FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

Zhu, Lihua Julie; Christensen, Ryan; Kazemian, Majid; Hull, C.J.; Enuameh, Metewo Selase; Basciotta, Matthew D.; Brasefield, Jessie A.; Zhu, Cong; Asriyan, Yuna; Lapointe, David S.; Sinha, Saurabh; Wolfe, Scot A.; Brodsky, Michael

doi:10.1093/nar/gkq858

Cited by 210 publications

(234 citation statements)

References 41 publications

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“…Sequences representing peaks identified in ChIP-seq experiments were entered as FASTA files. The program identified motifs relatively enriched in the data set compared to shuffled sequences, and also compared these motifs with a Drosophila database of known motifs combined from the OnTheFly_2014, Fly Factor Survey, FLYREG, iDMMPMM, and DMMPMM databases (Bergman et al 2005;Kulakovskii and Makeev 2009;Kulakovskiy et al 2009;Zhu et al 2011;Shazman et al 2014). Motifs are given with an e-value, calculated as the P-value of Fisher's Exact Test of motif enrichment multiplied by the number of candidate motifs.…”

Section: Motif Enrichmentmentioning

confidence: 99%

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

et al. 2017

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It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.

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Section: Motif Enrichmentmentioning

confidence: 99%

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

et al. 2017

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“…3M). Searching yR7 enh* for low-affinity Ss binding motifs (Zhu et al, 2011), we identified two putative sites (GTCTGA and GTGTGA), one of which is conserved (GTCTGA), suggesting that these cryptic/ low-affinity sites may drive very low level expression in the absence of core conserved (GCGTG) sites. Together, these data suggest that Ss directly binds the XRE sites in yR7 enh* to regulate expression.…”

Section: Two Enhancers Determine Yr7-and Outer Pr-specific Expressionmentioning

confidence: 99%

Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies

et al. 2017

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How differential levels of gene expression are controlled in postmitotic neurons is poorly understood. In the Drosophila retina, expression of the transcription factor Defective Proventriculus (Dve) at distinct cell type-specific levels is required for terminal differentiation of color-and motion-detecting photoreceptors. Here, we find that the activities of two cis-regulatory enhancers are coordinated to drive dve expression in the fly eye. Three transcription factors act on these enhancers to determine cell-type specificity. Negative autoregulation by Dve maintains expression from each enhancer at distinct homeostatic levels. One enhancer acts as an inducible backup ('dark' shadow enhancer) that is normally repressed but becomes active in the absence of the other enhancer. Thus, two enhancers integrate combinatorial transcription factor input, feedback and redundancy to generate cell type-specific levels of dve expression and stable photoreceptor fate. This regulatory logic may represent a general paradigm for how precise levels of gene expression are established and maintained in post-mitotic neurons.

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“…DNA sequences corresponding to the top 10,000 EF peaks were used as the control. The position weight matrices (PWMs) for these midline transcription factors were obtained from the Fly Factor Survey database (Zhu et al, 2011).…”

Section: Motif Predictionmentioning

confidence: 99%

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers

et al. 2016

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One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.

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FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

Cited by 210 publications

References 41 publications

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers

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