The transcriptional diversity of 25 Drosophila cell lines (original) (raw)

  1. Aarron Willingham2,11,
  2. Dayu Zhang1,
  3. Li Yang3,
  4. Yi Zou1,
  5. Brian D. Eads4,
  6. Joseph W. Carlson5,
  7. Jane M. Landolin5,
  8. Philipp Kapranov2,12,
  9. Jacqueline Dumais2,
  10. Anastasia Samsonova6,
  11. Jeong-Hyeon Choi1,
  12. Johnny Roberts1,
  13. Carrie A. Davis7,
  14. Haixu Tang1,8,
  15. Marijke J. van Baren9,13,
  16. Srinka Ghosh2,14,
  17. Alexander Dobin7,
  18. Kim Bell7,
  19. Wei Lin7,
  20. Laura Langton9,
  21. Michael O. Duff3,
  22. Aaron E. Tenney9,
  23. Chris Zaleski7,
  24. Michael R. Brent9,
  25. Roger A. Hoskins5,
  26. Thomas C. Kaufman4,
  27. Justen Andrews4,
  28. Brenton R. Graveley3,
  29. Norbert Perrimon6,10,
  30. Susan E. Celniker5,
  31. Thomas R. Gingeras2,7 and
  32. Peter Cherbas1,4,15
  33. 1 Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA;
  34. 2 Affymetrix Inc., Santa Clara, California 95051, USA;
  35. 3 Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06030-3301, USA;
  36. 4 Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
  37. 5 Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
  38. 6 Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
  39. 7 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
  40. 8 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47408, USA;
  41. 9 Center for Genome Sciences and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA;
  42. 10 Howard Hughes Medical Institute, Boston, Massachusetts, 02115, USA

Abstract

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are “off” and survival/growth pathways “on.” Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common “cell line“ gene expression pattern.

Footnotes

Freely available online through the Genome Research Open Access option.