. Ashburner and C. M. Bergman (2005)
Genome Res. 15, 1661-1667
   Abstract »    Full Text »    PDF »
Intragenic Hill-Robertson Interference Influences Selection Intensity on Synonymous Mutations in Drosophila.
J. M. Comeron and T. B. Guthrie (2005)
Mol. Biol. Evol. 22, 2519-2530
   Abstract »    Full Text »    PDF »
Dicer-Dependent Turnover of Intergenic Transcripts from the Human {beta}-Globin Gene Cluster.
D. Haussecker and N. J. Proudfoot (2005)
Mol. Cell. Biol. 25, 9724-9733
   Abstract »    Full Text »    PDF »
The Functional Genomics of Noncoding RNA.
J. S. Mattick (2005)
Science 309, 1527-1528
   Abstract »    Full Text »    PDF »
Genome-wide HP1 binding in Drosophila: Developmental plasticity and genomic targeting signals.
E. de Wit, F. Greil, and B. van Steensel (2005)
Genome Res. 15, 1265-1273
   Abstract »    Full Text »    PDF »
Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs.
Z.-P. HUANG, H. ZHOU, H.-L. HE, C.-L. CHEN, D. LIANG, and L.-H. QU (2005)
RNA 11, 1303-1316
   Abstract »    Full Text »    PDF »
Detecting novel low-abundant transcripts in Drosophila.
S. LEE, J. BAO, G. ZHOU, J. SHAPIRO, J. XU, R. Z. SHI, X. LU, T. CLARK, D. JOHNSON, Y. C. KIM, et al. (2005)
RNA 11, 939-946
   Abstract »    Full Text »    PDF »
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila.
M. Blanchette, R. E. Green, S. E. Brenner, and D. C. Rio (2005)
Genes & Dev. 19, 1306-1314
   Abstract »    Full Text »    PDF »
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution.
J. Cheng, P. Kapranov, J. Drenkow, S. Dike, S. Brubaker, S. Patel, J. Long, D. Stern, H. Tammana, G. Helt, et al. (2005)
Science 308, 1149-1154
   Abstract »    Full Text »    PDF »
Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.
J. L. Tupy, A. M. Bailey, G. Dailey, M. Evans-Holm, C. W. Siebel, S. Misra, S. E. Celniker, and G. M. Rubin (2005)
PNAS 102, 5495-5500
   Abstract »    Full Text »    PDF »
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays.
V. Stolc, M. P. Samanta, W. Tongprasit, H. Sethi, S. Liang, D. C. Nelson, A. Hegeman, C. Nelson, D. Rancour, S. Bednarek, et al. (2005)
PNAS 102, 4453-4458
   Abstract »    Full Text »    PDF »
Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes.
V. Stolc, M. P. Samanta, W. Tongprasit, and W. F. Marshall (2005)
PNAS 102, 3703-3707
   Abstract »    Full Text »    PDF »
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome.
M. Yandell, A. M. Bailey, S. Misra, S. Shu, C. Wiel, M. Evans-Holm, S. E. Celniker, and G. M. Rubin (2005)
PNAS 102, 1566-1571
   Abstract »    Full Text »    PDF »


ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)