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.

Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila

“…Abl stimulates Eya tyrosine phosphorylation and cytoplasmic accumulation (Xiong et al 2009 and Figure 6, A vs. B, quantified in N) and thus should enhance SH2/PTB-pY-Eya interactions. Abl is expressed endogenously in S2 cells (Cherbas et al 2011), and some tyrosine phosphorylation of Eya can be detected in cells transfected with Eya alone (Tootle et al 2003), perhaps explaining the low levels of Socs36E and Socs44A CoIP detected when Abl was not supplied by cotransfection (Figure 5, C and D). The Abl independence of the Eya-Hop CoIP ( Figure 5A) suggests that either Hop phosphorylates Eya at different tyrosine residues, or that pY-SH2 interactions do not drive the CoIP.…”

A conserved role for Snail as a potentiator of active transcription

“…2). Kc cells, which are thought to be of hematopoietic origin (Echalier and Ohanessian 1969), do not express detectable levels of Snail, Twist, or Dorsal (data not shown), while the corepressors dCtBP and Ebi are present (Cherbas et al 2011). First, we tested the ability of Snail to repress the Dorsaldependent wntD-lacZ enhancer in this system (Zeitlinger et al 2007).…”

The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation

“…Since Dmel2 cells express endogenous Brat and Pum (Cherbas et al 2011;Harris et al 2011;Weidmann and Goldstrohm 2012), we also performed knockdown experiments. As we lacked an antibody against endogenous Pum, we confirmed knockdown efficiency by the downregulation of coexpressed HA-tagged Pum (Fig.…”