The transcriptional diversity of 25 Drosophila cell lines

Lucy Cherbas, Aarron Willingham, Dayu Zhang, Li Yang, Yi Zou, Brian D. Eads, Joseph W. Carlson, Jane M. Landolin, Philipp Kapranov, Jacqueline Dumais, Anastasia Samsonova, Jeong-Hyeon Choi, Johnny Roberts, Carrie A. Davis, Haixu Tang, Marijke J. Van Baren, Srinka Ghosh, Alexander Dobin, Kim Bell, Wei Lin & 13 others Laura Langton, Michael O. Duff, Aaron E. Tenney, Chris Zaleski, Michael R. Brent, Roger A. Hoskins, Thomas C. Kaufman, Justen Andrews, Brenton R. Graveley, Norbert Perrimon, Susan E. Celniker, Thomas R. Gingeras, Peter Cherbas

Research output: Contribution to journalArticle

138 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)301-314
Number of pages14
JournalGenome Research
Volume21
Issue number2
DOIs
StatePublished - Feb 1 2011

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Drosophila
Cell Line
Genes
Exons
Imaginal Discs
Gene Expression
Drosophila melanogaster
Individuality
Transcription Factors
Growth

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., ... Cherbas, P. (2011). The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21(2), 301-314. https://doi.org/10.1101/gr.112961.110

The transcriptional diversity of 25 Drosophila cell lines. / Cherbas, Lucy; Willingham, Aarron; Zhang, Dayu; Yang, Li; Zou, Yi; Eads, Brian D.; Carlson, Joseph W.; Landolin, Jane M.; Kapranov, Philipp; Dumais, Jacqueline; Samsonova, Anastasia; Choi, Jeong-Hyeon; Roberts, Johnny; Davis, Carrie A.; Tang, Haixu; Van Baren, Marijke J.; Ghosh, Srinka; Dobin, Alexander; Bell, Kim; Lin, Wei; Langton, Laura; Duff, Michael O.; Tenney, Aaron E.; Zaleski, Chris; Brent, Michael R.; Hoskins, Roger A.; Kaufman, Thomas C.; Andrews, Justen; Graveley, Brenton R.; Perrimon, Norbert; Celniker, Susan E.; Gingeras, Thomas R.; Cherbas, Peter.

In: Genome Research, Vol. 21, No. 2, 01.02.2011, p. 301-314.

Research output: Contribution to journalArticle

Cherbas, L, Willingham, A, Zhang, D, Yang, L, Zou, Y, Eads, BD, Carlson, JW, Landolin, JM, Kapranov, P, Dumais, J, Samsonova, A, Choi, J-H, Roberts, J, Davis, CA, Tang, H, Van Baren, MJ, Ghosh, S, Dobin, A, Bell, K, Lin, W, Langton, L, Duff, MO, Tenney, AE, Zaleski, C, Brent, MR, Hoskins, RA, Kaufman, TC, Andrews, J, Graveley, BR, Perrimon, N, Celniker, SE, Gingeras, TR & Cherbas, P 2011, 'The transcriptional diversity of 25 Drosophila cell lines', Genome Research, vol. 21, no. 2, pp. 301-314. https://doi.org/10.1101/gr.112961.110
Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Research. 2011 Feb 1;21(2):301-314. https://doi.org/10.1101/gr.112961.110
Cherbas, Lucy ; Willingham, Aarron ; Zhang, Dayu ; Yang, Li ; Zou, Yi ; Eads, Brian D. ; Carlson, Joseph W. ; Landolin, Jane M. ; Kapranov, Philipp ; Dumais, Jacqueline ; Samsonova, Anastasia ; Choi, Jeong-Hyeon ; Roberts, Johnny ; Davis, Carrie A. ; Tang, Haixu ; Van Baren, Marijke J. ; Ghosh, Srinka ; Dobin, Alexander ; Bell, Kim ; Lin, Wei ; Langton, Laura ; Duff, Michael O. ; Tenney, Aaron E. ; Zaleski, Chris ; Brent, Michael R. ; Hoskins, Roger A. ; Kaufman, Thomas C. ; Andrews, Justen ; Graveley, Brenton R. ; Perrimon, Norbert ; Celniker, Susan E. ; Gingeras, Thomas R. ; Cherbas, Peter. / The transcriptional diversity of 25 Drosophila cell lines. In: Genome Research. 2011 ; Vol. 21, No. 2. pp. 301-314.
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AU - Carlson, Joseph W.

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AU - Samsonova, Anastasia

AU - Choi, Jeong-Hyeon

AU - Roberts, Johnny

AU - Davis, Carrie A.

AU - Tang, Haixu

AU - Van Baren, Marijke J.

AU - Ghosh, Srinka

AU - Dobin, Alexander

AU - Bell, Kim

AU - Lin, Wei

AU - Langton, Laura

AU - Duff, Michael O.

AU - Tenney, Aaron E.

AU - Zaleski, Chris

AU - Brent, Michael R.

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AU - Kaufman, Thomas C.

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