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Papers

Recent advances in functional assays of transcriptional enhancers

Genomics 2015
Babbitt C., Markstein M., Gray J.

In this special edition of Genomics,we present reviews of the current state of the field in identifying and functionally understanding transcriptional enhancers in cells and developing tissues. Typically several enhancers coordinate the expression of an individual target gene, each controlling that gene’s expression in specific cell types at specific times. Until recently, identifying each gene’s enhancers had been challenging because enhancers do not occupy prescribed locations relative to their target genes. Recently there have been powerful advances in DNA sequencing and other technologies that make it possible to identify the majority of enhancers in virtually any cell type of interest. The reviews in this edition of Genomics highlight some of these new and powerful approaches. 
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Genomics2015-CoverFORWEB

 

Gene expression profiling identifies the zinc-finger protein Charlatan as a regulator of intestinal stem cells in Drosophila

Development 2014
Amcheslavsky A., Nie Y., Li Q., He F., Tsuda L., Markstein M., Ip YT.

Intestinal stem cells (ISCs) in the adult Drosophila midgut can respond to tissue damage and support repair. We used genetic manipulation to increase the number of ISC-like cells in the adult midgut and performed gene expression profiling to identify potential ISC regulators. A detailed analysis of one of these potential regulators, the zinc-finger protein Charlatan, was carried out…
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Development2014-CoverFORWEB 

Systematic screen of chemotherapeutics in Drosophila stem cell tumors

PNAS 2014
Markstein M*, Dettorre S, Cho J, Neumüller RA, Craig-Müller S, Perrimon N*.

*Corresponding Authors

Here we report the development of an in vivo system to study the interaction of stem cells with drugs using a tumor model in the adult Drosophila intestine. Strikingly, we find that some Food and Drug Administration-approved chemotherapeutics that can inhibit the growth of Drosophila tumor stem cells can paradoxically promote the hyperproliferation of their wild-type counterparts. These results reveal an unanticipated side…
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PNAS2014-545Wide

Modeling colorectal cancer as a 3-dimensional disease in a dish: the case for drug screening using organoids, zebrafish, and fruit flies

Drug Development Today: Technologies 2013
Michele Markstein
This review discusses recent shifts in the understanding of colorectal cancer as a stem cell based disease, based on findings that tie patient prognosis to the presence of cancer stem cells in colorectal tumors. Currently no drugs specifically target CSCs in colorectal tumors. However, recent advances in the culturing of colorectal stem cells using mammalian organoids, zebrafish, and Drosophila offer promising avenues for…
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Complementary genomic screens identify SERCA as a therapeutic target in NOTCH1 mutated cancer

Cancer Cell 2013
Roti G, Carlton A, Ross KN, Markstein M, Pajcini K, Su AH, Perrimon N, Pear WS, Kung AL, Blacklow SC, Aster JC, Stegmaier K.
Notch1 is a rational therapeutic target in several human cancers, but as a transcriptional regulator, it poses a drug discovery challenge. To identify Notch1 modulators, we performed two cell-based, high-throughput screens for small-molecule inhibitors and cDNA enhancers of a NOTCH1 allele bearing a leukemia-associated mutation. Sarco/endoplasmic reticulum calcium ATPase (SERCA) channels emerged at the intersection of…
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A Drosophila resource of transgenic RNAi lines for neurogenetics

Genetics 2009
Ni JQ, Liu LP, Binari R, Hardy R, Shim HS, Cavallaro A, Booker M, Pfeiffer BD, Markstein M, Wang H, Villalta C, Laverty TR, Perkins LA, Perrimon N.
Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS…
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Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes.

Nature Genetics 2008
Markstein M*, Pitsouli C, Villalta C, Celniker SE, Perrimon N.

*Corresponding Author

A major obstacle to creating precisely expressed transgenes lies in the epigenetic effects of the host chromatin that surrounds them. Here we present a strategy to overcome this problem, employing a Gal4-inducible luciferase assay to systematically quantify position effects of host chromatin and the ability of insulators to counteract these effects at phiC31 integration loci randomly distributed throughout the…
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Nature Genetics News and Views: PDF

Nature Methods Research Highlight: PDF

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Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster

Nature Methods 2008
Ni JQ*, Markstein M*, Binari R*, Pfeiffer B, Liu LP, Villalta C, Booker M, Perkins L, Perrimon N

*Co-first Authors

The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site-driven RNA interference constructs have been inserted into the genome randomly using P-element-mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a…
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A regulatory code for neurogenic gene expression in the Drosophila embryo

Development 2004
Markstein M*, Zinzen R, Markstein P, Yee KP, Erives A, Stathopoulos A, Levine M*.

*Corresponding Authors

Bioinformatics methods have identified enhancers that mediate restricted expression in the Drosophila embryo. However, only a small fraction of the predicted enhancers actually work when tested in vivo. In the present study, co-regulated neurogenic enhancers that are activated by intermediate levels of the Dorsal regulatory gradient are shown to contain several shared sequence motifs. These motifs permitted the…
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Immunity regulatory DNAs share common organizational features in Drosophila

Molecular Cell 2004
Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, Levine M.
Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, Berkeley, CA 94720, USA. Comment in Mol Cell. 2004 Jan 16;13(1):1-2. Infection results in the rapid activation of immunity genes in the Drosophila fat body. Two classes of transcription factors have been implicated in this process: the REL-containing proteins, Dorsal, Dif, and Relish, and the GATA factor Serpent…
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Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo

Cell 2002
Stathopoulos A, Van Drenth M, Erives A, Markstein M, Levine M.
The maternal Dorsal regulatory gradient initiates the differentiation of several tissues in the early Drosophila embryo. Whole-genome microarray assays identified as many as 40 new Dorsal target genes, which encode a broad spectrum of cell signaling proteins and transcription factors. Evidence is presented that a tissue-specific form of the NF-Y transcription complex is essential for the activation of gene expression in the…
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Decoding cis-regulatory DNAs in the Drosophila genome

Current Opinion in Genes and Development
Markstein M, Levine M.
Cis-regulatory DNAs control the timing and sites of gene expression during metazoan development. Changes in gene expression are responsible for the morphological diversification of metazoan body plans. However, traditional methods for the identification and characterization of cis-regulatory DNAs are tedious. During the past year, computational methods have been used to identify novel cis-DNAs within the entire Drosophila…
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Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

 PNAS 2002
Markstein M, Markstein P, Markstein V, Levine MS.
Metazoan genomes contain vast tracts of cis-regulatory DNA that have been identified typically through tedious functional assays. As a result, it has not been possible to uncover a cis-regulatory code that links primary DNA sequences to gene expression patterns. In an initial effort to determine whether coordinately regulated genes share a common “grammar,” we have examined the distribution of Dorsal recognition…
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