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The transcriptional diversity of 25 Drosophila cell lines.

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.

SUBMITTER: Cherbas L

PROVIDER: S-EPMC3032933 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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The transcriptional diversity of 25 Drosophila cell lines.

Cherbas Lucy L Willingham Aarron A Zhang Dayu D Yang Li L Zou Yi Y Eads Brian D BD Carlson Joseph W JW Landolin Jane M JM Kapranov Philipp P Dumais Jacqueline J Samsonova Anastasia A Choi Jeong-Hyeon JH Roberts Johnny J Davis Carrie A CA Tang Haixu H van Baren Marijke J MJ Ghosh Srinka S Dobin Alexander A Bell Kim K Lin Wei W Langton Laura L Duff Michael O MO Tenney Aaron E AE Zaleski Chris C Brent Michael R MR Hoskins Roger A RA Kaufman Thomas C TC Andrews Justen J Graveley Brenton R BR Perrimon Norbert N Celniker Susan E SE Gingeras Thomas R TR Cherbas Peter P

Genome research 20101222 2

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 ...[more]

PMID: 21177962

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The transcriptional diversity of 25 Drosophila cell lines.

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The transcriptional diversity of 25 Drosophila cell lines.

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