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.
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Justin Crocker's reading list...
Wednesday, February 2, 2011
The transcriptional diversity of 25 Drosophila cell lines [RESOURCES]
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans [RESEARCH]
Regulation of gene expression by sequence-specific transcription factors is central to developmental programs and depends on the binding of transcription factors with target sites in the genome. To date, most such analyses in Caenorhabditis elegans have focused on the interactions between a single transcription factor with one or a few select target genes. As part of the modENCODE Consortium, we have used chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) to determine the genome-wide binding sites of 22 transcription factors (ALR-1, BLMP-1, CEH-14, CEH-30, EGL-27, EGL-5, ELT-3, EOR-1, GEI-11, HLH-1, LIN-11, LIN-13, LIN-15B, LIN-39, MAB-5, MDL-1, MEP-1, PES-1, PHA-4, PQM-1, SKN-1, and UNC-130) at diverse developmental stages. For each factor we determined candidate gene targets, both coding and non-coding. The typical binding sites of almost all factors are within a few hundred nucleotides of the transcript start site. Most factors target a mixture of coding and non-coding target genes, although one factor preferentially binds to non-coding RNA genes. We built a regulatory network among the 22 factors to determine their functional relationships to each other and found that some factors appear to act preferentially as regulators and others as target genes. Examination of the binding targets of three related HOX factors—LIN-39, MAB-5, and EGL-5—indicates that these factors regulate genes involved in cellular migration, neuronal function, and vulval differentiation, consistent with their known roles in these developmental processes. Ultimately, the comprehensive mapping of transcription factor binding sites will identify features of transcriptional networks that regulate C. elegans developmental processes.
"Tuesday, February 1, 2011
Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay
Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels.
Results:
Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners.
Conclusion:
Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development."
Modularity of gene-regulatory networks revealed in sea-star development
Corrigendum: Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior
Corrigendum: Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior
Nature Methods 8, 184 (2011). doi:10.1038/nmeth0211-184b
Author: Johannes D Seelig, M Eugenia Chiappe, Gus K Lott, Anirban Dutta, Jason E Osborne, Michael B Reiser & Vivek Jayaraman
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A microfluidic array for large-scale ordering and orientation of embryos
A microfluidic array for large-scale ordering and orientation of embryos
Nature Methods 8, 171 (2011). doi:10.1038/nmeth.1548
Authors: Kwanghun Chung, Yoosik Kim, Jitendra S Kanodia, Emily Gong, Stanislav Y Shvartsman & Hang Lu
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One genome, two haplotypes
One genome, two haplotypes
Nature Methods 8, 107 (2011). doi:10.1038/nmeth0211-107
Author: Nicole Rusk
Two approaches using either fosmid clones or a microfluidic device are used to tackle the challenge of a haplotype-resolved human genome.
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